5HAU

Crystal structure of antimicrobial peptide Bac7(1-19) bound to the Thermus thermophilus 70S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition.

Gagnon, M.G.Roy, R.N.Lomakin, I.B.Florin, T.Mankin, A.S.Steitz, T.A.

(2016) Nucleic Acids Res 44: 2439-2450

  • DOI: 10.1093/nar/gkw018
  • Primary Citation of Related Structures:  
    5HAU, 5HCQ, 5HCP, 5HD1, 5HCR

  • PubMed Abstract: 
  • With bacterial resistance becoming a serious threat to global public health, antimicrobial peptides (AMPs) have become a promising area of focus in antibiotic research. AMPs are derived from a diverse range of species, from prokaryotes to humans, with a mechanism of action that often involves disruption of the bacterial cell membrane ...

    With bacterial resistance becoming a serious threat to global public health, antimicrobial peptides (AMPs) have become a promising area of focus in antibiotic research. AMPs are derived from a diverse range of species, from prokaryotes to humans, with a mechanism of action that often involves disruption of the bacterial cell membrane. Proline-rich antimicrobial peptides (PrAMPs) are instead actively transported inside the bacterial cell where they bind and inactivate specific targets. Recently, it was reported that some PrAMPs, such as Bac71 -35, oncocins and apidaecins, bind and inactivate the bacterial ribosome. Here we report the crystal structures of Bac71 -35, Pyrrhocoricin, Metalnikowin and two oncocin derivatives, bound to the Thermus thermophilus 70S ribosome. Each of the PrAMPs blocks the peptide exit tunnel of the ribosome by simultaneously occupying three well characterized antibiotic-binding sites and interferes with the initiation step of translation, thereby revealing a common mechanism of action used by these PrAMPs to inactivate protein synthesis. Our study expands the repertoire of PrAMPs and provides a framework for designing new-generation therapeutics.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA thomas.steitz@yale.edu.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L1 1C2C229Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
Find proteins for Q5SLP7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2 1D2D276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3 1E2E206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4 1F2F210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5 1G2G182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6 1H2H180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
Find proteins for P0DOY8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10 1J2J173Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplJTTHA0209
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11 1K2K147Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplKTTHA0247
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13 1L2L140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14 1M2M122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15 1N2N150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
Find proteins for Q5SHQ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16 1O2O141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17 1P2P118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18 1Q2Q112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19 1R2R146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20 1S2S118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 19
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50S ribosomal protein L21 1T2T101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22 1U2U113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23 1V2V96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24 1W2W110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25 1X2X206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27 1Y2Y85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28 1Z2Z98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29 102072Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30 112160Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31 122271Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32 132360Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33 142454Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
Find proteins for P35871 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34 152549Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35 162665Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36 172737Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
Find proteins for Q5SHR2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2 1b2b256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3 1c2c239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 37
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30S ribosomal protein S4 1d2d209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5 1e2e162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6 1f2f101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7 1g2g156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8 1h2h138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 42
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30S ribosomal protein S9 1i2i128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 43
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30S ribosomal protein S10 1j2j105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 44
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30S ribosomal protein S11 1k2k129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 45
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30S ribosomal protein S12 1l2l132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 46
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30S ribosomal protein S13 1m2m126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 47
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30S ribosomal protein S14 type Z 1n2n61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
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30S ribosomal protein S15 1o2o89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 49
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30S ribosomal protein S16 1p2p88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 50
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30S ribosomal protein S17 1q2q105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 51
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30S ribosomal protein S18 1r2r88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 52
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30S ribosomal protein S19 1s2s93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 53
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30S ribosomal protein S20 1t2t106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 54
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30S ribosomal protein Thx 1u2u27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 55
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Chimera protein of 50S ribosomal protein L9 and Elongation factor G 1z2z758Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242fusAfusTTHA1695
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Find proteins for Q5SHN5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q5SHN5
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  • Reference Sequence
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
Cathelicidin-3 1x2x35Bos taurusMutation(s): 0 
Gene Names: CATHL3BAC7
Find proteins for P19661 (Bos taurus)
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S Ribosomal RNA1A, 2A2915Thermus thermophilus HB8
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S Ribosomal RNA1B, 2B121Thermus thermophilus HB8
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Entity ID: 34
MoleculeChainsLengthOrganismImage
16S Ribosomal RNA1a, 2a1521Thermus thermophilus HB8
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Entity ID: 56
MoleculeChainsLengthOrganismImage
mRNA1y, 2y24Escherichia virus T4
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Entity ID: 57
MoleculeChainsLengthOrganismImage
P-site tRNA1w, 2w77Escherichia coli
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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1z, 2z
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
SF4
Query on SF4

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1d, 2d
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

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12, 13, 14, 17, 1W, 1n, 22, 23, 24, 27, 2W, 2n
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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