SMTL ID : 1kw8.1

Crystal structure of BphC-2,3-dihydroxybiphenyl-NO complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-octamer

Ligands

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

FE2.1: 6 residues within 4Å: Chain A: H.145, H.209, Y.249, E.260 Ligands: NO.2, BPY.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.145, A:H.209, A:E.260, NO.2 FE2.4: 6 residues within 4Å: Chain B: H.145, H.209, Y.249, E.260 Ligands: NO.5, BPY.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.145, B:H.209, B:E.260, NO.5 FE2.7: 6 residues within 4Å: Chain C: H.145, H.209, Y.249, E.260 Ligands: NO.8, BPY.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.145, C:H.209, C:E.260, NO.8 FE2.10: 6 residues within 4Å: Chain D: H.145, H.209, Y.249, E.260 Ligands: NO.11, BPY.12 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.145, D:H.209, D:E.260, NO.11 FE2.13: 6 residues within 4Å: Chain E: H.145, H.209, Y.249, E.260 Ligands: NO.14, BPY.15 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:H.145, E:H.209, E:E.260, NO.14 FE2.16: 6 residues within 4Å: Chain F: H.145, H.209, Y.249, E.260 Ligands: NO.17, BPY.18 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:H.145, F:H.209, F:E.260, NO.17 FE2.19: 6 residues within 4Å: Chain G: H.145, H.209, Y.249, E.260 Ligands: NO.20, BPY.21 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Ligand interactions Metal complexes: G:H.145, G:H.209, G:E.260, NO.20 FE2.22: 6 residues within 4Å: Chain H: H.145, H.209, Y.249, E.260 Ligands: NO.23, BPY.24 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Ligand interactions Metal complexes: H:H.145, H:H.209, H:E.260, NO.23

8 x NO: NITRIC OXIDE(Non-covalent)

NO.2: 9 residues within 4Å: Chain A: H.145, V.147, F.186, H.194, A.197, H.209, E.260 Ligands: FE2.1, BPY.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.194 NO.5: 9 residues within 4Å: Chain B: H.145, V.147, F.186, H.194, A.197, H.209, E.260 Ligands: FE2.4, BPY.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.194 NO.8: 9 residues within 4Å: Chain C: H.145, V.147, F.186, H.194, A.197, H.209, E.260 Ligands: FE2.7, BPY.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.194 NO.11: 9 residues within 4Å: Chain D: H.145, V.147, F.186, H.194, A.197, H.209, E.260 Ligands: FE2.10, BPY.12 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.194 NO.14: 9 residues within 4Å: Chain E: H.145, V.147, F.186, H.194, A.197, H.209, E.260 Ligands: FE2.13, BPY.15 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.194 NO.17: 9 residues within 4Å: Chain F: H.145, V.147, F.186, H.194, A.197, H.209, E.260 Ligands: FE2.16, BPY.18 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.194 NO.20: 9 residues within 4Å: Chain G: H.145, V.147, F.186, H.194, A.197, H.209, E.260 Ligands: FE2.19, BPY.21 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:H.194 NO.23: 9 residues within 4Å: Chain H: H.145, V.147, F.186, H.194, A.197, H.209, E.260 Ligands: FE2.22, BPY.24 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:H.194

8 x BPY: BIPHENYL-2,3-DIOL(Non-covalent)

BPY.3: 14 residues within 4Å: Chain A: H.145, I.172, F.186, H.194, F.201, H.208, H.209, H.240, N.242, Y.249, E.260, T.280 Ligands: FE2.1, NO.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.172, A:F.186, A:F.186, A:F.201, A:T.280 pi-Stacking: A:H.240 BPY.6: 14 residues within 4Å: Chain B: H.145, I.172, F.186, H.194, F.201, H.208, H.209, H.240, N.242, Y.249, E.260, T.280 Ligands: FE2.4, NO.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.172, B:F.186, B:F.186, B:F.201, B:T.280 pi-Stacking: B:H.240 BPY.9: 14 residues within 4Å: Chain C: H.145, I.172, F.186, H.194, F.201, H.208, H.209, H.240, N.242, Y.249, E.260, T.280 Ligands: FE2.7, NO.8 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.172, C:F.186, C:F.186, C:F.201, C:T.280 pi-Stacking: C:H.240 BPY.12: 14 residues within 4Å: Chain D: H.145, I.172, F.186, H.194, F.201, H.208, H.209, H.240, N.242, Y.249, E.260, T.280 Ligands: FE2.10, NO.11 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:I.172, D:F.186, D:F.186, D:F.201, D:T.280 pi-Stacking: D:H.240 BPY.15: 14 residues within 4Å: Chain E: H.145, I.172, F.186, H.194, F.201, H.208, H.209, H.240, N.242, Y.249, E.260, T.280 Ligands: FE2.13, NO.14 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:I.172, E:F.186, E:F.186, E:F.201, E:T.280 Hydrogen bonds: E:Y.249 pi-Stacking: E:H.240 BPY.18: 14 residues within 4Å: Chain F: H.145, I.172, F.186, H.194, F.201, H.208, H.209, H.240, N.242, Y.249, E.260, T.280 Ligands: FE2.16, NO.17 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:I.172, F:F.186, F:F.186, F:F.201, F:T.280 Hydrogen bonds: F:Y.249 pi-Stacking: F:H.240 BPY.21: 14 residues within 4Å: Chain G: H.145, I.172, F.186, H.194, F.201, H.208, H.209, H.240, N.242, Y.249, E.260, T.280 Ligands: FE2.19, NO.20 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:I.172, G:F.186, G:F.186, G:F.201, G:T.280 Hydrogen bonds: G:Y.249 pi-Stacking: G:H.240 BPY.24: 14 residues within 4Å: Chain H: H.145, I.172, F.186, H.194, F.201, H.208, H.209, H.240, N.242, Y.249, E.260, T.280 Ligands: FE2.22, NO.23 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:I.172, H:F.186, H:F.186, H:F.201, H:T.280 Hydrogen bonds: H:Y.249 pi-Stacking: H:H.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sato, N. et al., Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase. J.Mol.Biol. (2002)

Release Date

2003-01-29

Peptides

2,3-Dihydroxybiphenyl dioxygenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

E
B

F
B

G
B

H
B

2,3-Dihydroxybiphenyl dioxygenase

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