5E7K

Structure of T. thermophilus 70S ribosome complex with mRNA and cognate tRNALys in the A-site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.

Rozov, A., Demeshkina, N., Khusainov, I., Westhof, E., Yusupov, M., Yusupova, G.

(2016) Nat Commun 7: 10457-10457

  • DOI: https://doi.org/10.1038/ncomms10457
  • Primary Citation of Related Structures:  
    5E7K, 5E81, 5EL4, 5EL5, 5EL6, 5EL7

  • PubMed Abstract: 

    Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNA(Lys)(UUU) with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm(5)s(2)U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.

    • Organizational Affiliation: 

    Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, BP 10142, Illkirch 67404, France.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth 1E],
EB [auth 12]		256Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth 2E],
FB [auth 22]		239Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth 3E],
GB [auth 32]		209Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth 4E],
HB [auth 42]		162Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth 5E],
IB [auth 52]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth 6E],
JB [auth 62]		156Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth 7E],
KB [auth 72]		138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth 8E],
LB [auth 82]		128Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth 1I],
MB [auth 1A]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth 2I],
NB [auth 2A]		129Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth 3I],
OB [auth 3A]		132Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth 4I],
PB [auth 4A]		126Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN [auth 5I],
QB [auth 5A]		61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth 6I],
RB [auth 6A]		89Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth 7I],
SB [auth 7A]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth 8I],
TB [auth 8A]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth 9I],
UB [auth 9A]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth AI],
VB [auth AA]		93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth BI],
WB [auth BA]		106Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxU [auth 1F],
XB [auth 1B]		27Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1BA [auth 71],
EC [auth 79]		229Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2CA [auth 11],
FC [auth 19]		276Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3DA [auth 21],
GC [auth 29]		206Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4EA [auth 31],
HC [auth 39]		210Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5FA [auth 41],
IC [auth 49]		182Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6GA [auth 51],
JC [auth 59]		180Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9HA [auth 61],
KC [auth 69]		148Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13IA [auth 58],
