SMTL ID : 1i0b.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 7 residues within 4Å: Chain A: H.22, H.24, K.136, D.268 Ligands: MN.2, EDO.4, FMT.17 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.22, A:H.24, A:D.268, H2O.11 MN.2: 4 residues within 4Å: Chain A: H.168, H.197 Ligands: MN.1, FMT.17 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.168, A:H.197, H2O.8, H2O.11, H2O.11 MN.18: 6 residues within 4Å: Chain B: H.22, H.24, D.268 Ligands: MN.19, EDO.21, FMT.36 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.22, B:H.24, B:D.268, H2O.25 MN.19: 5 residues within 4Å: Chain B: H.168, H.197 Ligands: MN.18, EDO.21, FMT.36 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.168, B:H.197, H2O.25, H2O.25, H2O.25

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

NA.3: 4 residues within 4Å: Chain A: N.5, I.121, Q.122, R.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.5 Water bridges: A:R.131 NA.20: 4 residues within 4Å: Chain B: N.5, I.121, Q.122, R.131 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.122 Water bridges: B:N.5

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

EDO.4: 7 residues within 4Å: Chain A: H.24, W.98, D.268, F.273, S.275 Ligands: MN.1, FMT.17 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: R.156 Ligands: EDO.8 Ligand excluded by PLIP EDO.8: 1 residues within 4Å: Ligands: EDO.7 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: S.14, E.15, A.16, G.17, R.63, H.90 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: R.8, G.9, P.10 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: F.39, F.40, G.272, F.273, M.281 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: I.300, R.304, Q.310, L.313, A.314 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: S.191, K.261, R.323 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: G.41, A.45 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: E.177, A.209, L.210, R.213 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain B: H.24, I.73, W.98, F.273, S.275 Ligands: MN.18, MN.19, FMT.36 Ligand excluded by PLIP EDO.22: 1 residues within 4Å: Chain B: T.114 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain B: R.43, K.44, E.82 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 A: D.100, P.101, P.102 Chain B: D.100, P.101, P.102 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: S.14, E.15, G.17, R.63, H.90 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: P.37, E.38, S.42, R.43 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain B: N.232, S.234, V.277, T.278, N.279, I.280, V.283 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain B: P.301, E.305 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain B: V.318, T.319, A.322 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain A: F.71, R.75, E.126 Chain B: G.31, R.34, A.35 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain B: K.252, D.256, K.306, G.307, V.308 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain B: G.41, A.45 Ligand excluded by PLIP EDO.34: 1 residues within 4Å: Chain B: R.85 Ligand excluded by PLIP

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

PEL.16: 7 residues within 4Å: Chain A: M.260, K.261, 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.35: 9 residues within 4Å: Chain B: M.260, K.261, E.311, T.312, G.315, I.316, T.319, 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.17: 10 residues within 4Å: Chain A: H.22, H.24, I.73, W.98, K.136, H.168, H.197 Ligands: MN.1, MN.2, EDO.4 No protein-ligand interaction detected (PLIP) FMT.36: 11 residues within 4Å: Chain B: H.22, H.24, V.68, I.73, W.98, K.136, H.168, H.197 Ligands: MN.18, MN.19, EDO.21 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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