SMTL ID : 2bmo.1

The Crystal Structure of Nitrobenzene Dioxygenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

hetero-3-3-mer

Ligands

3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 8 residues within 4Å: Chain A: C.79, H.81, R.82, C.99, Y.101, H.102, G.103, W.104 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.79, A:H.81, A:C.99, A:H.102 FES.25: 8 residues within 4Å: Chain C: C.79, H.81, R.82, C.99, Y.101, H.102, G.103, W.104 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.79, C:H.81, C:C.99, C:H.102 FES.49: 8 residues within 4Å: Chain E: C.79, H.81, R.82, C.99, Y.101, H.102, G.103, W.104 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.79, E:H.81, E:C.99, E:H.102

3 x FE: FE (III) ION(Non-covalent)

FE.2: 4 residues within 4Å: Chain A: H.206, H.211, D.360 Ligands: EDO.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.206, A:H.211, A:D.360, A:D.360, H2O.17 FE.26: 4 residues within 4Å: Chain C: H.206, H.211, D.360 Ligands: EDO.27 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.206, C:H.211, C:D.360, C:D.360, H2O.45 FE.50: 4 residues within 4Å: Chain E: H.206, H.211, D.360 Ligands: EDO.51 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.206, E:H.211, E:D.360, E:D.360, H2O.73

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

EDO.3: 7 residues within 4Å: Chain A: N.199, F.200, D.203, H.206, N.295, D.360 Ligands: FE.2 Ligand excluded by PLIP EDO.4: 9 residues within 4Å: Chain A: V.53, K.54, E.90, P.184, K.186, W.325 Chain B: E.70, R.183 Ligands: EOH.6 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: K.30, R.35, D.151, S.425, N.426 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain B: M.2, N.4, E.7 Chain F: H.56 Ligands: NI.60 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain B: Y.50, Y.88, Q.102, L.191, V.192, F.193 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain B: T.35, T.39, V.120, V.123 Chain D: T.121, N.122 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: D.46, R.115, F.116 Chain D: T.158 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: P.47, S.48, D.51 Chain B: R.78, Y.79, Q.80, L.81 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain C: N.199, F.200, D.203, H.206, N.295, D.360 Ligands: FE.26 Ligand excluded by PLIP EDO.28: 9 residues within 4Å: Chain C: V.53, K.54, E.90, P.184, K.186, W.325 Chain D: E.70, R.183 Ligands: EOH.30 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain C: K.30, R.35, D.151, S.425, N.426 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain B: H.56 Chain D: M.2, N.4, E.7 Ligands: NI.12 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain D: Y.50, Y.88, Q.102, L.191, V.192, F.193 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain D: T.35, T.39, V.120, V.123 Chain F: T.121, N.122 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain D: D.46, R.115, F.116 Chain F: T.158 Ligand excluded by PLIP EDO.41: 7 residues within 4Å: Chain C: P.47, S.48, D.51 Chain D: R.78, Y.79, Q.80, L.81 Ligand excluded by PLIP EDO.51: 7 residues within 4Å: Chain E: N.199, F.200, D.203, H.206, N.295, D.360 Ligands: FE.50 Ligand excluded by PLIP EDO.52: 9 residues within 4Å: Chain E: V.53, K.54, E.90, P.184, K.186, W.325 Chain F: E.70, R.183 Ligands: EOH.54 Ligand excluded by PLIP EDO.53: 5 residues within 4Å: Chain E: K.30, R.35, D.151, S.425, N.426 Ligand excluded by PLIP EDO.61: 5 residues within 4Å: Chain D: H.56 Chain F: M.2, N.4, E.7 Ligands: NI.36 Ligand excluded by PLIP EDO.62: 6 residues within 4Å: Chain F: Y.50, Y.88, Q.102, L.191, V.192, F.193 Ligand excluded by PLIP EDO.63: 6 residues within 4Å: Chain B: T.121, N.122 Chain F: T.35, T.39, V.120, V.123 Ligand excluded by PLIP EDO.64: 4 residues within 4Å: Chain B: T.158 Chain F: D.46, R.115, F.116 Ligand excluded by PLIP EDO.65: 7 residues within 4Å: Chain E: P.47, S.48, D.51 Chain F: R.78, Y.79, Q.80, L.81 Ligand excluded by PLIP

36 x EOH: ETHANOL(Non-functional Binders)