LC [auth 15]		140Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14JA [auth 68],
MC [auth 25]		122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15KA [auth 78],
NC [auth 35]		150Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16LA [auth 88],
OC [auth 45]		141Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17MA [auth 98],
PC [auth 55]		118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18NA [auth A8],
QC [auth 65]		112Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19OA [auth B8],
RC [auth 75]		146Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20PA [auth C8],
SC [auth 85]		118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21QA [auth D8],
TC [auth 95]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22RA [auth E8],
UC [auth A5]		113Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23SA [auth F8],
VC [auth B5]		96Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24TA [auth G8],
WC [auth C5]		110Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25UA [auth H8],
XC [auth D5]		206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27VA [auth I8],
YC [auth E5]		85Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28WA [auth J8],
ZC [auth F5]		98Thermus thermophilus HB8Mutation(s): 0 
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UniProt GroupP60494
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29AD [auth G5],
XA [auth K8]		72Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SHP6
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30BD [auth H5],
YA [auth L8]		60Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q5SHQ6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SHQ6
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31ZA [auth M8]71Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SJE1
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32AB [auth N8],
CD [auth J5]		60Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80339
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BB [auth P8],
DD [auth L5]		49Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for P80340 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80340
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CB [auth Q8],
ED [auth M5]		65Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SKU1
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth 13],
DB [auth 1G]		1,522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
tRNALysV [auth 1K]75Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
tRNAfMetW [auth 2K],
ZB [auth 2L]		77Escherichia coli
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Entity ID: 24
MoleculeChains LengthOrganismImage
tRNALysX [auth 3K]76Escherichia coli
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Entity ID: 25
MoleculeChains LengthOrganismImage
mRNABC [auth 4L],
Y [auth 4K]		27Escherichia coli
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Entity ID: 26
