SMTL ID : 2ei0.1

Anaerobic Crystal Structure Analysis of 1,2-dihydroxynaphthalene dioxygenase from Pseudomonas sp. strain C18 complexed with 3,4-dihydroxybiphenyl

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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: BP7.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.152, A:H.215, A:E.266 FE2.7: 5 residues within 4Å: Chain B: H.152, H.215, Y.256, E.266 Ligands: BP7.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.152, B:H.215, B:E.266 FE2.13: 5 residues within 4Å: Chain C: H.152, H.215, Y.256, E.266 Ligands: BP7.15 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.152, C:H.215, C:E.266 FE2.19: 5 residues within 4Å: Chain D: H.152, H.215, Y.256, E.266 Ligands: BP7.21 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.152, D:H.215, D:E.266 FE2.25: 5 residues within 4Å: Chain E: H.152, H.215, Y.256, E.266 Ligands: BP7.27 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.152, E:H.215, E:E.266 FE2.31: 5 residues within 4Å: Chain F: H.152, H.215, Y.256, E.266 Ligands: BP7.33 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.152, F:H.215, F:E.266 FE2.37: 5 residues within 4Å: Chain G: H.152, H.215, Y.256, E.266 Ligands: BP7.39 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.152, G:H.215, G:E.266 FE2.43: 5 residues within 4Å: Chain H: H.152, H.215, Y.256, E.266 Ligands: BP7.45 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:H.152, H:H.215, H:E.266

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.2, H2O.3, H2O.4, H2O.5, H2O.6 MG.8: 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.351, H2O.352, H2O.353, H2O.354, H2O.355 MG.14: 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.700, H2O.701, H2O.702, H2O.703, H2O.704 MG.20: 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.1049, H2O.1050, H2O.1051, H2O.1052, H2O.1053 MG.26: 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.1398, H2O.1399, H2O.1400, H2O.1401, H2O.1402 MG.32: 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.1747, H2O.1748, H2O.1749, H2O.1750, H2O.1751 MG.38: 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.2096, H2O.2097, H2O.2098, H2O.2099, H2O.2100 MG.44: 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.2445, H2O.2446, H2O.2447, H2O.2448, H2O.2449

24 x BP7: 1,1'-BIPHENYL-3,4-DIOL(Non-covalent)

