SMTL ID : 2ei2.1

Crystal Structure Analysis of the 1,2-dihydroxynaphthalene dioxygenase from Pseudomonas sp. stain C18

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 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.3, H2O.4, H2O.5, H2O.6, H2O.30 MG.5: 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.270, H2O.271, H2O.272, H2O.273, H2O.297 MG.9: 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.537, H2O.538, H2O.539, H2O.540, H2O.564 MG.13: 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.804, H2O.805, H2O.806, H2O.807, H2O.831 MG.17: 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.1071, H2O.1072, H2O.1073, H2O.1074, H2O.1098 MG.21: 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.1338, H2O.1339, H2O.1340, H2O.1341, H2O.1365 MG.25: 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.1605, H2O.1606, H2O.1607, H2O.1608, H2O.1632 MG.29: 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.1872, H2O.1873, H2O.1874, H2O.1875, H2O.1899

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

FE2.2: 5 residues within 4Å: Chain A: H.152, H.215, Y.256, E.266 Ligands: GOL.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.152, A:H.215, A:E.266, H2O.1, H2O.2 FE2.6: 5 residues within 4Å: Chain B: H.152, H.215, Y.256, E.266 Ligands: GOL.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.152, B:H.215, B:E.266, H2O.268, H2O.269 FE2.10: 5 residues within 4Å: Chain C: H.152, H.215, Y.256, E.266 Ligands: GOL.12 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.152, C:H.215, C:E.266, H2O.535, H2O.536 FE2.14: 5 residues within 4Å: Chain D: H.152, H.215, Y.256, E.266 Ligands: GOL.16 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.152, D:H.215, D:E.266, H2O.802, H2O.803 FE2.18: 5 residues within 4Å: Chain E: H.152, H.215, Y.256, E.266 Ligands: GOL.20 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.152, E:H.215, E:E.266, H2O.1069, H2O.1070 FE2.22: 5 residues within 4Å: Chain F: H.152, H.215, Y.256, E.266 Ligands: GOL.24 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.152, F:H.215, F:E.266, H2O.1336, H2O.1337 FE2.26: 5 residues within 4Å: Chain G: H.152, H.215, Y.256, E.266 Ligands: GOL.28 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:H.152, G:H.215, G:E.266, H2O.1603, H2O.1604 FE2.30: 5 residues within 4Å: Chain H: H.152, H.215, Y.256, E.266 Ligands: GOL.32 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:H.152, H:H.215, H:E.266, H2O.1870, H2O.1871

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: Y.178, L.190, F.192, H.247, Y.256, L.297 Ligands: FE2.2 Ligand excluded by PLIP GOL.7: 9 residues within 4Å: Chain B: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain B: Y.178, L.190, F.192, H.247, Y.256, L.297 Ligands: FE2.6 Ligand excluded by PLIP GOL.11: 9 residues within 4Å: Chain C: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain C: Y.178, L.190, F.192, H.247, Y.256, L.297 Ligands: FE2.10 Ligand excluded by PLIP GOL.15: 9 residues within 4Å: Chain D: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain D: Y.178, L.190, F.192, H.247, Y.256, L.297 Ligands: FE2.14 Ligand excluded by PLIP GOL.19: 9 residues within 4Å: Chain E: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain E: Y.178, L.190, F.192, H.247, Y.256, L.297 Ligands: FE2.18 Ligand excluded by PLIP GOL.23: 9 residues within 4Å: Chain F: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain F: Y.178, L.190, F.192, H.247, Y.256, L.297 Ligands: FE2.22 Ligand excluded by PLIP GOL.27: 9 residues within 4Å: Chain G: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain G: Y.178, L.190, F.192, H.247, Y.256, L.297 Ligands: FE2.26 Ligand excluded by PLIP GOL.31: 9 residues within 4Å: Chain H: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126 Ligand excluded by PLIP GOL.32: 7 residues within 4Å: Chain H: Y.178, L.190, F.192, H.247, Y.256, L.297 Ligands: FE2.30 Ligand excluded by PLIP

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