MoleculeChains LengthOrganismImage
23S rRNACC [auth 14],
Z [auth 1H]		2,917Thermus thermophilus HB8
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Entity ID: 27
MoleculeChains LengthOrganismImage
5S rRNAAA [auth 16],
DC [auth 1J]		122Thermus thermophilus HB8
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Entity ID: 56
MoleculeChains LengthOrganismImage
tRNALysYB [auth 1L]76Escherichia coli
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Entity ID: 57
MoleculeChains LengthOrganismImage
tRNALysAC [auth 3L]76Escherichia coli
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
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II [auth 3E],
YEA [auth 32]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN
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DVA [auth C5],
EBA [auth G8],
KI [auth 5I],
ZEA [auth 5A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AAA [auth 1H]
ABA [auth 41]
ACA [auth 1G]
ADA [auth 1G]
AE [auth 13]
AAA [auth 1H],
ABA [auth 41],
ACA [auth 1G],
ADA [auth 1G],
AE [auth 13],
AEA [auth 1G],
AF [auth 13],
AFA [auth 6A],
AG [auth 13],
AGA [auth 14],
AH [auth 13],
AHA [auth 14],
AI [auth 13],
AIA [auth 14],
AJ [auth 1H],
AJA [auth 14],
AK [auth 1H],
AKA [auth 14],
AL [auth 1H],
ALA [auth 14],
AM [auth 1H],
AMA [auth 14],
AN [auth 1H],
ANA [auth 14],
AO [auth 1H],
AOA [auth 14],
AP [auth 1H],
APA [auth 14],
AQ [auth 1H],
AQA [auth 14],
AR [auth 1H],
ARA [auth 14],
AS [auth 1H],
ASA [auth 14],
AT [auth 1H],
ATA [auth 14],
AU [auth 1H],
AUA [auth 14],
AV [auth 1H],
AVA [auth 45],
AW [auth 1H],
AX [auth 1H],
AY [auth 1H],
AZ [auth 1H],
BAA [auth 1H],
BBA [auth 78],
BCA [auth 1G],
BDA [auth 1G],
BE [auth 13],
BEA [auth 1G],
BF [auth 13],
BFA [auth 2L],
BG [auth 13],
BGA [auth 14],
BH [auth 13],
BHA [auth 14],
BI [auth 13],
BIA [auth 14],
BJ [auth 1H],
BJA [auth 14],
BK [auth 1H],
BKA [auth 14],
BL [auth 1H],
BLA [auth 14],
BM [auth 1H],
BMA [auth 14],
BN [auth 1H],
BNA [auth 14],
BO [auth 1H],
BOA [auth 14],
BP [auth 1H],
BPA [auth 14],
BQ [auth 1H],
BQA [auth 14],
BR [auth 1H],
BRA [auth 14],
BS [auth 1H],
BSA [auth 14],
BT [auth 1H],
BTA [auth 14],
BU [auth 1H],
BUA [auth 14],
BV [auth 1H],
BVA [auth 45],
BW [auth 1H],
BX [auth 1H],
BY [auth 1H],
BZ [auth 1H],
CAA [auth 1H],
CBA [auth 88],
CCA [auth 1G],
CDA [auth 1G],
CE [auth 13],
CEA [auth 1G],
CF [auth 13],
CFA [auth 2L],
CG [auth 13],
CGA [auth 14],
CH [auth 13],
CHA [auth 14],
CI [auth 13],
CIA [auth 14],
CJ [auth 1H],
CJA [auth 14],
CK [auth 1H],
CKA [auth 14],
CL [auth 1H],
CLA [auth 14],
CM [auth 1H],
CMA [auth 14],
CN [auth 1H],
CNA [auth 14],
CO [auth 1H],
COA [auth 14],
CP [auth 1H],
CPA [auth 14],
CQ [auth 1H],
CQA [auth 14],
CR [auth 1H],
CRA [auth 14],
CS [auth 1H],
CSA [auth 14],
CT [auth 1H],
CTA [auth 14],
CU [auth 1H],
CUA [auth 14],
CV [auth 1H],
CVA [auth 55],
CW [auth 1H],
CX [auth 1H],
CY [auth 1H],
CZ [auth 1H],
DAA [auth 1H],
DBA [auth 98],
DCA [auth 1G],
DDA [auth 1G],
DE [auth 13],
