4WOI

4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.174 

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This is version 1.4 of the entry. See complete history


Literature

Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions.

Wasserman, M.R.Pulk, A.Zhou, Z.Altman, R.B.Zinder, J.C.Green, K.D.Garneau-Tsodikova, S.Doudna Cate, J.H.Blanchard, S.C.

(2015) Nat Commun 6: 7896-7896

  • DOI: https://doi.org/10.1038/ncomms8896
  • Primary Citation of Related Structures:  
    4WOI

  • PubMed Abstract: 

    Dynamic remodelling of intersubunit bridge B2, a conserved RNA domain of the bacterial ribosome connecting helices 44 (h44) and 69 (H69) of the small and large subunit, respectively, impacts translation by controlling intersubunit rotation. Here we show that aminoglycosides chemically related to neomycin-paromomycin, ribostamycin and neamine-each bind to sites within h44 and H69 to perturb bridge B2 and affect subunit rotation. Neomycin and paromomycin, which only differ by their ring-I 6'-polar group, drive subunit rotation in opposite directions. This suggests that their distinct actions hinge on the 6'-substituent and the drug's net positive charge. By solving the crystal structure of the paromomycin-ribosome complex, we observe specific contacts between the apical tip of H69 and the 6'-hydroxyl on paromomycin from within the drug's canonical h44-binding site. These results indicate that aminoglycoside actions must be framed in the context of bridge B2 and their regulation of subunit rotation.


