SMTL ID : 3gzx.1

Crystal Structure of the Biphenyl Dioxygenase in complex with Biphenyl from Comamonas testosteroni Sp. Strain B-356

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

hetero-3-3-mer

Ligands

3 x FE2: FE (II) ION(Non-covalent)

FE2.1: 4 residues within 4Å: Chain A: Q.226, H.233, H.239, D.386 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.233, A:H.239, A:D.386, A:D.386, H2O.1 FE2.7: 4 residues within 4Å: Chain C: Q.226, H.233, H.239, D.386 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.233, C:H.239, C:D.386, C:D.386, H2O.25 FE2.13: 4 residues within 4Å: Chain E: Q.226, H.233, H.239, D.386 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.233, E:H.239, E:D.386, E:D.386, H2O.50

3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.2: 8 residues within 4Å: Chain A: C.100, H.102, R.103, M.105, C.120, Y.122, H.123, W.125 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.100, A:H.102, A:C.120, A:H.123 FES.8: 8 residues within 4Å: Chain C: C.100, H.102, R.103, M.105, C.120, Y.122, H.123, W.125 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.100, C:H.102, C:C.120, C:H.123 FES.14: 8 residues within 4Å: Chain E: C.100, H.102, R.103, M.105, C.120, Y.122, H.123, W.125 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.100, E:H.102, E:C.120, E:H.123

3 x BNL: BIPHENYL(Non-covalent)

BNL.3: 9 residues within 4Å: Chain A: Q.226, F.227, D.230, H.233, A.234, G.319, H.321, L.331, F.376 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.234, A:H.321, A:L.331, A:F.376 pi-Stacking: A:F.227, A:H.233 BNL.9: 9 residues within 4Å: Chain C: Q.226, F.227, D.230, H.233, A.234, G.319, H.321, L.331, F.376 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.234, C:H.321, C:L.331, C:F.376 pi-Stacking: C:F.227, C:H.233 BNL.15: 9 residues within 4Å: Chain E: Q.226, F.227, D.230, H.233, A.234, G.319, H.321, L.331, F.376 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:A.234, E:H.321, E:L.331, E:F.376 pi-Stacking: E:F.227, E:H.233

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: H.66, Y.73, L.74, D.111, G.112, G.113, I.211 Chain B: R.62 Ligands: GOL.5 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.73, A:G.113 Water bridges: A:D.111, A:D.111, A:I.211, A:I.211, A:I.211, A:K.213, A:K.213, B:R.62, B:R.62 GOL.5: 5 residues within 4Å: Chain A: H.66, P.68, K.69, D.72 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.66, A:K.69, A:D.72 GOL.10: 9 residues within 4Å: Chain C: H.66, Y.73, L.74, D.111, G.112, G.113, I.211 Chain D: R.62 Ligands: GOL.11 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.73, C:G.113 Water bridges: C:D.111, C:D.111, C:I.211, C:I.211, C:I.211, C:K.213, C:K.213, D:R.62, D:R.62 GOL.11: 5 residues within 4Å: Chain C: H.66, P.68, K.69, D.72 Ligands: GOL.10 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.66, C:K.69, C:D.72 GOL.16: 9 residues within 4Å: Chain E: H.66, Y.73, L.74, D.111, G.112, G.113, I.211 Chain F: R.62 Ligands: GOL.17 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:Y.73, E:G.113 Water bridges: E:D.111, E:D.111, E:I.211, E:I.211, E:I.211, E:K.213, E:K.213, F:R.62, F:R.62 GOL.17: 5 residues within 4Å: Chain E: H.66, P.68, K.69, D.72 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:H.66, E:K.69, E:D.72

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.6: 3 residues within 4Å: Chain B: R.118, M.120, D.121 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.121, B:D.121 Water bridges: B:T.122 Salt bridges: B:R.118, B:D.121 MES.12: 3 residues within 4Å: Chain D: R.118, M.120, D.121 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.121, D:D.121 Water bridges: D:T.122 Salt bridges: D:R.118, D:D.121 MES.18: 3 residues within 4Å: Chain F: R.118, M.120, D.121 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:D.121, F:D.121 Water bridges: F:T.122 Salt bridges: F:R.118, F:D.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Colbert, C.L. et al., Structural Characterization of Pandoraea pnomenusa B-356 Biphenyl Dioxygenase Reveals Features of Potent Polychlorinated Biphenyl-Degrading Enzymes. Plos One (2013)

Release Date

2010-05-05

Peptides

Biphenyl dioxygenase subunit alpha: ACE
Biphenyl dioxygenase subunit beta: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Biphenyl dioxygenase subunit alpha

Biphenyl dioxygenase subunit beta

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