DEA [auth 1G],
DF [auth 13],
DFA [auth 14],
DG [auth 13],
DGA [auth 14],
DH [auth 13],
DHA [auth 14],
DI [auth 13],
DIA [auth 14],
DJ [auth 1H],
DJA [auth 14],
DK [auth 1H],
DKA [auth 14],
DL [auth 1H],
DLA [auth 14],
DM [auth 1H],
DMA [auth 14],
DN [auth 1H],
DNA [auth 14],
DO [auth 1H],
DOA [auth 14],
DP [auth 1H],
DPA [auth 14],
DQ [auth 1H],
DQA [auth 14],
DR [auth 1H],
DRA [auth 14],
DS [auth 1H],
DSA [auth 14],
DT [auth 1H],
DTA [auth 14],
DU [auth 1H],
DUA [auth 14],
DV [auth 1H],
DW [auth 1H],
DX [auth 1H],
DY [auth 1H],
DZ [auth 1H],
EAA [auth 1H],
ECA [auth 1G],
EDA [auth 1G],
EE [auth 13],
EEA [auth 1G],
EF [auth 13],
EFA [auth 14],
EG [auth 13],
EGA [auth 14],
EH [auth 13],
EHA [auth 14],
EI [auth 13],
EIA [auth 14],
EJ [auth 1H],
EJA [auth 14],
EK [auth 1H],
EKA [auth 14],
EL [auth 1H],
ELA [auth 14],
EM [auth 1H],
EMA [auth 14],
EN [auth 1H],
ENA [auth 14],
EO [auth 1H],
EOA [auth 14],
EP [auth 1H],
EPA [auth 14],
EQ [auth 1H],
EQA [auth 14],
ER [auth 1H],
ERA [auth 14],
ES [auth 1H],
ESA [auth 14],
ET [auth 1H],
ETA [auth 14],
EU [auth 1H],
EUA [auth 14],
EV [auth 1H],
EVA [auth E5],
EW [auth 1H],
EX [auth 1H],
EY [auth 1H],
EZ [auth 1H],
FAA [auth 1H],
FBA [auth I8],
FCA [auth 1G],
FD [auth 13],
FDA [auth 1G],
FE [auth 13],
FEA [auth 1G],
FF [auth 13],
FFA [auth 14],
FG [auth 13],
FGA [auth 14],
FH [auth 13],
FHA [auth 14],
FI [auth 13],
FIA [auth 14],
FJ [auth 1H],
FJA [auth 14],
FK [auth 1H],
FKA [auth 14],
FL [auth 1H],
FLA [auth 14],
FM [auth 1H],
FMA [auth 14],
FN [auth 1H],
FNA [auth 14],
FO [auth 1H],
FOA [auth 14],
FP [auth 1H],
FPA [auth 14],
FQ [auth 1H],
FQA [auth 14],
FR [auth 1H],
FRA [auth 14],
FS [auth 1H],
FSA [auth 14],
FT [auth 1H],
FTA [auth 14],
FU [auth 1H],
FUA [auth 14],
FV [auth 1H],
FW [auth 1H],
FX [auth 1H],
FY [auth 1H],
FZ [auth 1H],
GAA [auth 1H],
GBA [auth I8],
GCA [auth 1G],
GD [auth 13],
GDA [auth 1G],
GE [auth 13],
GEA [auth 1G],
GF [auth 13],
GFA [auth 14],
GG [auth 13],
GGA [auth 14],
GH [auth 13],
GHA [auth 14],
GI [auth 13],
GIA [auth 14],
GJ [auth 1H],
GJA [auth 14],
GK [auth 1H],
GKA [auth 14],
GL [auth 1H],
GLA [auth 14],
GM [auth 1H],
GMA [auth 14],
GN [auth 1H],
GNA [auth 14],
GO [auth 1H],
GOA [auth 14],
GP [auth 1H],
GPA [auth 14],
GQ [auth 1H],
GQA [auth 14],
GR [auth 1H],
GRA [auth 14],
GS [auth 1H],
GSA [auth 14],
GT [auth 1H],
GTA [auth 14],
GU [auth 1H],
GUA [auth 14],
GV [auth 1H],
GW [auth 1H],
GX [auth 1H],
GY [auth 1H],
GZ [auth 1H],
HAA [auth 1H],
HBA [auth I8],
HCA [auth 1G],
HD [auth 13],
HDA [auth 1G],
HE [auth 13],
HEA [auth 1G],
HF [auth 13],
HFA [auth 14],
HG [auth 13],
HGA [auth 14],
HH [auth 13],
HHA [auth 14],
HI [auth 1E],
HIA [auth 14],
HJ [auth 1H],
HJA [auth 14],
HK [auth 1H],
HKA [auth 14],
HL [auth 1H],
HLA [auth 14],
HM [auth 1H],
HMA [auth 14],
HN [auth 1H],
HNA [auth 14],
HO [auth 1H],
HOA [auth 14],
HP [auth 1H],
HPA [auth 14],
HQ [auth 1H],
HQA [auth 14],
HR [auth 1H],
HRA [auth 14],
HS [auth 1H],
