SMTL ID : 1han.1

CRYSTAL STRUCTURE OF THE BIPHENYL-CLEAVING EXTRADIOL DIOXYGENASE FROM A PCB-DEGRADING PSEUDOMONAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-octamer

Ligands

16 x FE: FE (III) ION(Non-covalent)

FE.1: 4 residues within 4Å: Chain A: H.145, H.209, Y.249, E.259 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.145, A:H.209, A:E.259, H2O.2, H2O.2 FE.2: 1 residues within 4Å: Chain A: H.188 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.188 FE.4: 4 residues within 4Å: Chain B: H.145, H.209, Y.249, E.259 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.145, B:H.209, B:E.259, H2O.7, H2O.7 FE.5: 1 residues within 4Å: Chain B: H.188 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.188 FE.7: 4 residues within 4Å: Chain C: H.145, H.209, Y.249, E.259 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.145, C:H.209, C:E.259, H2O.13, H2O.13 FE.8: 1 residues within 4Å: Chain C: H.188 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.188 FE.10: 4 residues within 4Å: Chain D: H.145, H.209, Y.249, E.259 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.145, D:H.209, D:E.259, H2O.18, H2O.18 FE.11: 1 residues within 4Å: Chain D: H.188 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.188 FE.13: 4 residues within 4Å: Chain E: H.145, H.209, Y.249, E.259 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.145, E:H.209, E:E.259, H2O.23, H2O.23 FE.14: 1 residues within 4Å: Chain E: H.188 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.188 FE.16: 4 residues within 4Å: Chain F: H.145, H.209, Y.249, E.259 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.145, F:H.209, F:E.259, H2O.29, H2O.29 FE.17: 1 residues within 4Å: Chain F: H.188 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:H.188 FE.19: 4 residues within 4Å: Chain G: H.145, H.209, Y.249, E.259 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:H.145, G:H.209, G:E.259, H2O.34, H2O.34 FE.20: 1 residues within 4Å: Chain G: H.188 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:H.188 FE.22: 4 residues within 4Å: Chain H: H.145, H.209, Y.249, E.259 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:H.145, H:H.209, H:E.259, H2O.39, H2O.40 FE.23: 1 residues within 4Å: Chain H: H.188 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:H.188

8 x TBU: TERTIARY-BUTYL ALCOHOL(Non-functional Binders)

TBU.3: 8 residues within 4Å: Chain A: V.147, M.174, F.186, F.201, H.208, H.209, Y.249, P.279 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.147, A:F.186, A:F.201, A:P.279 Hydrogen bonds: A:H.208 TBU.6: 8 residues within 4Å: Chain B: V.147, M.174, F.186, F.201, H.208, H.209, Y.249, P.279 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.147, B:F.186, B:F.201, B:P.279 Hydrogen bonds: B:H.208 TBU.9: 8 residues within 4Å: Chain C: V.147, M.174, F.186, F.201, H.208, H.209, Y.249, P.279 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.147, C:F.186, C:F.201, C:P.279 Hydrogen bonds: C:H.208 TBU.12: 8 residues within 4Å: Chain D: V.147, M.174, F.186, F.201, H.208, H.209, Y.249, P.279 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.147, D:F.186, D:F.201, D:P.279 Hydrogen bonds: D:H.208 TBU.15: 8 residues within 4Å: Chain E: V.147, M.174, F.186, F.201, H.208, H.209, Y.249, P.279 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:V.147, E:F.186, E:F.201, E:P.279 Hydrogen bonds: E:H.209, E:Y.249 TBU.18: 8 residues within 4Å: Chain F: V.147, M.174, F.186, F.201, H.208, H.209, Y.249, P.279 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:V.147, F:F.186, F:F.201, F:P.279 Hydrogen bonds: F:H.209, F:Y.249 TBU.21: 8 residues within 4Å: Chain G: V.147, M.174, F.186, F.201, H.208, H.209, Y.249, P.279 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:V.147, G:F.186, G:F.201, G:P.279 Hydrogen bonds: G:H.209, G:Y.249 TBU.24: 8 residues within 4Å: Chain H: V.147, M.174, F.186, F.201, H.208, H.209, Y.249, P.279 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:V.147, H:F.186, H:F.201, H:P.279 Hydrogen bonds: H:H.209, H:Y.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, S. et al., Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad. Science (1995)

Release Date

1995-11-14

Peptides

2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE

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