SMTL ID : 2ei1.1

Anaerobic Crystal Structure Analysis of the 1,2-dihydroxynaphthalene dioxygeanse of Pseudomonas sp. strain C18 complexes to 1,2-dihydroxynaphthalene

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-octamer

Ligands

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

FE2.1: 5 residues within 4Å: Chain A: H.152, H.215, Y.256, E.266 Ligands: D1N.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.152, A:H.215, A:E.266, H2O.1 FE2.5: 5 residues within 4Å: Chain B: H.152, H.215, Y.256, E.266 Ligands: D1N.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.152, B:H.215, B:E.266, H2O.11 FE2.9: 5 residues within 4Å: Chain C: H.152, H.215, Y.256, E.266 Ligands: D1N.11 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.152, C:H.215, C:E.266, H2O.22 FE2.13: 5 residues within 4Å: Chain D: H.152, H.215, Y.256, E.266 Ligands: D1N.15 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.152, D:H.215, D:E.266, H2O.33 FE2.17: 5 residues within 4Å: Chain E: H.152, H.215, Y.256, E.266 Ligands: D1N.19 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.152, E:H.215, E:E.266, H2O.44 FE2.21: 5 residues within 4Å: Chain F: H.152, H.215, Y.256, E.266 Ligands: D1N.23 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.152, F:H.215, F:E.266, H2O.54 FE2.25: 5 residues within 4Å: Chain G: H.152, H.215, Y.256, E.266 Ligands: D1N.27 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.152, G:H.215, G:E.266, H2O.65 FE2.29: 5 residues within 4Å: Chain H: H.152, H.215, Y.256, E.266 Ligands: D1N.31 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.152, H:H.215, H:E.266, H2O.76

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.177, D.199 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.177, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1 MG.6: 2 residues within 4Å: Chain B: E.177, D.199 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.177, H2O.11, H2O.11, H2O.11, H2O.11, H2O.11 MG.10: 2 residues within 4Å: Chain C: E.177, D.199 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:E.177, H2O.22, H2O.22, H2O.22, H2O.22, H2O.22 MG.14: 2 residues within 4Å: Chain D: E.177, D.199 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:E.177, H2O.33, H2O.33, H2O.33, H2O.33, H2O.33 MG.18: 2 residues within 4Å: Chain E: E.177, D.199 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:E.177, H2O.44, H2O.44, H2O.44, H2O.44, H2O.44 MG.22: 2 residues within 4Å: Chain F: E.177, D.199 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:E.177, H2O.54, H2O.54, H2O.54, H2O.55, H2O.55 MG.26: 2 residues within 4Å: Chain G: E.177, D.199 6 PLIP interactions: 1 interactions with chain G, 5 Ligand-Water interactions Metal complexes: G:E.177, H2O.65, H2O.65, H2O.65, H2O.65, H2O.65 MG.30: 2 residues within 4Å: Chain H: E.177, D.199 6 PLIP interactions: 1 interactions with chain H, 5 Ligand-Water interactions Metal complexes: H:E.177, H2O.76, H2O.76, H2O.76, H2O.76, H2O.76

8 x D1N: NAPHTHALENE-1,2-DIOL(Non-covalent)

D1N.3: 11 residues within 4Å: Chain A: H.152, Y.178, L.190, F.192, H.200, H.215, H.247, N.249, Y.256, E.266 Ligands: FE2.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.178, A:L.190, A:F.192, A:F.192 pi-Stacking: A:Y.178, A:H.247 D1N.7: 11 residues within 4Å: Chain B: H.152, Y.178, L.190, F.192, H.200, H.215, H.247, N.249, Y.256, E.266 Ligands: FE2.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.178, B:L.190, B:F.192, B:F.192 pi-Stacking: B:Y.178, B:H.247 D1N.11: 11 residues within 4Å: Chain C: H.152, Y.178, L.190, F.192, H.200, H.215, H.247, N.249, Y.256, E.266 Ligands: FE2.9 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.178, C:L.190, C:F.192, C:F.192 pi-Stacking: C:Y.178, C:H.247 D1N.15: 11 residues within 4Å: Chain D: H.152, Y.178, L.190, F.192, H.200, H.215, H.247, N.249, Y.256, E.266 Ligands: FE2.13 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:Y.178, D:L.190, D:F.192, D:F.192 pi-Stacking: D:Y.178, D:H.247 D1N.19: 11 residues within 4Å: Chain E: H.152, Y.178, L.190, F.192, H.200, H.215, H.247, N.249, Y.256, E.266 Ligands: FE2.17 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:Y.178, E:L.190, E:F.192, E:F.192 Hydrogen bonds: E:Y.256 pi-Stacking: E:Y.178, E:H.247 D1N.23: 11 residues within 4Å: Chain F: H.152, Y.178, L.190, F.192, H.200, H.215, H.247, N.249, Y.256, E.266 Ligands: FE2.21 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:Y.178, F:L.190, F:F.192, F:F.192 Hydrogen bonds: F:Y.256 pi-Stacking: F:Y.178, F:H.247 D1N.27: 11 residues within 4Å: Chain G: H.152, Y.178, L.190, F.192, H.200, H.215, H.247, N.249, Y.256, E.266 Ligands: FE2.25 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:Y.178, G:L.190, G:F.192, G:F.192 Hydrogen bonds: G:Y.256 pi-Stacking: G:Y.178, G:H.247 D1N.31: 11 residues within 4Å: Chain H: H.152, Y.178, L.190, F.192, H.200, H.215, H.247, N.249, Y.256, E.266 Ligands: FE2.29 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:Y.178, H:L.190, H:F.192, H:F.192 Hydrogen bonds: H:H.152, H:Y.256 Water bridges: H:H.247, H:D.250 pi-Stacking: H:Y.178, H:H.247

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.52, A:H.53, A:R.126 GOL.8: 9 residues within 4Å: Chain B: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.52, B:H.53, B:R.126 GOL.12: 9 residues within 4Å: Chain C: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.52, C:H.53, C:R.126 GOL.16: 9 residues within 4Å: Chain D: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.52, D:H.53, D:R.126 GOL.20: 9 residues within 4Å: Chain E: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:H.52, E:H.53, E:R.126 GOL.24: 9 residues within 4Å: Chain F: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:H.52, F:H.53, F:R.126 GOL.28: 9 residues within 4Å: Chain G: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:H.52, G:H.53, G:R.126 GOL.32: 9 residues within 4Å: Chain H: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:H.52, H:H.53, H:R.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neau, D.B. et al., Structural explanation for success and failure in the enzymatic ring-cleavage of 3,4 dihydroxybiphenyl and related PCB metabolites. To be Published

Release Date

2008-02-19

Peptides

1,2-dihydroxynaphthalene 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

1,2-dihydroxynaphthalene dioxygenase

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