HSA [auth 14],
HT [auth 1H],
HTA [auth 14],
HU [auth 1H],
HUA [auth 14],
HV [auth 1H],
HW [auth 1H],
HX [auth 1H],
HY [auth 1H],
HZ [auth 1H],
IAA [auth 1H],
IBA [auth J8],
ICA [auth 1G],
ID [auth 13],
IDA [auth 1G],
IE [auth 13],
IEA [auth 1G],
IF [auth 13],
IFA [auth 14],
IG [auth 13],
IGA [auth 14],
IH [auth 13],
IHA [auth 14],
IIA [auth 14],
IJ [auth 1H],
IJA [auth 14],
IK [auth 1H],
IKA [auth 14],
IL [auth 1H],
ILA [auth 14],
IM [auth 1H],
IMA [auth 14],
IN [auth 1H],
INA [auth 14],
IO [auth 1H],
IOA [auth 14],
IP [auth 1H],
IPA [auth 14],
IQ [auth 1H],
IQA [auth 14],
IR [auth 1H],
IRA [auth 14],
IS [auth 1H],
ISA [auth 14],
IT [auth 1H],
ITA [auth 14],
IU [auth 1H],
IUA [auth 14],
IV [auth 1H],
IW [auth 1H],
IX [auth 1H],
IY [auth 1H],
IZ [auth 1H],
JAA [auth 1H],
JBA [auth L8],
JCA [auth 1G],
JD [auth 13],
JDA [auth 1G],
JE [auth 13],
JEA [auth 1G],
JF [auth 13],
JFA [auth 14],
JG [auth 13],
JGA [auth 14],
JH [auth 13],
JHA [auth 14],
JI [auth 5E],
JIA [auth 14],
JJ [auth 1H],
JJA [auth 14],
JK [auth 1H],
JKA [auth 14],
JL [auth 1H],
JLA [auth 14],
JM [auth 1H],
JMA [auth 14],
JN [auth 1H],
JNA [auth 14],
JO [auth 1H],
JOA [auth 14],
JP [auth 1H],
JPA [auth 14],
JQ [auth 1H],
JQA [auth 14],
JR [auth 1H],
JRA [auth 14],
JS [auth 1H],
JSA [auth 14],
JT [auth 1H],
JTA [auth 14],
JU [auth 1H],
JUA [auth 14],
JV [auth 1H],
JW [auth 1H],
JX [auth 1H],
JY [auth 1H],
JZ [auth 1H],
KAA [auth 1H],
KBA [auth P8],
KCA [auth 1G],
KD [auth 13],
KDA [auth 1G],
KE [auth 13],
KEA [auth 1G],
KF [auth 13],
KFA [auth 14],
KG [auth 13],
KGA [auth 14],
KH [auth 13],
KHA [auth 14],
KIA [auth 14],
KJ [auth 1H],
KJA [auth 14],
KK [auth 1H],
KKA [auth 14],
KL [auth 1H],
KLA [auth 14],
KM [auth 1H],
KMA [auth 14],
KN [auth 1H],
KNA [auth 14],
KO [auth 1H],
KOA [auth 14],
KP [auth 1H],
KPA [auth 14],
KQ [auth 1H],
KQA [auth 14],
KR [auth 1H],
KRA [auth 14],
KS [auth 1H],
KSA [auth 14],
KT [auth 1H],
KTA [auth 14],
KU [auth 1H],
KUA [auth 14],
KV [auth 1H],
KW [auth 1H],
KX [auth 1H],
KY [auth 1H],
KZ [auth 1H],
LAA [auth 1H],
LBA [auth Q8],
LCA [auth 1G],
LD [auth 13],
LDA [auth 1G],
LE [auth 13],
LEA [auth 1G],
LF [auth 13],
LFA [auth 14],
LG [auth 13],
LGA [auth 14],
LH [auth 13],
LHA [auth 14],
LI [auth 1K],
LIA [auth 14],
LJ [auth 1H],
LJA [auth 14],
LK [auth 1H],
LKA [auth 14],
LL [auth 1H],
LLA [auth 14],
LM [auth 1H],
LMA [auth 14],
LN [auth 1H],
LNA [auth 14],
LO [auth 1H],
LOA [auth 14],
LP [auth 1H],
LPA [auth 14],
LQ [auth 1H],
LQA [auth 14],
LR [auth 1H],
LRA [auth 14],
LS [auth 1H],
LSA [auth 14],
LT [auth 1H],
LTA [auth 14],
LU [auth 1H],
LUA [auth 14],
LV [auth 1H],
LW [auth 1H],
LX [auth 1H],
LY [auth 1H],
LZ [auth 1H],
MAA [auth 1H],
MBA [auth 1G],
MCA [auth 1G],
MD [auth 13],
MDA [auth 1G],
ME [auth 13],
MEA [auth 1G],
MF [auth 13],
MFA [auth 14],
MG [auth 13],
MGA [auth 14],
MH [auth 13],
MHA [auth 14],
MI [auth 2K],
MIA [auth 14],
MJ [auth 1H],
MJA [auth 14],
MK [auth 1H],
MKA [auth 14],
