SMTL ID : 3f9o.2 (1 other biounit)

Crystal Structure of the Di-Zinc Carbapenemase CphA from Aeromonas Hydrophila

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-dimer

Ligands

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 8 residues within 4Å: Chain A: W.41, H.70, D.72, H.147, C.166, H.204 Ligands: ZN.13, ZN.14 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.147, A:H.204 SO4.2: 2 residues within 4Å: Chain A: H.127, D.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.126, A:D.128 Water bridges: A:G.129 Salt bridges: A:H.127 SO4.3: 4 residues within 4Å: Chain A: A.178, D.179, V.180, K.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.179, A:V.180, A:K.181 SO4.4: 4 residues within 4Å: Chain A: F.29, G.30, S.57, K.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.57, A:S.57 Water bridges: A:K.59 Salt bridges: A:K.59 SO4.16: 8 residues within 4Å: Chain B: W.41, H.70, D.72, H.147, C.166, H.204 Ligands: ZN.28, ZN.29 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.147, B:H.204 SO4.17: 2 residues within 4Å: Chain B: H.127, D.128 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.126, B:D.128 Water bridges: B:G.129 Salt bridges: B:H.127 SO4.18: 4 residues within 4Å: Chain B: A.178, D.179, V.180, K.181 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.179, B:D.179, B:V.180, B:K.181 SO4.19: 4 residues within 4Å: Chain B: F.29, G.30, S.57, K.59 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.57, B:S.57 Water bridges: B:K.59 Salt bridges: B:K.59

4 x CO3: CARBONATE ION(Non-functional Binders)

CO3.5: 6 residues within 4Å: Chain A: L.190, K.191, K.194, L.195, I.197, I.214 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.190, A:L.195, A:L.195 CO3.6: 3 residues within 4Å: Chain A: R.109, P.116, D.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.117 CO3.20: 6 residues within 4Å: Chain B: L.190, K.191, K.194, L.195, I.197, I.214 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.190, B:L.195, B:L.195 CO3.21: 3 residues within 4Å: Chain B: R.109, P.116, D.117 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.117

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 7 residues within 4Å: Chain A: N.68, H.147, T.148, G.151, N.165, C.166, I.167 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: R.109 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: Q.7 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Ligands: CL.11, ZN.15 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain A: H.209, E.212, L.213 Ligands: CL.10, CL.12, ZN.15 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: H.209, G.210 Ligands: CL.11, ZN.15 Ligand excluded by PLIP CL.22: 7 residues within 4Å: Chain B: N.68, H.147, T.148, G.151, N.165, C.166, I.167 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain B: R.109 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain B: Q.7 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Ligands: CL.26, ZN.30 Ligand excluded by PLIP CL.26: 6 residues within 4Å: Chain B: H.209, E.212, L.213 Ligands: CL.25, CL.27, ZN.30 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain B: H.209, G.210 Ligands: CL.26, ZN.30 Ligand excluded by PLIP

6 x ZN: ZINC ION(Non-covalent)

ZN.13: 5 residues within 4Å: Chain A: D.72, R.73, C.166, H.204 Ligands: SO4.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.72, A:C.166, A:H.204 ZN.14: 3 residues within 4Å: Chain A: H.70, H.147 Ligands: SO4.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.70, A:H.147, H2O.8 ZN.15: 4 residues within 4Å: Chain A: H.209 Ligands: CL.10, CL.11, CL.12 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.209 ZN.28: 5 residues within 4Å: Chain B: D.72, R.73, C.166, H.204 Ligands: SO4.16 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.72, B:C.166, B:H.204 ZN.29: 3 residues within 4Å: Chain B: H.70, H.147 Ligands: SO4.16 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.70, B:H.147, H2O.16 ZN.30: 4 residues within 4Å: Chain B: H.209 Ligands: CL.25, CL.26, CL.27 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bebrone, C. et al., The structure of the dizinc subclass B2 metallo-beta-lactamase CphA reveals that the second inhibitory zinc ion binds in the histidine site. Antimicrob.Agents Chemother. (2009)

Release Date

2009-09-01

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-lactamase

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