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

The Di Zinc Carbapenemase CphA N220G mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.72, R.73, C.166, H.204 Ligands: SO4.11 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.72, A:C.166, A:H.204, H2O.2 ZN.2: 3 residues within 4Å: Chain A: H.70, H.147 Ligands: SO4.11 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.70, A:H.147, H2O.8, H2O.10 ZN.3: 4 residues within 4Å: Chain A: H.209 Ligands: CL.4, CL.5, CL.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.209, H2O.10 ZN.21: 5 residues within 4Å: Chain B: D.72, R.73, C.166, H.204 Ligands: SO4.31 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.72, B:C.166, B:H.204, H2O.12 ZN.22: 3 residues within 4Å: Chain B: H.70, H.147 Ligands: SO4.31 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.70, B:H.147, H2O.18, H2O.20 ZN.23: 4 residues within 4Å: Chain B: H.209 Ligands: CL.24, CL.25, CL.26 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.209, H2O.20

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

CL.4: 2 residues within 4Å: Ligands: ZN.3, CL.5 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain A: H.209, E.212, L.213, H.216 Ligands: ZN.3, CL.4 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: H.209, G.210 Ligands: ZN.3 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: N.68, T.148, G.151, C.166, I.167 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: S.57, K.59 Ligands: CL.9 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: S.57, R.58 Ligands: CL.8 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: R.109 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Ligands: ZN.23, CL.25 Ligand excluded by PLIP CL.25: 6 residues within 4Å: Chain B: H.209, E.212, L.213, H.216 Ligands: ZN.23, CL.24 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: H.209, G.210 Ligands: ZN.23 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain B: N.68, T.148, G.151, C.166, I.167 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain B: S.57, K.59 Ligands: CL.29 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain B: S.57, R.58 Ligands: CL.28 Ligand excluded by PLIP CL.30: 1 residues within 4Å: Chain B: R.109 Ligand excluded by PLIP

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

SO4.11: 7 residues within 4Å: Chain A: H.70, D.72, H.147, C.166, H.204 Ligands: ZN.1, ZN.2 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.72 Salt bridges: A:H.147, A:H.204 SO4.12: 4 residues within 4Å: Chain A: E.48, K.51, L.52, R.55 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.48 Water bridges: A:E.48 Salt bridges: A:R.55 SO4.13: 4 residues within 4Å: Chain A: K.81, L.120, V.121, L.122 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.122 Water bridges: A:K.81 Salt bridges: A:K.81 SO4.14: 3 residues within 4Å: Chain A: R.91, R.94, V.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.94 Salt bridges: A:R.91 SO4.15: 4 residues within 4Å: Chain A: H.127, D.128, G.129, D.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.128, A:G.129 Salt bridges: A:H.127 SO4.16: 1 residues within 4Å: Chain A: K.98 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.98 SO4.17: 3 residues within 4Å: Chain A: R.109, P.116, D.117 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.117 Water bridges: A:R.109, A:E.114 Salt bridges: A:R.109 SO4.31: 7 residues within 4Å: Chain B: H.70, D.72, H.147, C.166, H.204 Ligands: ZN.21, ZN.22 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.72 Water bridges: B:H.147 Salt bridges: B:H.147, B:H.204 SO4.32: 4 residues within 4Å: Chain B: E.48, K.51, L.52, R.55 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.48 Salt bridges: B:R.55 SO4.33: 4 residues within 4Å: Chain B: K.81, L.120, V.121, L.122 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.122 Water bridges: B:K.81 Salt bridges: B:K.81 SO4.34: 3 residues within 4Å: Chain B: R.91, R.94, V.126 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.94 Salt bridges: B:R.91 SO4.35: 4 residues within 4Å: Chain B: H.127, D.128, G.129, D.130 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.128, B:D.128, B:G.129 Salt bridges: B:H.127 SO4.36: 1 residues within 4Å: Chain B: K.98 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.98 SO4.37: 3 residues within 4Å: Chain B: R.109, P.116, D.117 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.117 Water bridges: B:R.109, B:E.114 Salt bridges: B:R.109

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 6 residues within 4Å: Chain A: K.32, E.63, T.132, L.133, Q.134, E.135 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.63, A:Q.134, A:E.135 Water bridges: A:T.132, A:E.135 GOL.19: 4 residues within 4Å: Chain A: D.130, R.139, F.141, Y.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.130, A:R.139 GOL.20: 3 residues within 4Å: Chain A: K.171, L.172, G.173 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.173 Water bridges: A:L.172, A:L.172, A:G.173 GOL.38: 6 residues within 4Å: Chain B: K.32, E.63, T.132, L.133, Q.134, E.135 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.63, B:Q.134, B:E.135 Water bridges: B:T.132, B:T.132, B:E.135 GOL.39: 4 residues within 4Å: Chain B: D.130, R.139, F.141, Y.155 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.130, B:D.130, B:R.139 GOL.40: 3 residues within 4Å: Chain B: K.171, L.172, G.173 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.173 Water bridges: B:L.172, B:L.172, B:G.173

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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