ML [auth 1H],
MLA [auth 14],
MM [auth 1H],
MMA [auth 14],
MN [auth 1H],
MNA [auth 14],
MO [auth 1H],
MOA [auth 14],
MP [auth 1H],
MPA [auth 14],
MQ [auth 1H],
MQA [auth 14],
MR [auth 1H],
MRA [auth 14],
MS [auth 1H],
MSA [auth 14],
MT [auth 1H],
MTA [auth 14],
MU [auth 1H],
MUA [auth 1J],
MV [auth 1H],
MW [auth 1H],
MX [auth 1H],
MY [auth 1H],
MZ [auth 1H],
NAA [auth 1H],
NBA [auth 1G],
NCA [auth 1G],
ND [auth 13],
NDA [auth 1G],
NE [auth 13],
NEA [auth 1G],
NF [auth 13],
NFA [auth 14],
NG [auth 13],
NGA [auth 14],
NH [auth 13],
NHA [auth 14],
NI [auth 2K],
NIA [auth 14],
NJ [auth 1H],
NJA [auth 14],
NK [auth 1H],
NKA [auth 14],
NL [auth 1H],
NLA [auth 14],
NM [auth 1H],
NMA [auth 14],
NN [auth 1H],
NNA [auth 14],
NO [auth 1H],
NOA [auth 14],
NP [auth 1H],
NPA [auth 14],
NQ [auth 1H],
NQA [auth 14],
NR [auth 1H],
NRA [auth 14],
NS [auth 1H],
NSA [auth 14],
NT [auth 1H],
NTA [auth 14],
NU [auth 1H],
NUA [auth 1J],
NV [auth 1H],
NW [auth 1H],
NX [auth 1H],
NY [auth 1H],
NZ [auth 1H],
OAA [auth 1H],
OBA [auth 1G],
OCA [auth 1G],
OD [auth 13],
ODA [auth 1G],
OE [auth 13],
OEA [auth 1G],
OF [auth 13],
OFA [auth 14],
OG [auth 13],
OGA [auth 14],
OH [auth 13],
OHA [auth 14],
OI [auth 2K],
OIA [auth 14],
OJ [auth 1H],
OJA [auth 14],
OK [auth 1H],
OKA [auth 14],
OL [auth 1H],
OLA [auth 14],
OM [auth 1H],
OMA [auth 14],
ON [auth 1H],
ONA [auth 14],
OO [auth 1H],
OOA [auth 14],
OP [auth 1H],
OPA [auth 14],
OQ [auth 1H],
OQA [auth 14],
OR [auth 1H],
ORA [auth 14],
OS [auth 1H],
OSA [auth 14],
OT [auth 1H],
OTA [auth 14],
OU [auth 1H],
OUA [auth 1J],
OV [auth 1H],
OW [auth 1H],
OX [auth 1H],
OY [auth 1H],
OZ [auth 1H],
PAA [auth 16],
PBA [auth 1G],
PCA [auth 1G],
PD [auth 13],
PDA [auth 1G],
PE [auth 13],
PEA [auth 1G],
PF [auth 13],
PFA [auth 14],
PG [auth 13],
PGA [auth 14],
PH [auth 13],
PHA [auth 14],
PI [auth 3K],
PIA [auth 14],
PJ [auth 1H],
PJA [auth 14],
PK [auth 1H],
PKA [auth 14],
PL [auth 1H],
PLA [auth 14],
PM [auth 1H],
PMA [auth 14],
PN [auth 1H],
PNA [auth 14],
PO [auth 1H],
POA [auth 14],
PP [auth 1H],
PPA [auth 14],
PQ [auth 1H],
PQA [auth 14],
PR [auth 1H],
PRA [auth 14],
PS [auth 1H],
PSA [auth 14],
PT [auth 1H],
PTA [auth 14],
PU [auth 1H],
PUA [auth 1J],
PV [auth 1H],
PW [auth 1H],
PX [auth 1H],
PY [auth 1H],
PZ [auth 1H],
QAA [auth 16],
QBA [auth 1G],
QCA [auth 1G],
QD [auth 13],
QDA [auth 1G],
QE [auth 13],
QEA [auth 1G],
QF [auth 13],
QFA [auth 14],
QG [auth 13],
QGA [auth 14],
QH [auth 13],
QHA [auth 14],
QI [auth 1H],
QIA [auth 14],
QJ [auth 1H],
QJA [auth 14],
QK [auth 1H],
QKA [auth 14],
QL [auth 1H],
QLA [auth 14],
QM [auth 1H],
QMA [auth 14],
QN [auth 1H],
QNA [auth 14],
QO [auth 1H],
QOA [auth 14],
QP [auth 1H],
QPA [auth 14],
QQ [auth 1H],
QQA [auth 14],
QR [auth 1H],
QRA [auth 14],
QS [auth 1H],
QSA [auth 14],
QT [auth 1H],
QTA [auth 14],
QU [auth 1H],
QUA [auth 1J],
QV [auth 1H],
QW [auth 1H],
QX [auth 1H],
QY [auth 1H],
QZ [auth 1H],
RAA [auth 16],
RBA [auth 1G],
