SMTL ID : 1hzy.1

HIGH RESOLUTION STRUCTURE OF THE ZINC-CONTAINING PHOSPHOTRIESTERASE FROM PSEUDOMONAS DIMINUTA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.22, H.24, D.268 Ligands: ZN.2, EDO.4, FMT.16 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.22, A:H.24, A:D.268, H2O.9 ZN.2: 6 residues within 4Å: Chain A: H.22, H.168, H.197 Ligands: ZN.1, EDO.4, FMT.16 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.168, A:H.197, H2O.9, H2O.10 ZN.17: 7 residues within 4Å: Chain B: H.22, H.24, D.268 Ligands: ZN.18, EDO.20, EDO.27, FMT.30 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.22, B:H.24, B:D.268, H2O.23 ZN.18: 5 residues within 4Å: Chain B: H.168, H.197 Ligands: ZN.17, EDO.20, FMT.30 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.168, B:H.197, H2O.23, H2O.24

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 2 residues within 4Å: Chain A: N.5, I.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.121 Water bridges: A:R.131 NA.19: 2 residues within 4Å: Chain B: N.5, I.121 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.5 Water bridges: B:N.5, B:R.131

20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 9 residues within 4Å: Chain A: H.24, I.73, W.98, F.273 Ligands: ZN.1, ZN.2, EDO.13, EDO.14, FMT.16 Ligand excluded by PLIP EDO.5: 1 residues within 4Å: Chain A: L.149 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: A.47, E.48, V.51, E.82, A.86 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: T.114, R.156 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: D.100, P.101, P.102 Chain B: D.100, P.101, P.102 Ligand excluded by PLIP EDO.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: A.233, S.234, S.236, A.237 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: S.243, T.246 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: P.223, W.244, V.287, N.288, F.294 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: H.221, H.224, L.238, D.268, F.273 Ligands: EDO.4 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: W.98, F.99, F.273, S.275, Y.276 Ligands: EDO.4 Ligand excluded by PLIP EDO.20: 10 residues within 4Å: Chain B: H.24, I.73, W.98, F.273, S.275 Ligands: ZN.17, ZN.18, EDO.26, EDO.27, FMT.30 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain B: T.114, R.156 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: R.43, K.44, A.47, E.82 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: F.39, F.40, G.272, F.273, M.281 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: P.223, W.244, V.287, N.288, F.294 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: W.98, F.99, P.101, T.144, F.146, Q.147 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain A: L.103 Chain B: W.98, F.273, S.275, Y.276 Ligands: EDO.20 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: H.221, H.224, D.268, L.270 Ligands: ZN.17, EDO.20 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain B: S.14, E.15, G.17, R.63 Ligand excluded by PLIP

2 x PEL: 2-PHENYL-ETHANOL(Non-covalent)

PEL.15: 8 residues within 4Å: Chain A: M.260, K.261, E.311, T.312, G.315, I.316, N.320, R.323 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:M.260, A:K.261 Hydrogen bonds: A:K.261, A:K.261 PEL.29: 8 residues within 4Å: Chain B: M.260, K.261, E.311, T.312, G.315, I.316, N.320, R.323 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.261

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.16: 11 residues within 4Å: Chain A: H.22, H.24, V.68, I.73, W.98, K.136, H.168, H.197 Ligands: ZN.1, ZN.2, EDO.4 No protein-ligand interaction detected (PLIP) FMT.30: 11 residues within 4Å: Chain B: H.22, H.24, V.68, I.73, W.98, K.136, H.168, H.197 Ligands: ZN.17, ZN.18, EDO.20 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benning, M.M. et al., High resolution X-ray structures of different metal-substituted forms of phosphotriesterase from Pseudomonas diminuta. Biochemistry (2001)

Release Date

2001-04-04

Peptides

PHOSPHOTRIESTERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PHOSPHOTRIESTERASE

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