SMTL ID : 2b24.1

Crystal structure of naphthalene 1,2-dioxygenase from Rhodococcus sp. bound to indole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-3-3-mer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: N.209, H.216, H.221, D.372 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.216, A:H.221, A:D.372, A:D.372 FE.4: 4 residues within 4Å: Chain C: N.209, H.216, H.221, D.372 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.216, C:H.221, C:D.372, C:D.372 FE.7: 4 residues within 4Å: Chain E: N.209, H.216, H.221, D.372 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.216, E:H.221, E:D.372, E:D.372

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

FES.2: 9 residues within 4Å: Chain A: C.88, H.90, R.91, G.92, C.108, Y.110, H.111, G.112, W.113 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.88, A:H.90, A:C.108, A:H.111 FES.5: 9 residues within 4Å: Chain C: C.88, H.90, R.91, G.92, C.108, Y.110, H.111, G.112, W.113 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.88, C:H.90, C:C.108, C:H.111 FES.8: 8 residues within 4Å: Chain E: C.88, H.90, R.91, C.108, Y.110, H.111, G.112, W.113 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.88, E:H.90, E:C.108, E:H.111

3 x IND: INDOLE(Non-covalent)

IND.3: 5 residues within 4Å: Chain A: D.213, A.214, T.217, H.295, F.307 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.214, A:F.307, A:F.307 Hydrogen bonds: A:H.295 pi-Stacking: A:F.210, A:H.216 IND.6: 5 residues within 4Å: Chain C: D.213, A.214, T.217, H.295, F.307 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.214, C:F.307, C:F.307 Hydrogen bonds: C:H.295 pi-Stacking: C:H.216 IND.9: 5 residues within 4Å: Chain E: D.213, A.214, T.217, H.295, F.307 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:A.214, E:F.307, E:F.307 Hydrogen bonds: E:H.295 pi-Stacking: E:F.210, E:H.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gakhar, L. et al., Structure and Increased Thermostability of Rhodococcus sp. Naphthalene 1,2-Dioxygenase. J.Bacteriol. (2005)

Release Date

2005-10-04

Peptides

naphthalene dioxygenase large subunit: ACE
naphthalene dioxygenase small subunit: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

naphthalene dioxygenase large subunit

naphthalene dioxygenase small subunit

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