RCA [auth 1G],
RD [auth 13],
RDA [auth 1G],
RE [auth 13],
REA [auth 1G],
RF [auth 13],
RFA [auth 14],
RG [auth 13],
RGA [auth 14],
RH [auth 13],
RHA [auth 14],
RI [auth 1H],
RIA [auth 14],
RJ [auth 1H],
RJA [auth 14],
RK [auth 1H],
RKA [auth 14],
RL [auth 1H],
RLA [auth 14],
RM [auth 1H],
RMA [auth 14],
RN [auth 1H],
RNA [auth 14],
RO [auth 1H],
ROA [auth 14],
RP [auth 1H],
RPA [auth 14],
RQ [auth 1H],
RQA [auth 14],
RR [auth 1H],
RRA [auth 14],
RS [auth 1H],
RSA [auth 14],
RT [auth 1H],
RTA [auth 14],
RU [auth 1H],
RUA [auth 29],
RV [auth 1H],
RW [auth 1H],
RX [auth 1H],
RY [auth 1H],
RZ [auth 1H],
SAA [auth 16],
SBA [auth 1G],
SCA [auth 1G],
SD [auth 13],
SDA [auth 1G],
SE [auth 13],
SEA [auth 1G],
SF [auth 13],
SFA [auth 14],
SG [auth 13],
SGA [auth 14],
SH [auth 13],
SHA [auth 14],
SI [auth 1H],
SIA [auth 14],
SJ [auth 1H],
SJA [auth 14],
SK [auth 1H],
SKA [auth 14],
SL [auth 1H],
SLA [auth 14],
SM [auth 1H],
SMA [auth 14],
SN [auth 1H],
SNA [auth 14],
SO [auth 1H],
SOA [auth 14],
SP [auth 1H],
SPA [auth 14],
SQ [auth 1H],
SQA [auth 14],
SR [auth 1H],
SRA [auth 14],
SS [auth 1H],
SSA [auth 14],
ST [auth 1H],
STA [auth 14],
SU [auth 1H],
SUA [auth 29],
SV [auth 1H],
SW [auth 1H],
SX [auth 1H],
SY [auth 1H],
SZ [auth 1H],
TAA [auth 16],
TBA [auth 1G],
TCA [auth 1G],
TD [auth 13],
TDA [auth 1G],
TE [auth 13],
TEA [auth 1G],
TF [auth 13],
TFA [auth 14],
TG [auth 13],
TGA [auth 14],
TH [auth 13],
THA [auth 14],
TI [auth 1H],
TIA [auth 14],
TJ [auth 1H],
TJA [auth 14],
TK [auth 1H],
TKA [auth 14],
TL [auth 1H],
TLA [auth 14],
TM [auth 1H],
TMA [auth 14],
TN [auth 1H],
TNA [auth 14],
TO [auth 1H],
TOA [auth 14],
TP [auth 1H],
TPA [auth 14],
TQ [auth 1H],
TQA [auth 14],
TR [auth 1H],
TRA [auth 14],
TS [auth 1H],
TSA [auth 14],
TT [auth 1H],
TTA [auth 14],
TU [auth 1H],
TUA [auth 29],
TV [auth 1H],
TW [auth 1H],
TX [auth 1H],
TY [auth 1H],
TZ [auth 1H],
UAA [auth 16],
UBA [auth 1G],
UCA [auth 1G],
UD [auth 13],
UDA [auth 1G],
UE [auth 13],
UEA [auth 1G],
UF [auth 13],
UFA [auth 14],
UG [auth 13],
UGA [auth 14],
UH [auth 13],
UHA [auth 14],
UI [auth 1H],
UIA [auth 14],
UJ [auth 1H],
UJA [auth 14],
UK [auth 1H],
UKA [auth 14],
UL [auth 1H],
ULA [auth 14],
UM [auth 1H],
UMA [auth 14],
UN [auth 1H],
UNA [auth 14],
UO [auth 1H],
UOA [auth 14],
UP [auth 1H],
UPA [auth 14],
UQ [auth 1H],
UQA [auth 14],
UR [auth 1H],
URA [auth 14],
US [auth 1H],
USA [auth 14],
UT [auth 1H],
UTA [auth 14],
UU [auth 1H],
UUA [auth 29],
UV [auth 1H],
UW [auth 1H],
UX [auth 1H],
UY [auth 1H],
UZ [auth 1H],
VAA [auth 16],
VBA [auth 1G],
VCA [auth 1G],
VD [auth 13],
VDA [auth 1G],
VE [auth 13],
VEA [auth 1G],
VF [auth 13],
VFA [auth 14],
VG [auth 13],
VGA [auth 14],
VH [auth 13],
VHA [auth 14],
VI [auth 1H],
VIA [auth 14],
VJ [auth 1H],
VJA [auth 14],
VK [auth 1H],
VKA [auth 14],
VL [auth 1H],
VLA [auth 14],
VM [auth 1H],
VMA [auth 14],
VN [auth 1H],
VNA [auth 14],
VO [auth 1H],
VOA [auth 14],
VP [auth 1H],
VPA [auth 14],
