SMTL ID : 2ehz.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 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: MCT.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.152, A:H.215, A:E.266 FE2.10: 5 residues within 4Å: Chain B: H.152, H.215, Y.256, E.266 Ligands: MCT.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.152, B:H.215, B:E.266 FE2.19: 5 residues within 4Å: Chain C: H.152, H.215, Y.256, E.266 Ligands: MCT.21 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.152, C:H.215, C:E.266 FE2.28: 5 residues within 4Å: Chain D: H.152, H.215, Y.256, E.266 Ligands: MCT.30 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.152, D:H.215, D:E.266 FE2.37: 5 residues within 4Å: Chain E: H.152, H.215, Y.256, E.266 Ligands: MCT.39 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.152, E:H.215, E:E.266 FE2.46: 5 residues within 4Å: Chain F: H.152, H.215, Y.256, E.266 Ligands: MCT.48 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.152, F:H.215, F:E.266 FE2.55: 5 residues within 4Å: Chain G: H.152, H.215, Y.256, E.266 Ligands: MCT.57 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.152, G:H.215, G:E.266 FE2.64: 5 residues within 4Å: Chain H: H.152, H.215, Y.256, E.266 Ligands: MCT.66 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.11: 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.313, H2O.314, H2O.315, H2O.316, H2O.317 MG.20: 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.624, H2O.625, H2O.626, H2O.627, H2O.628 MG.29: 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.935, H2O.936, H2O.937, H2O.938, H2O.939 MG.38: 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.1246, H2O.1247, H2O.1248, H2O.1249, H2O.1250 MG.47: 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.1557, H2O.1558, H2O.1559, H2O.1560, H2O.1561 MG.56: 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.1868, H2O.1869, H2O.1870, H2O.1871, H2O.1872 MG.65: 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.2179, H2O.2180, H2O.2181, H2O.2182, H2O.2183

48 x MCT: 4-METHYLCATECHOL(Non-covalent)

MCT.3: 12 residues within 4Å: Chain A: H.152, I.154, Y.178, F.192, H.200, H.215, H.247, N.249, Y.256, E.266, L.301 Ligands: FE2.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.192, A:F.192, A:L.301 pi-Stacking: A:H.247 MCT.4: 10 residues within 4Å: Chain A: I.154, V.155, R.156, L.190, F.204, G.205, M.207, A.209, N.214, L.297 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.154, A:L.190, A:M.207, A:N.214, A:L.297 Hydrogen bonds: A:V.155, A:G.205, A:G.205 Water bridges: A:Q.157, A:M.207 MCT.5: 10 residues within 4Å: Chain A: L.244, G.245, L.253, F.286 Chain G: M.223, G.227, H.230, Q.231, L.244, L.253 8 PLIP interactions: 5 interactions with chain G, 3 interactions with chain A Hydrophobic interactions: G:H.230, G:L.244, G:L.253, A:L.244, A:L.253, A:F.286 Hydrogen bonds: G:H.230, G:Q.231 MCT.6: 6 residues within 4Å: Chain A: R.43, H.58, E.66, Y.67, E.102, R.103 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.103, A:R.103 Water bridges: A:E.102, A:K.110, A:K.110 pi-Cation interactions: A:H.58 MCT.7: 6 residues within 4Å: Chain A: H.194, N.196, A.197, A.274, I.275, D.276 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.197, A:A.274 Water bridges: A:C.195, A:A.197 MCT.8: 6 residues within 4Å: Chain A: S.16, Q.62, D.64, L.65, E.66, R.212 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.62, A:D.64 Hydrogen bonds: A:D.64, A:E.66 Water bridges: A:R.212 pi-Cation interactions: A:R.212 MCT.12: 12 residues within 4Å: Chain B: H.152, I.154, Y.178, F.192, H.200, H.215, H.247, N.249, Y.256, E.266, L.301 Ligands: FE2.10 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.192, B:F.192, B:L.301 pi-Stacking: B:H.247 MCT.13: 10 residues within 4Å: Chain B: I.154, V.155, R.156, L.190, F.204, G.205, M.207, A.209, N.214, L.297 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.154, B:L.190, B:M.207, B:N.214, B:L.297 Hydrogen bonds: B:V.155, B:G.205, B:G.205 Water bridges: B:Q.157, B:M.207 MCT.14: 10 residues within 4Å: Chain B: L.244, G.245, L.253, F.286 Chain H: M.223, G.227, H.230, Q.231, L.244, L.253 8 PLIP interactions: 5 interactions with chain H, 3 interactions with chain B Hydrophobic interactions: H:H.230, H:L.244, H:L.253, B:L.244, B:L.253, B:F.286 Hydrogen bonds: H:H.230, H:Q.231 MCT.15: 6 residues within 4Å: Chain B: R.43, H.58, E.66, Y.67, E.102, R.103 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.103, B:R.103 Water bridges: B:E.102, B:K.110, B:K.110 pi-Cation interactions: B:H.58 MCT.16: 6 residues within 4Å: Chain B: H.194, N.196, A.197, A.274, I.275, D.276 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.197, B:A.274 Water bridges: B:C.195, B:A.197 MCT.17: 6 residues within 4Å: Chain B: S.16, Q.62, D.64, L.65, E.66, R.212 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Q.62, B:D.64 Hydrogen bonds: B:D.64, B:E.66 Water bridges: B:R.212 pi-Cation interactions: B:R.212 MCT.21: 12 residues within 4Å: Chain C: H.152, I.154, Y.178, F.192, H.200, H.215, H.247, N.249, Y.256, E.266, L.301 Ligands: FE2.19 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.192, C:F.192, C:L.301 pi-Stacking: C:H.247 MCT.22: 10 residues within 4Å: Chain C: I.154, V.155, R.156, L.190, F.204, G.205, M.207, A.209, N.214, L.297 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.154, C:L.190, C:M.207, C:N.214, C:L.297 Hydrogen bonds: C:V.155, C:G.205, C:G.205 Water bridges: C:Q.157, C:M.207 MCT.23: 10 residues within 4Å: Chain C: L.244, G.245, L.253, F.286 Chain E: M.223, G.227, H.230, Q.231, L.244, L.253 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain E Hydrophobic interactions: C:L.244, C:L.253, C:F.286, E:H.230, E:L.244, E:L.253 Hydrogen bonds: E:H.230, E:Q.231 MCT.24: 6 residues within 4Å: Chain C: R.43, H.58, E.66, Y.67, E.102, R.103 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.103, C:R.103 Water bridges: C:E.102, C:K.110, C:K.110 pi-Cation interactions: C:H.58 MCT.25: 6 residues within 4Å: Chain C: H.194, N.196, A.197, A.274, I.275, D.276 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.197, C:A.274 Water bridges: C:C.195, C:A.197 MCT.26: 6 residues within 4Å: Chain C: S.16, Q.62, D.64, L.65, E.66, R.212 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Q.62, C:D.64 Hydrogen bonds: C:D.64, C:E.66 Water bridges: C:R.212 pi-Cation interactions: C:R.212 MCT.30: 12 residues within 4Å: Chain D: H.152, I.154, Y.178, F.192, H.200, H.215, H.247, N.249, Y.256, E.266, L.301 Ligands: FE2.28 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.192, D:F.192, D:L.301 pi-Stacking: D:H.247 MCT.31: 10 residues within 4Å: Chain D: I.154, V.155, R.156, L.190, F.204, G.205, M.207, A.209, N.214, L.297 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:I.154, D:L.190, D:M.207, D:N.214, D:L.297 Hydrogen bonds: D:V.155, D:G.205, D:G.205 Water bridges: D:Q.157, D:M.207 MCT.32: 10 residues within 4Å: Chain D: L.244, G.245, L.253, F.286 Chain F: M.223, G.227, H.230, Q.231, L.244, L.253 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain D Hydrophobic interactions: F:H.230, F:L.244, F:L.253, D:L.244, D:L.253, D:F.286 Hydrogen bonds: F:H.230, F:Q.231 MCT.33: 6 residues within 4Å: Chain D: R.43, H.58, E.66, Y.67, E.102, R.103 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.103, D:R.103 Water bridges: D:E.102, D:K.110, D:K.110 pi-Cation interactions: D:H.58 MCT.34: 6 residues within 4Å: Chain D: H.194, N.196, A.197, A.274, I.275, D.276 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:A.197, D:A.274 Water bridges: D:C.195, D:A.197 MCT.35: 6 residues within 4Å: Chain D: S.16, Q.62, D.64, L.65, E.66, R.212 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:Q.62, D:D.64 Hydrogen bonds: D:D.64, D:E.66 Water bridges: D:R.212 pi-Cation interactions: D:R.212 MCT.39: 12 residues within 4Å: Chain E: H.152, I.154, Y.178, F.192, H.200, H.215, H.247, N.249, Y.256, E.266, L.301 Ligands: FE2.37 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:F.192, E:F.192, E:L.301 Hydrogen bonds: E:Y.256 pi-Stacking: E:H.247 MCT.40: 10 residues within 4Å: Chain E: I.154, V.155, R.156, L.190, F.204, G.205, M.207, A.209, N.214, L.297 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:I.154, E:L.190, E:M.207, E:N.214, E:L.297 Hydrogen bonds: E:V.155, E:G.205, E:G.205 Water bridges: E:Q.157, E:M.207 MCT.41: 10 residues within 4Å: Chain C: M.223, G.227, H.230, Q.231, L.244, L.253 Chain E: L.244, G.245, L.253, F.286 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain E Hydrophobic interactions: C:H.230, C:L.244, C:L.253, E:L.244, E:L.253, E:F.286 Hydrogen bonds: C:Q.231 MCT.42: 6 residues within 4Å: Chain E: R.43, H.58, E.66, Y.67, E.102, R.103 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:R.103, E:R.103 Water bridges: E:E.102, E:K.110, E:K.110 pi-Cation interactions: E:H.58 MCT.43: 6 residues within 4Å: Chain E: H.194, N.196, A.197, A.274, I.275, D.276 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:A.197, E:A.274 Water bridges: E:C.195, E:A.197 MCT.44: 6 residues within 4Å: Chain E: S.16, Q.62, D.64, L.65, E.66, R.212 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:Q.62, E:D.64 Hydrogen bonds: E:D.64, E:E.66 Water bridges: E:R.212 pi-Cation interactions: E:R.212 MCT.48: 12 residues within 4Å: Chain F: H.152, I.154, Y.178, F.192, H.200, H.215, H.247, N.249, Y.256, E.266, L.301 Ligands: FE2.46 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:F.192, F:F.192, F:L.301 Hydrogen bonds: F:Y.256 pi-Stacking: F:H.247 MCT.49: 10 residues within 4Å: Chain F: I.154, V.155, R.156, L.190, F.204, G.205, M.207, A.209, N.214, L.297 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:I.154, F:L.190, F:M.207, F:N.214, F:L.297 Hydrogen bonds: F:V.155, F:G.205, F:G.205 Water bridges: F:Q.157, F:M.207 MCT.50: 10 residues within 4Å: Chain D: M.223, G.227, H.230, Q.231, L.244, L.253 Chain F: L.244, G.245, L.253, F.286 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: D:H.230, D:L.244, D:L.253, F:L.244, F:L.253, F:F.286 Hydrogen bonds: D:Q.231 MCT.51: 6 residues within 4Å: Chain F: R.43, H.58, E.66, Y.67, E.102, R.103 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:R.103, F:R.103 Water bridges: F:E.102, F:K.110, F:K.110 pi-Cation interactions: F:H.58 MCT.52: 6 residues within 4Å: Chain F: H.194, N.196, A.197, A.274, I.275, D.276 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:A.197, F:A.274 Water bridges: F:C.195, F:A.197 MCT.53: 6 residues within 4Å: Chain F: S.16, Q.62, D.64, L.65, E.66, R.212 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:Q.62, F:D.64 Hydrogen bonds: F:D.64, F:E.66 Water bridges: F:R.212 pi-Cation interactions: F:R.212 MCT.57: 12 residues within 4Å: Chain G: H.152, I.154, Y.178, F.192, H.200, H.215, H.247, N.249, Y.256, E.266, L.301 Ligands: FE2.55 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:F.192, G:F.192, G:L.301 Hydrogen bonds: G:Y.256 pi-Stacking: G:H.247 MCT.58: 10 residues within 4Å: Chain G: I.154, V.155, R.156, L.190, F.204, G.205, M.207, A.209, N.214, L.297 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:I.154, G:L.190, G:M.207, G:N.214, G:L.297 Hydrogen bonds: G:V.155, G:G.205, G:G.205 Water bridges: G:Q.157, G:M.207 MCT.59: 10 residues within 4Å: Chain A: M.223, G.227, H.230, Q.231, L.244, L.253 Chain G: L.244, G.245, L.253, F.286 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain G Hydrophobic interactions: A:H.230, A:L.244, A:L.253, G:L.244, G:L.253, G:F.286 Hydrogen bonds: A:Q.231 MCT.60: 6 residues within 4Å: Chain G: R.43, H.58, E.66, Y.67, E.102, R.103 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:R.103, G:R.103 Water bridges: G:E.102, G:K.110, G:K.110 pi-Cation interactions: G:H.58 MCT.61: 6 residues within 4Å: Chain G: H.194, N.196, A.197, A.274, I.275, D.276 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:A.197, G:A.274 Water bridges: G:C.195, G:A.197 MCT.62: 6 residues within 4Å: Chain G: S.16, Q.62, D.64, L.65, E.66, R.212 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:Q.62, G:D.64 Hydrogen bonds: G:D.64, G:E.66 Water bridges: G:R.212 pi-Cation interactions: G:R.212 MCT.66: 12 residues within 4Å: Chain H: H.152, I.154, Y.178, F.192, H.200, H.215, H.247, N.249, Y.256, E.266, L.301 Ligands: FE2.64 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:F.192, H:F.192, H:L.301 Hydrogen bonds: H:Y.256 pi-Stacking: H:H.247 MCT.67: 10 residues within 4Å: Chain H: I.154, V.155, R.156, L.190, F.204, G.205, M.207, A.209, N.214, L.297 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:I.154, H:L.190, H:M.207, H:N.214, H:L.297 Hydrogen bonds: H:V.155, H:G.205, H:G.205 Water bridges: H:Q.157, H:M.207 MCT.68: 10 residues within 4Å: Chain B: M.223, G.227, H.230, Q.231, L.244, L.253 Chain H: L.244, G.245, L.253, F.286 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain H Hydrophobic interactions: B:H.230, B:L.244, B:L.253, H:L.244, H:L.253, H:F.286 Hydrogen bonds: B:Q.231 MCT.69: 6 residues within 4Å: Chain H: R.43, H.58, E.66, Y.67, E.102, R.103 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:R.103, H:R.103 Water bridges: H:E.102, H:K.110, H:K.110 pi-Cation interactions: H:H.58 MCT.70: 6 residues within 4Å: Chain H: H.194, N.196, A.197, A.274, I.275, D.276 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:A.197, H:A.274 Water bridges: H:C.195, H:A.197 MCT.71: 6 residues within 4Å: Chain H: S.16, Q.62, D.64, L.65, E.66, R.212 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:Q.62, H:D.64 Hydrogen bonds: H:D.64, H:E.66 Water bridges: H:R.212 pi-Cation interactions: H:R.212

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 8 residues within 4Å: Chain A: W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.52, A:H.53, A:H.53, A:M.104, A:R.126 EDO.18: 8 residues within 4Å: Chain B: W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.52, B:H.53, B:H.53, B:M.104, B:R.126 EDO.27: 8 residues within 4Å: Chain C: W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.52, C:H.53, C:H.53, C:M.104, C:R.126 EDO.36: 8 residues within 4Å: Chain D: W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.52, D:H.53, D:H.53, D:M.104, D:R.126 EDO.45: 8 residues within 4Å: Chain E: W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:H.52, E:H.53, E:H.53, E:M.104, E:R.126 EDO.54: 8 residues within 4Å: Chain F: W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:H.52, F:H.53, F:H.53, F:M.104, F:R.126 EDO.63: 8 residues within 4Å: Chain G: W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:H.52, G:H.53, G:H.53, G:M.104, G:R.126 EDO.72: 8 residues within 4Å: Chain H: W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:H.52, H:H.53, H:H.53, H:M.104, 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

Related Entries With Identical Sequence