  • Organizational Affiliation

    Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth AB],
KC [auth DB]
241Escherichia coli K-12Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth AC],
LC [auth DC]
233Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7V3 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth AD],
MC [auth DD]
206Escherichia coli K-12Mutation(s): 0 
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Find proteins for P0A7V8 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth AE],
NC [auth DE]
167Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth AF],
OC [auth DF]
135Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P02358 (Escherichia coli (strain K12))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth AG],
PC [auth DG]
179Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P02359 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth AH],
QC [auth DH]
130Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth AI],
RC [auth DI]
130Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7X3 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth AJ],
SC [auth DJ]
103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth AK],
TC [auth DK]
129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth AL],
UC [auth DL]
124Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth AM],
VC [auth DM]
118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth AN],
WC [auth DN]
101Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth AO],
XC [auth DO]
89Escherichia coli O157:H7 str. TW14359Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth AP],
YC [auth DP]
82Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth AQ],
ZC [auth DQ]
84Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18AD [auth DR],
R [auth AR]
75Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19BD [auth DS],
S [auth AS]
92Escherichia coli K-12Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20CD [auth DT],
T [auth AT]
87Escherichia coli K-12Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21DD [auth DU],
U [auth AU]
71Escherichia coli K-12Mutation(s): 0 
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Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome-recycling factorV [auth AV]185Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A805 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2AA [auth BC],
GB [auth CC]
273Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3BA [auth BD],
HB [auth CD]
209Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4CA [auth BE],
IB [auth CE]
201Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5DA [auth BF],
JB [auth CF]
179Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6EA [auth BG],
KB [auth CG]
177Escherichia coli K-12Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9FA [auth BH],
LB [auth CH]
149Escherichia coli K-12Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11GA [auth BI],
MB [auth CI]
142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13HA [auth BJ],
NB [auth CJ]
142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14IA [auth BK],
OB [auth CK]
123Escherichia coli K-12Mutation(s): 0 
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Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15JA [auth BL],
PB [auth CL]
144Escherichia coli K-12Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16KA [auth BM],
QB [auth CM]
136Escherichia coli K-12Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17LA [auth BN],
RB [auth CN]
127Escherichia coli K-12Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18MA [auth BO],
SB [auth CO]
117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19NA [auth BP],
TB [auth CP]
115Escherichia coli K-12Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20OA [auth BQ],
UB [auth CQ]
118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21PA [auth BR],
VB [auth CR]
103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22QA [auth BS],
WB [auth CS]
110Escherichia coli K-12Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23RA [auth BT],
XB [auth CT]
100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24SA [auth BU],
YB [auth CU]
104Escherichia coli K-12Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25TA [auth BV],
ZB [auth CV]
94Escherichia coli K-12Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27AC [auth CW],
UA [auth BW]
85Escherichia coli K-12Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28BC [auth CX],
VA [auth BX]
78Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29CC [auth CY],
WA [auth BY]
63Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12))
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UniProt GroupP0A7M6
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30DC [auth CZ],
XA [auth BZ]
