SMTL ID : 1jgm.1

High Resolution Structure of the Cadmium-containing Phosphotriesterase from Pseudomonas diminuta

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 6 residues within 4Å: Chain A: H.26, H.28, K.140, D.272 Ligands: CD.2, EDO.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.26, A:H.28, A:D.272, H2O.9 CD.2: 5 residues within 4Å: Chain A: K.140, H.172, H.201 Ligands: CD.1, EDO.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.172, A:H.201, H2O.9, H2O.11, H2O.13 CD.21: 7 residues within 4Å: Chain B: H.26, H.28, K.140, D.272 Ligands: CD.22, EDO.24, EDO.30 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.26, B:H.28, B:D.272, H2O.28 CD.22: 4 residues within 4Å: Chain B: K.140, H.172, H.201 Ligands: CD.21 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.172, B:H.201, H2O.23, H2O.26, H2O.28

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

NA.3: 2 residues within 4Å: Chain A: N.9, I.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.125 Water bridges: A:R.135 NA.23: 2 residues within 4Å: Chain B: N.9, I.125 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.125 Water bridges: B:N.9, B:R.135

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

EDO.4: 9 residues within 4Å: Chain A: H.28, I.77, W.102, K.140, F.277, S.279 Ligands: CD.1, CD.2, EDO.12 Ligand excluded by PLIP EDO.5: 1 residues within 4Å: Chain A: L.153 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: A.51, E.52, V.55, E.86, A.90 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: T.118, R.160 Ligands: EDO.8 Ligand excluded by PLIP EDO.8: 1 residues within 4Å: Ligands: EDO.7 Ligand excluded by PLIP EDO.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: P.227, W.248, V.291, N.292, F.298 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: R.12, G.13, P.14 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: W.102, F.103, F.277, S.279, Y.280 Chain B: L.107 Ligands: EDO.4 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: S.195, R.196, L.220, R.327, F.328 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: A.237, S.240, A.241 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: F.44, G.45, S.46, A.49 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: K.256, I.259, D.260, V.312, P.313 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: F.43, F.44, G.276, F.277, S.278, M.285 Ligand excluded by PLIP EDO.18: 1 residues within 4Å: Chain A: T.144 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain B: H.28, W.102, K.140, F.277, S.279 Ligands: CD.21, EDO.30, EDO.35 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain B: T.118, R.160 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: R.47, K.48, A.51, E.86 Ligands: EDO.31 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: F.44, G.276, F.277, M.285 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: P.227, W.248, V.291, N.292, F.298 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain A: D.104, P.105, P.106 Chain B: D.104, P.105, P.106 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: H.228, D.272, F.277 Ligands: CD.21, EDO.24 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain B: A.51, E.52, V.55, E.86, A.90 Ligands: EDO.26 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain A: E.42 Chain B: R.123, Y.127 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain A: R.123, Y.127 Chain B: E.42 Ligand excluded by PLIP EDO.34: 1 residues within 4Å: Chain B: Y.127 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain A: L.107 Chain B: W.102, F.277, S.279, Y.280 Ligands: EDO.24 Ligand excluded by PLIP

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

PEL.19: 8 residues within 4Å: Chain A: M.264, K.265, E.315, T.316, G.319, I.320, N.324, R.327 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.264, A:K.265 PEL.20: 3 residues within 4Å: Chain A: R.56, R.59, R.60 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.59 PEL.36: 8 residues within 4Å: Chain B: M.264, K.265, E.315, T.316, G.319, I.320, N.324, R.327 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.265

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

2001-07-04

Peptides

Phosphotriesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphotriesterase