SMTL ID : 1eg9.1 (1 other biounit)

NAPHTHALENE 1,2-DIOXYGENASE WITH INDOLE BOUND IN THE ACTIVE SITE.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-oligomer

Ligands

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain B: Q.63, Q.65 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.63, B:Q.65 Water bridges: B:Q.63, B:Q.65 SO4.2: 5 residues within 4Å: Chain B: G.59, S.60, E.61, K.164, K.172 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.60 Water bridges: B:K.164, B:K.164 Salt bridges: B:K.164, B:K.172 SO4.3: 4 residues within 4Å: Chain A: L.128, N.129, K.130, K.131 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.128, A:N.129, A:K.130, A:K.131 Water bridges: A:K.130 Salt bridges: A:K.130, A:K.131 SO4.7: 2 residues within 4Å: Chain D: Q.63, Q.65 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.63, D:Q.65 Water bridges: D:Q.63, D:Q.65 SO4.8: 5 residues within 4Å: Chain D: G.59, S.60, E.61, K.164, K.172 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.60 Water bridges: D:K.164, D:K.164 Salt bridges: D:K.164, D:K.172 SO4.9: 4 residues within 4Å: Chain C: L.128, N.129, K.130, K.131 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:L.128, C:N.129, C:K.130, C:K.131 Water bridges: C:K.130 Salt bridges: C:K.130, C:K.131 SO4.13: 2 residues within 4Å: Chain F: Q.63, Q.65 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.63, F:Q.65 Water bridges: F:Q.63, F:Q.65 SO4.14: 5 residues within 4Å: Chain F: G.59, S.60, E.61, K.164, K.172 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.60 Water bridges: F:K.164, F:K.164 Salt bridges: F:K.164, F:K.172 SO4.15: 4 residues within 4Å: Chain E: L.128, N.129, K.130, K.131 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:L.128, E:N.129, E:K.130, E:K.131 Water bridges: E:K.130 Salt bridges: E:K.130, E:K.131

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

FE.4: 4 residues within 4Å: Chain A: N.201, H.208, H.213, D.362 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.208, A:H.213, A:D.362, A:D.362, H2O.430 FE.10: 4 residues within 4Å: Chain C: N.201, H.208, H.213, D.362 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.208, C:H.213, C:D.362, C:D.362, H2O.1042 FE.16: 4 residues within 4Å: Chain E: N.201, H.208, H.213, D.362 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.208, E:H.213, E:D.362, E:D.362, H2O.1654

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

FES.5: 10 residues within 4Å: Chain A: C.81, H.83, R.84, G.85, K.86, C.101, Y.103, H.104, G.105, W.106 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.81, A:H.83, A:C.101, A:H.104 FES.11: 10 residues within 4Å: Chain C: C.81, H.83, R.84, G.85, K.86, C.101, Y.103, H.104, G.105, W.106 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.81, C:H.83, C:C.101, C:H.104 FES.17: 10 residues within 4Å: Chain E: C.81, H.83, R.84, G.85, K.86, C.101, Y.103, H.104, G.105, W.106 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.81, E:H.83, E:C.101, E:H.104

3 x IND: INDOLE(Non-covalent)

IND.6: 7 residues within 4Å: Chain A: N.201, D.205, H.208, V.209, H.295, N.297, L.307 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.209, A:N.297, A:L.307 Hydrogen bonds: A:N.297 pi-Stacking: A:H.208 IND.12: 7 residues within 4Å: Chain C: N.201, D.205, H.208, V.209, H.295, N.297, L.307 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.209, C:N.297, C:L.307 Hydrogen bonds: C:N.297 pi-Stacking: C:H.208 IND.18: 7 residues within 4Å: Chain E: N.201, D.205, H.208, V.209, H.295, N.297, L.307 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:V.209, E:N.297, E:L.307 Hydrogen bonds: E:N.297 pi-Stacking: E:H.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carredano, E. et al., Substrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding. J.Mol.Biol. (2000)

Release Date

2000-05-24

Peptides

PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT): ACE
PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT): BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT)

PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT)

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