59Escherichia coli K-12Mutation(s): 0 
UniProt
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UniProt GroupP0AG51
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32EC [auth C0],
YA [auth B0]
57Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33FC [auth C1],
ZA [auth B1]
55Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34AB [auth B2],
GC [auth C2]
46Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35BB [auth B3],
HC [auth C3]
65Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36CB [auth B4],
IC [auth C4]
38Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1DB [auth B5]228Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth AA],
JC [auth DA]
1,542Escherichia coli str. K-12 substr. MDS42
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Entity ID: 23
MoleculeChains LengthOrganismImage
Messenger RNAED [auth DV],
W [auth AW]
16Enterobacteria phage L1
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Entity ID: 24
MoleculeChains LengthOrganismImage
Phenylalanine specific transfer RNA, tRNA-PheFD [auth DW],
X [auth AX]
76Escherichia coli str. K-12 substr. MDS42
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Entity ID: 25
MoleculeChains LengthOrganismImage
23S ribosomal RNAEB [auth CA],
Y [auth BA]
2,904Escherichia coli str. K-12 substr. MDS42
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Entity ID: 26
MoleculeChains LengthOrganismImage
5S ribosomal RNAFB [auth CB],
Z [auth BB]
120Escherichia coli str. K-12 substr. MDS42
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download Ideal Coordinates CCD File 
BG [auth BA]
CG [auth BA]
DG [auth BA]
EG [auth BA]
FG [auth BA]
BG [auth BA],
CG [auth BA],
DG [auth BA],
EG [auth BA],
FG [auth BA],
FU [auth CA],
GU [auth CA],
HU [auth CA],
IU [auth CA],
JU [auth CA],
RW [auth DA],
SW [auth DA],
ZF [auth AA]
PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
PU [auth C4],
VN [auth B4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AE [auth AA]
AF [auth AA]
AG [auth AN]
AH [auth BA]
AI [auth BA]
AE [auth AA],
AF [auth AA],
AG [auth AN],
AH [auth BA],
AI [auth BA],
AJ [auth BA],
AK [auth BA],
AL [auth BA],
AM [auth BA],
AN [auth BA],
AO [auth CA],
AP [auth CA],
AQ [auth CA],
AR [auth CA],
AS [auth CA],
AT [auth CA],
AU [auth CA],
AV [auth DA],
AW [auth DA],
BE [auth AA],
BF [auth AA],
BH [auth BA],
BI [auth BA],
BJ [auth BA],
BK [auth BA],
BL [auth BA],
BM [auth BA],
BN [auth BA],
BO [auth CA],
BP [auth CA],
BQ [auth CA],
BR [auth CA],
BS [auth CA],
BT [auth CA],
BU [auth CA],
BV [auth DA],
BW [auth DA],
CE [auth AA],
CF [auth AA],
CH [auth BA],
CI [auth BA],
CJ [auth BA],
CK [auth BA],
CL [auth BA],
CM [auth BA],
CN [auth BA],
CO [auth CA],
CP [auth CA],
CQ [auth CA],
CR [auth CA],
CS [auth CA],
CT [auth CA],
CU [auth CA],
CV [auth DA],
CW [auth DA],
DE [auth AA],
DF [auth AA],
DH [auth BA],
DI [auth BA],
DJ [auth BA],
DK [auth BA],
DL [auth BA],
DM [auth BA],
DN [auth BA],
DO [auth CA],
DP [auth CA],
DQ [auth CA],
DR [auth CA],
DS [auth CA],
DT [auth CA],
DU [auth CA],
DV [auth DA],
DW [auth DA],
EE [auth AA],
EF [auth AA],
EH [auth BA],
EI [auth BA],
EJ [auth BA],
EK [auth BA],
EL [auth BA],
EM [auth BA],
EN [auth BA],
EO [auth CA],
EP [auth CA],
EQ [auth CA],
ER [auth CA],
ES [auth CA],
ET [auth CA],
EU [auth CA],
EV [auth DA],
EW [auth DA],
FE [auth AA],
FF [auth AA],
FH [auth BA],
FI [auth BA],
FJ [auth BA],
FK [auth BA],
FL [auth BA],
FM [auth BA],
FN [auth BA],
FO [auth CA],
FP [auth CA],
FQ [auth CA],
FR [auth CA],
FS [auth CA],
FT [auth CA],
FV [auth DA],
FW [auth DA],
GD [auth AA],
GE [auth AA],
GF [auth AA],
GG [auth BA],
GH [auth BA],
GI [auth BA],
GJ [auth BA],
GK [auth BA],
GL [auth BA],
GM [auth BA],
GN [auth BA],
GO [auth CA],
GP [auth CA],
GQ [auth CA],
GR [auth CA],
GS [auth CA],
GT [auth CA],
GV [auth DA],
GW [auth DA],
HD [auth AA],
HE [auth AA],
HF [auth AA],
HG [auth BA],
HH [auth BA],
HI [auth BA],
HJ [auth BA],
HK [auth BA],
HL [auth BA],
HM [auth BA],
HN [auth BA],
HO [auth CA],
HP [auth CA],
HQ [auth CA],
HR [auth CA],
HS [auth CA],
HT [auth CA],
HV [auth DA],
HW [auth DA],
ID [auth AA],
IE [auth AA],
IF [auth AA],
IG [auth BA],
IH [auth BA],
II [auth BA],
IJ [auth BA],
IK [auth BA],
IL [auth BA],
IM [auth BA],
IN [auth BA],
IO [auth CA],
IP [auth CA],
IQ [auth CA],
IR [auth CA],
IS [auth CA],
IT [auth CA],
IV [auth DA],
IW [auth DA],
JD [auth AA],
JE [auth AA],
JF [auth AA],
JG [auth BA],
JH [auth BA],
JI [auth BA],
JJ [auth BA],
JK [auth BA],
JL [auth BA],
JM [auth BA],
JN [auth BA],
JO [auth CA],
JP [auth CA],
JQ [auth CA],
JR [auth CA],
JS [auth CA],
JT [auth CA],
JV [auth DA],
JW [auth DA],
KD [auth AA],
KE [auth AA],
KF [auth AA],
KG [auth BA],
KH [auth BA],
KI [auth BA],
KJ [auth BA],
KK [auth BA],
KL [auth BA],
KM [auth BA],
KN [auth BA],
KO [auth CA],
KP [auth CA],