VQ [auth 1H],
VQA [auth 14],
VR [auth 1H],
VRA [auth 14],
VS [auth 1H],
VSA [auth 14],
VT [auth 1H],
VTA [auth 14],
VU [auth 1H],
VUA [auth 39],
VV [auth 1H],
VW [auth 1H],
VX [auth 1H],
VY [auth 1H],
VZ [auth 1H],
WAA [auth 16],
WBA [auth 1G],
WCA [auth 1G],
WD [auth 13],
WDA [auth 1G],
WE [auth 13],
WEA [auth 1G],
WF [auth 13],
WFA [auth 14],
WG [auth 13],
WGA [auth 14],
WH [auth 13],
WHA [auth 14],
WI [auth 1H],
WIA [auth 14],
WJ [auth 1H],
WJA [auth 14],
WK [auth 1H],
WKA [auth 14],
WL [auth 1H],
WLA [auth 14],
WM [auth 1H],
WMA [auth 14],
WN [auth 1H],
WNA [auth 14],
WO [auth 1H],
WOA [auth 14],
WP [auth 1H],
WPA [auth 14],
WQ [auth 1H],
WQA [auth 14],
WR [auth 1H],
WRA [auth 14],
WS [auth 1H],
WSA [auth 14],
WT [auth 1H],
WTA [auth 14],
WU [auth 1H],
WUA [auth 25],
WV [auth 1H],
WW [auth 1H],
WX [auth 1H],
WY [auth 1H],
WZ [auth 1H],
XAA [auth 16],
XBA [auth 1G],
XCA [auth 1G],
XD [auth 13],
XDA [auth 1G],
XE [auth 13],
XEA [auth 1G],
XF [auth 13],
XFA [auth 14],
XG [auth 13],
XGA [auth 14],
XH [auth 13],
XHA [auth 14],
XI [auth 1H],
XIA [auth 14],
XJ [auth 1H],
XJA [auth 14],
XK [auth 1H],
XKA [auth 14],
XL [auth 1H],
XLA [auth 14],
XM [auth 1H],
XMA [auth 14],
XN [auth 1H],
XNA [auth 14],
XO [auth 1H],
XOA [auth 14],
XP [auth 1H],
XPA [auth 14],
XQ [auth 1H],
XQA [auth 14],
XR [auth 1H],
XRA [auth 14],
XS [auth 1H],
XSA [auth 14],
XT [auth 1H],
XTA [auth 14],
XU [auth 1H],
XUA [auth 35],
XV [auth 1H],
XW [auth 1H],
XX [auth 1H],
XY [auth 1H],
XZ [auth 1H],
YAA [auth 21],
YBA [auth 1G],
YCA [auth 1G],
YD [auth 13],
YDA [auth 1G],
YE [auth 13],
YF [auth 13],
YFA [auth 14],
YG [auth 13],
YGA [auth 14],
YH [auth 13],
YHA [auth 14],
YI [auth 1H],
YIA [auth 14],
YJ [auth 1H],
YJA [auth 14],
YK [auth 1H],
YKA [auth 14],
YL [auth 1H],
YLA [auth 14],
YM [auth 1H],
YMA [auth 14],
YN [auth 1H],
YNA [auth 14],
YO [auth 1H],
YOA [auth 14],
YP [auth 1H],
YPA [auth 14],
YQ [auth 1H],
YQA [auth 14],
YR [auth 1H],
YRA [auth 14],
YS [auth 1H],
YSA [auth 14],
YT [auth 1H],
YTA [auth 14],
YU [auth 1H],
YUA [auth 35],
YV [auth 1H],
YW [auth 1H],
YX [auth 1H],
YY [auth 1H],
YZ [auth 1H],
ZAA [auth 21],
ZBA [auth 1G],
ZCA [auth 1G],
ZD [auth 13],
ZDA [auth 1G],
ZE [auth 13],
ZF [auth 13],
ZFA [auth 14],
ZG [auth 13],
ZGA [auth 14],
ZH [auth 13],
ZHA [auth 14],
ZI [auth 1H],
ZIA [auth 14],
ZJ [auth 1H],
ZJA [auth 14],
ZK [auth 1H],
ZKA [auth 14],
ZL [auth 1H],
ZLA [auth 14],
ZM [auth 1H],
ZMA [auth 14],
ZN [auth 1H],
ZNA [auth 14],
ZO [auth 1H],
ZOA [auth 14],
ZP [auth 1H],
ZPA [auth 14],
ZQ [auth 1H],
ZQA [auth 14],
ZR [auth 1H],
ZRA [auth 14],
ZS [auth 1H],
ZSA [auth 14],
ZT [auth 1H],
ZTA [auth 14],
ZU [auth 1H],
ZUA [auth 35],
ZV [auth 1H],
ZW [auth 1H],
ZX [auth 1H],
ZY [auth 1H],
ZZ [auth 1H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.5α = 90
b = 450.1β = 90
c = 621.6γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-03
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description