SMTL ID : 1i0d.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.22, H.24, D.268 Ligands: CD.2, EDO.4, FMT.14 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.22, A:H.24, A:D.268, H2O.12 ZN.15: 6 residues within 4Å: Chain B: H.22, H.24, D.268 Ligands: CD.16, EDO.18, FMT.25 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.22, B:H.24, B:D.268, H2O.27

2 x CD: CADMIUM ION(Non-covalent)

CD.2: 5 residues within 4Å: Chain A: H.22, H.168, H.197 Ligands: ZN.1, FMT.14 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.168, A:H.197, H2O.9, H2O.12, H2O.13 CD.16: 4 residues within 4Å: Chain B: H.168, H.197 Ligands: ZN.15, FMT.25 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.168, B:H.197, H2O.27, H2O.27, H2O.27

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.17: 2 residues within 4Å: Chain B: N.5, I.121 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.121 Water bridges: B:R.131, B:R.131

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

EDO.4: 8 residues within 4Å: Chain A: H.24, W.98, D.268, F.273, S.275 Ligands: ZN.1, EDO.13, FMT.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.268 EDO.5: 1 residues within 4Å: Chain A: L.149 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: A.47, E.48, V.51, E.82, A.86 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.82 Water bridges: A:E.82, A:E.82, A:A.86 EDO.7: 3 residues within 4Å: Chain A: T.114, R.156 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.114, A:R.156 EDO.8: 1 residues within 4Å: Ligands: EDO.7 No protein-ligand interaction detected (PLIP) EDO.10: 6 residues within 4Å: Chain A: D.100, P.101, P.102 Chain B: D.100, P.101, P.102 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.100, B:D.100 Water bridges: B:R.106 EDO.11: 4 residues within 4Å: Chain A: S.14, E.15, G.17, R.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.63, A:H.90 EDO.12: 3 residues within 4Å: Chain A: R.8, G.9, P.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.10 EDO.13: 7 residues within 4Å: Chain A: W.98, F.99, F.273, S.275, Y.276 Chain B: L.103 Ligands: EDO.4 No protein-ligand interaction detected (PLIP) EDO.18: 8 residues within 4Å: Chain B: H.24, W.98, D.268, F.273, S.275 Ligands: ZN.15, EDO.24, FMT.25 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.24 Water bridges: B:S.275 EDO.19: 2 residues within 4Å: Chain B: T.114, R.156 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.114, B:R.156 EDO.20: 4 residues within 4Å: Chain B: R.43, K.44, A.47, E.82 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.43, B:E.82 EDO.21: 5 residues within 4Å: Chain B: P.223, W.244, V.287, N.288, F.294 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.223 Water bridges: B:V.287 EDO.23: 5 residues within 4Å: Chain B: S.14, E.15, G.17, R.63, H.90 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.90 EDO.24: 6 residues within 4Å: Chain B: H.224, D.268, L.270, F.273, M.284 Ligands: EDO.18 4 PLIP interactions: 4 interactions with chain B Water bridges: B:H.24, B:H.221, B:D.268, B:D.268

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

PEL.9: 7 residues within 4Å: Chain A: M.260, K.261, E.311, T.312, G.315, I.316, N.320 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.260, A:K.261 PEL.22: 8 residues within 4Å: Chain B: M.260, K.261, E.311, T.312, G.315, I.316, N.320, R.323 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:M.260, B:K.261 Hydrogen bonds: B:K.261, B:K.261

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

FMT.14: 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, CD.2, EDO.4 No protein-ligand interaction detected (PLIP) FMT.25: 11 residues within 4Å: Chain B: H.22, H.24, V.68, I.73, W.98, K.136, H.168, H.197 Ligands: ZN.15, CD.16, EDO.18 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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