KQ [auth CA],
KR [auth CA],
KS [auth CA],
KT [auth CA],
KU [auth CB],
KV [auth DA],
KW [auth DA],
LD [auth AA],
LE [auth AA],
LF [auth AA],
LG [auth BA],
LH [auth BA],
LI [auth BA],
LJ [auth BA],
LK [auth BA],
LL [auth BA],
LM [auth BA],
LN [auth BA],
LO [auth CA],
LP [auth CA],
LQ [auth CA],
LR [auth CA],
LS [auth CA],
LT [auth CA],
LU [auth CB],
LV [auth DA],
LW [auth DA],
MD [auth AA],
ME [auth AA],
MF [auth AA],
MG [auth BA],
MH [auth BA],
MI [auth BA],
MJ [auth BA],
MK [auth BA],
ML [auth BA],
MM [auth BA],
MN [auth BA],
MO [auth CA],
MP [auth CA],
MQ [auth CA],
MR [auth CA],
MS [auth CA],
MT [auth CA],
MU [auth CB],
MV [auth DA],
MW [auth DA],
ND [auth AA],
NE [auth AA],
NF [auth AA],
NG [auth BA],
NH [auth BA],
NI [auth BA],
NJ [auth BA],
NK [auth BA],
NL [auth BA],
NM [auth BA],
NN [auth BB],
NO [auth CA],
NP [auth CA],
NQ [auth CA],
NR [auth CA],
NS [auth CA],
NT [auth CA],
NU [auth CD],
NV [auth DA],
NW [auth DA],
OD [auth AA],
OE [auth AA],
OF [auth AA],
OG [auth BA],
OH [auth BA],
OI [auth BA],
OJ [auth BA],
OK [auth BA],
OL [auth BA],
OM [auth BA],
ON [auth BB],
OO [auth CA],
OP [auth CA],
OQ [auth CA],
OR [auth CA],
OS [auth CA],
OT [auth CA],
OU [auth CQ],
OV [auth DA],
OW [auth DA],
PD [auth AA],
PE [auth AA],
PF [auth AA],
PG [auth BA],
PH [auth BA],
PI [auth BA],
PJ [auth BA],
PK [auth BA],
PL [auth BA],
PM [auth BA],
PN [auth BB],
PO [auth CA],
PP [auth CA],
PQ [auth CA],
PR [auth CA],
PS [auth CA],
PT [auth CA],
PV [auth DA],
PW [auth DA],
QD [auth AA],
QE [auth AA],
QF [auth AA],
QG [auth BA],
QH [auth BA],
QI [auth BA],
QJ [auth BA],
QK [auth BA],
QL [auth BA],
QM [auth BA],
QN [auth BB],
QO [auth CA],
QP [auth CA],
QQ [auth CA],
QR [auth CA],
QS [auth CA],
QT [auth CA],
QU [auth DA],
QV [auth DA],
QW [auth DA],
RD [auth AA],
RE [auth AA],
RF [auth AA],
RG [auth BA],
RH [auth BA],
RI [auth BA],
RJ [auth BA],
RK [auth BA],
RL [auth BA],
RM [auth BA],
RN [auth BL],
RO [auth CA],
RP [auth CA],
RQ [auth CA],
RR [auth CA],
RS [auth CA],
RT [auth CA],
RU [auth DA],
RV [auth DA],
SD [auth AA],
SE [auth AA],
SF [auth AA],
SG [auth BA],
SH [auth BA],
SI [auth BA],
SJ [auth BA],
SK [auth BA],
SL [auth BA],
SM [auth BA],
SN [auth BL],
SO [auth CA],
SP [auth CA],
SQ [auth CA],
SR [auth CA],
SS [auth CA],
ST [auth CA],
SU [auth DA],
SV [auth DA],
TD [auth AA],
TE [auth AA],
TF [auth AA],
TG [auth BA],
TH [auth BA],
TI [auth BA],
TJ [auth BA],
TK [auth BA],
TL [auth BA],
TM [auth BA],
TN [auth BO],
TO [auth CA],
TP [auth CA],
TQ [auth CA],
TR [auth CA],
TS [auth CA],
TT [auth CA],
TU [auth DA],
TV [auth DA],
TW [auth DD],
UD [auth AA],
UE [auth AA],
UF [auth AA],
UG [auth BA],
UH [auth BA],
UI [auth BA],
UJ [auth BA],
UK [auth BA],
UL [auth BA],
UM [auth BA],
UN [auth BQ],
UO [auth CA],
UP [auth CA],
UQ [auth CA],
UR [auth CA],
US [auth CA],
UT [auth CA],
UU [auth DA],
UV [auth DA],
UW [auth DD],
VD [auth AA],
VE [auth AA],
VF [auth AA],
VG [auth BA],
VH [auth BA],
VI [auth BA],
VJ [auth BA],
VK [auth BA],
VL [auth BA],
VM [auth BA],
VO [auth CA],
VP [auth CA],
VQ [auth CA],
VR [auth CA],
VS [auth CA],
VT [auth CA],
VU [auth DA],
VV [auth DA],
VW [auth DN],
WD [auth AA],
WE [auth AA],
WF [auth AA],
WG [auth BA],
WH [auth BA],
WI [auth BA],
WJ [auth BA],
WK [auth BA],
WL [auth BA],
WM [auth BA],
WN [auth CA],
WO [auth CA],
WP [auth CA],
WQ [auth CA],
WR [auth CA],
WS [auth CA],
WT [auth CA],
WU [auth DA],
WV [auth DA],
XD [auth AA],
XE [auth AA],
XF [auth AA],
XG [auth BA],
XH [auth BA],
XI [auth BA],
XJ [auth BA],
XK [auth BA],
XL [auth BA],
XM [auth BA],
XN [auth CA],
XO [auth CA],
XP [auth CA],
XQ [auth CA],
XR [auth CA],
XS [auth CA],
XT [auth CA],
XU [auth DA],
XV [auth DA],
YD [auth AA],
YE [auth AA],
YF [auth AA],
YG [auth BA],
YH [auth BA],
YI [auth BA],
YJ [auth BA],
YK [auth BA],
YL [auth BA],
YM [auth BA],
YN [auth CA],
YO [auth CA],
YP [auth CA],
YQ [auth CA],
YR [auth CA],
YS [auth CA],
YT [auth CA],
YU [auth DA],
YV [auth DA],
ZD [auth AA],
ZE [auth AA],
ZG [auth BA],
ZH [auth BA],
ZI [auth BA],
ZJ [auth BA],
ZK [auth BA],
ZL [auth BA],
ZM [auth BA],
ZN [auth CA],
ZO [auth CA],
ZP [auth CA],
ZQ [auth CA],
ZR [auth CA],
ZS [auth CA],
ZT [auth CA],
ZU [auth DA],
ZV [auth DA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.1α = 90
b = 435.24β = 90
c = 614.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States2R01GM079238
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM65050
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R01AI090048
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA92584
Human Frontiers in Science ProgramUnited StatesRGY0088
National Science Foundation (NSF, United States)United States0644129
Department of Energy (DOE, United States)United StatesDE-AC0376SF00098

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Structure summary