EOH.6: 9 residues within 4Å: Chain A: K.54, A.55, K.56, E.61, E.90, K.186, W.325 Chain F: E.149 Ligands: EDO.4 Ligand excluded by PLIP EOH.7: 3 residues within 4Å: Chain A: S.141, F.142, H.143 Ligand excluded by PLIP EOH.8: 5 residues within 4Å: Chain A: D.163, Y.392, G.393, P.398, G.399 Ligand excluded by PLIP EOH.9: 4 residues within 4Å: Chain A: V.87, H.88, A.89 Chain F: N.111 Ligand excluded by PLIP EOH.10: 3 residues within 4Å: Chain A: W.252, R.288, Y.397 Ligand excluded by PLIP EOH.18: 5 residues within 4Å: Chain A: V.188, K.190 Chain B: Q.186, T.187, H.188 Ligand excluded by PLIP EOH.19: 7 residues within 4Å: Chain B: P.112, K.113, I.114, A.146, R.147, R.148 Chain D: L.71 Ligand excluded by PLIP EOH.20: 3 residues within 4Å: Chain B: E.17, E.18, R.21 Ligand excluded by PLIP EOH.21: 6 residues within 4Å: Chain A: G.92, N.93 Chain B: E.76, R.77, R.78, Y.79 Ligand excluded by PLIP EOH.22: 2 residues within 4Å: Chain B: N.4, Q.6 Ligand excluded by PLIP EOH.23: 4 residues within 4Å: Chain B: P.60, K.164, I.166, K.172 Ligand excluded by PLIP EOH.24: 1 residues within 4Å: Chain B: H.14 Ligand excluded by PLIP EOH.30: 9 residues within 4Å: Chain B: E.149 Chain C: K.54, A.55, K.56, E.61, E.90, K.186, W.325 Ligands: EDO.28 Ligand excluded by PLIP EOH.31: 3 residues within 4Å: Chain C: S.141, F.142, H.143 Ligand excluded by PLIP EOH.32: 5 residues within 4Å: Chain C: D.163, Y.392, G.393, P.398, G.399 Ligand excluded by PLIP EOH.33: 4 residues within 4Å: Chain B: N.111 Chain C: V.87, H.88, A.89 Ligand excluded by PLIP EOH.34: 3 residues within 4Å: Chain C: W.252, R.288, Y.397 Ligand excluded by PLIP EOH.42: 5 residues within 4Å: Chain C: V.188, K.190 Chain D: Q.186, T.187, H.188 Ligand excluded by PLIP EOH.43: 7 residues within 4Å: Chain D: P.112, K.113, I.114, A.146, R.147, R.148 Chain F: L.71 Ligand excluded by PLIP EOH.44: 3 residues within 4Å: Chain D: E.17, E.18, R.21 Ligand excluded by PLIP EOH.45: 6 residues within 4Å: Chain C: G.92, N.93 Chain D: E.76, R.77, R.78, Y.79 Ligand excluded by PLIP EOH.46: 2 residues within 4Å: Chain D: N.4, Q.6 Ligand excluded by PLIP EOH.47: 4 residues within 4Å: Chain D: P.60, K.164, I.166, K.172 Ligand excluded by PLIP EOH.48: 1 residues within 4Å: Chain D: H.14 Ligand excluded by PLIP EOH.54: 9 residues within 4Å: Chain D: E.149 Chain E: K.54, A.55, K.56, E.61, E.90, K.186, W.325 Ligands: EDO.52 Ligand excluded by PLIP EOH.55: 3 residues within 4Å: Chain E: S.141, F.142, H.143 Ligand excluded by PLIP EOH.56: 5 residues within 4Å: Chain E: D.163, Y.392, G.393, P.398, G.399 Ligand excluded by PLIP EOH.57: 4 residues within 4Å: Chain D: N.111 Chain E: V.87, H.88, A.89 Ligand excluded by PLIP EOH.58: 3 residues within 4Å: Chain E: W.252, R.288, Y.397 Ligand excluded by PLIP EOH.66: 5 residues within 4Å: Chain E: V.188, K.190 Chain F: Q.186, T.187, H.188 Ligand excluded by PLIP EOH.67: 7 residues within 4Å: Chain B: L.71 Chain F: P.112, K.113, I.114, A.146, R.147, R.148 Ligand excluded by PLIP EOH.68: 3 residues within 4Å: Chain F: E.17, E.18, R.21 Ligand excluded by PLIP EOH.69: 6 residues within 4Å: Chain E: G.92, N.93 Chain F: E.76, R.77, R.78, Y.79 Ligand excluded by PLIP EOH.70: 2 residues within 4Å: Chain F: N.4, Q.6 Ligand excluded by PLIP EOH.71: 4 residues within 4Å: Chain F: P.60, K.164, I.166, K.172 Ligand excluded by PLIP EOH.72: 1 residues within 4Å: Chain F: H.14 Ligand excluded by PLIP

6 x NI: NICKEL (II) ION(Non-covalent)

NI.11: 3 residues within 4Å: Chain B: H.14, E.18, E.160 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.14, B:E.160, H2O.19, H2O.19, H2O.27 NI.12: 4 residues within 4Å: Chain B: E.55, H.56 Chain D: M.2 Ligands: EDO.37 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.56, H2O.22, H2O.45, H2O.46 NI.35: 3 residues within 4Å: Chain D: H.14, E.18, E.160 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.14, D:E.160, H2O.47, H2O.47, H2O.55 NI.36: 4 residues within 4Å: Chain D: E.55, H.56 Chain F: M.2 Ligands: EDO.61 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.56, H2O.50, H2O.73, H2O.74 NI.59: 3 residues within 4Å: Chain F: H.14, E.18, E.160 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:H.14, F:E.160, H2O.75, H2O.75, H2O.84 NI.60: 4 residues within 4Å: Chain B: M.2 Chain F: E.55, H.56 Ligands: EDO.13 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:H.56, H2O.17, H2O.17, H2O.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Friemann, R. et al., Structural insight into the dioxygenation of nitroarene compounds: the crystal structure of nitrobenzene dioxygenase. J. Mol. Biol. (2005)

Release Date

2005-05-04

Peptides

OXYGENASE-ALPHA NBDO: ACE
OXYGENASE-BETA NBDO: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

OXYGENASE-ALPHA NBDO

OXYGENASE-BETA NBDO

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