BP7.3: 14 residues within 4Å: Chain A: H.152, Y.178, I.180, L.190, F.192, H.200, H.215, H.247, N.249, Y.256, E.266, D.284 Ligands: FE2.1, BP7.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.178, A:Y.178, A:I.180, A:L.190, A:F.192, A:F.192 pi-Stacking: A:H.247 BP7.4: 9 residues within 4Å: Chain A: I.154, L.190, F.192, A.203, F.204, G.205, M.207, N.214 Ligands: BP7.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.154, A:I.154, A:L.190, A:L.190, A:F.192, A:A.203 Hydrogen bonds: A:N.214 BP7.5: 9 residues within 4Å: Chain A: G.171, F.172, R.173, H.194, C.195, N.196, A.197, A.274, D.276 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.197 Hydrogen bonds: A:D.276 pi-Stacking: A:H.194 BP7.9: 14 residues within 4Å: Chain B: H.152, Y.178, I.180, L.190, F.192, H.200, H.215, H.247, N.249, Y.256, E.266, D.284 Ligands: FE2.7, BP7.10 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.178, B:Y.178, B:I.180, B:L.190, B:F.192, B:F.192 pi-Stacking: B:H.247 BP7.10: 9 residues within 4Å: Chain B: I.154, L.190, F.192, A.203, F.204, G.205, M.207, N.214 Ligands: BP7.9 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.154, B:I.154, B:L.190, B:L.190, B:F.192, B:A.203 Hydrogen bonds: B:N.214 BP7.11: 9 residues within 4Å: Chain B: G.171, F.172, R.173, H.194, C.195, N.196, A.197, A.274, D.276 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.197 Hydrogen bonds: B:D.276 pi-Stacking: B:H.194 BP7.15: 14 residues within 4Å: Chain C: H.152, Y.178, I.180, L.190, F.192, H.200, H.215, H.247, N.249, Y.256, E.266, D.284 Ligands: FE2.13, BP7.16 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.178, C:Y.178, C:I.180, C:L.190, C:F.192, C:F.192 pi-Stacking: C:H.247 BP7.16: 9 residues within 4Å: Chain C: I.154, L.190, F.192, A.203, F.204, G.205, M.207, N.214 Ligands: BP7.15 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.154, C:I.154, C:L.190, C:L.190, C:F.192, C:A.203 Hydrogen bonds: C:N.214 BP7.17: 9 residues within 4Å: Chain C: G.171, F.172, R.173, H.194, C.195, N.196, A.197, A.274, D.276 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.197 Hydrogen bonds: C:D.276 pi-Stacking: C:H.194 BP7.21: 14 residues within 4Å: Chain D: H.152, Y.178, I.180, L.190, F.192, H.200, H.215, H.247, N.249, Y.256, E.266, D.284 Ligands: FE2.19, BP7.22 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.178, D:Y.178, D:I.180, D:L.190, D:F.192, D:F.192 pi-Stacking: D:H.247 BP7.22: 9 residues within 4Å: Chain D: I.154, L.190, F.192, A.203, F.204, G.205, M.207, N.214 Ligands: BP7.21 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.154, D:I.154, D:L.190, D:L.190, D:F.192, D:A.203 Hydrogen bonds: D:N.214 BP7.23: 9 residues within 4Å: Chain D: G.171, F.172, R.173, H.194, C.195, N.196, A.197, A.274, D.276 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.197 Hydrogen bonds: D:D.276 pi-Stacking: D:H.194 BP7.27: 14 residues within 4Å: Chain E: H.152, Y.178, I.180, L.190, F.192, H.200, H.215, H.247, N.249, Y.256, E.266, D.284 Ligands: FE2.25, BP7.28 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:Y.178, E:Y.178, E:I.180, E:L.190, E:F.192, E:F.192 Hydrogen bonds: E:Y.256 pi-Stacking: E:H.247 BP7.28: 9 residues within 4Å: Chain E: I.154, L.190, F.192, A.203, F.204, G.205, M.207, N.214 Ligands: BP7.27 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:I.154, E:I.154, E:L.190, E:L.190, E:F.192, E:A.203 Hydrogen bonds: E:N.214 BP7.29: 9 residues within 4Å: Chain E: G.171, F.172, R.173, H.194, C.195, N.196, A.197, A.274, D.276 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:A.197 Hydrogen bonds: E:D.276 pi-Stacking: E:H.194 BP7.33: 14 residues within 4Å: Chain F: H.152, Y.178, I.180, L.190, F.192, H.200, H.215, H.247, N.249, Y.256, E.266, D.284 Ligands: FE2.31, BP7.34 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:Y.178, F:Y.178, F:I.180, F:L.190, F:F.192, F:F.192 Hydrogen bonds: F:Y.256 pi-Stacking: F:H.247 BP7.34: 9 residues within 4Å: Chain F: I.154, L.190, F.192, A.203, F.204, G.205, M.207, N.214 Ligands: BP7.33 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:I.154, F:I.154, F:L.190, F:L.190, F:F.192, F:A.203 Hydrogen bonds: F:N.214 BP7.35: 9 residues within 4Å: Chain F: G.171, F.172, R.173, H.194, C.195, N.196, A.197, A.274, D.276 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:A.197 Hydrogen bonds: F:D.276 pi-Stacking: F:H.194 BP7.39: 14 residues within 4Å: Chain G: H.152, Y.178, I.180, L.190, F.192, H.200, H.215, H.247, N.249, Y.256, E.266, D.284 Ligands: FE2.37, BP7.40 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:Y.178, G:Y.178, G:I.180, G:L.190, G:F.192, G:F.192 Hydrogen bonds: G:Y.256 pi-Stacking: G:H.247 BP7.40: 9 residues within 4Å: Chain G: I.154, L.190, F.192, A.203, F.204, G.205, M.207, N.214 Ligands: BP7.39 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:I.154, G:I.154, G:L.190, G:L.190, G:F.192, G:A.203 Hydrogen bonds: G:N.214 BP7.41: 9 residues within 4Å: Chain G: G.171, F.172, R.173, H.194, C.195, N.196, A.197, A.274, D.276 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:A.197 Hydrogen bonds: G:D.276 pi-Stacking: G:H.194 BP7.45: 14 residues within 4Å: Chain H: H.152, Y.178, I.180, L.190, F.192, H.200, H.215, H.247, N.249, Y.256, E.266, D.284 Ligands: FE2.43, BP7.46 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:Y.178, H:Y.178, H:I.180, H:L.190, H:F.192, H:F.192 Hydrogen bonds: H:Y.256 pi-Stacking: H:H.247 BP7.46: 9 residues within 4Å: Chain H: I.154, L.190, F.192, A.203, F.204, G.205, M.207, N.214 Ligands: BP7.45 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:I.154, H:I.154, H:L.190, H:L.190, H:F.192, H:A.203 Hydrogen bonds: H:N.214 BP7.47: 9 residues within 4Å: Chain H: G.171, F.172, R.173, H.194, C.195, N.196, A.197, A.274, D.276 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:A.197 Hydrogen bonds: H:D.276 pi-Stacking: H:H.194

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 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.12: 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.18: 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.24: 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.30: 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.36: 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.42: 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.48: 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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