SMTL ID : 1uuv.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-3-3-mer

Ligands

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

FES.1: 9 residues within 4Å: Chain A: C.81, H.83, R.84, G.85, 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.13: 9 residues within 4Å: Chain C: C.81, H.83, R.84, G.85, 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.25: 9 residues within 4Å: Chain E: C.81, H.83, R.84, G.85, 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

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

EDO.2: 10 residues within 4Å: Chain A: L.31, F.35, A.36, M.59, G.60, I.61, D.62, F.152 Chain C: Y.376, Q.377 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:I.61, A:D.62, A:D.62, C:Q.377 EDO.3: 7 residues within 4Å: Chain A: H.18, S.381, D.382, L.383 Chain E: V.80, C.81, R.82 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:H.18, A:S.381, E:R.82 Water bridges: A:D.382, E:R.82 EDO.4: 7 residues within 4Å: Chain A: T.56, E.92, P.186, K.188, W.327 Chain B: E.70, R.183 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.70, B:E.70, B:R.183, A:T.56, A:T.56, A:K.188 EDO.8: 6 residues within 4Å: Chain B: Y.50, Y.88, Q.102, M.191, V.192, F.193 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.50, B:Y.88, B:Y.88 Water bridges: B:F.193 EDO.9: 3 residues within 4Å: Chain A: R.343 Chain B: N.91, Q.94 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Water bridges: A:D.264, A:R.350, A:R.350, A:R.350, B:N.91 Hydrogen bonds: B:N.91, B:Q.94 EDO.14: 10 residues within 4Å: Chain C: L.31, F.35, A.36, M.59, G.60, I.61, D.62, F.152 Chain E: Y.376, Q.377 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:I.61, C:D.62, C:D.62, E:Q.377 EDO.15: 7 residues within 4Å: Chain A: V.80, C.81, R.82 Chain C: H.18, S.381, D.382, L.383 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:R.82, C:H.18, C:S.381 Water bridges: A:R.82, C:D.382 EDO.16: 7 residues within 4Å: Chain C: T.56, E.92, P.186, K.188, W.327 Chain D: E.70, R.183 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:T.56, C:T.56, C:K.188, D:E.70, D:E.70, D:R.183 EDO.20: 6 residues within 4Å: Chain D: Y.50, Y.88, Q.102, M.191, V.192, F.193 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.50, D:Y.88, D:Y.88 Water bridges: D:F.193 EDO.21: 3 residues within 4Å: Chain C: R.343 Chain D: N.91, Q.94 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Water bridges: C:D.264, C:R.350, C:R.350, C:R.350, D:N.91 Hydrogen bonds: D:N.91, D:Q.94 EDO.26: 10 residues within 4Å: Chain A: Y.376, Q.377 Chain E: L.31, F.35, A.36, M.59, G.60, I.61, D.62, F.152 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:I.61, E:D.62, E:D.62, A:Q.377 EDO.27: 7 residues within 4Å: Chain C: V.80, C.81, R.82 Chain E: H.18, S.381, D.382, L.383 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:H.18, E:S.381, C:R.82 Water bridges: E:D.382, C:R.82 EDO.28: 7 residues within 4Å: Chain E: T.56, E.92, P.186, K.188, W.327 Chain F: E.70, R.183 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:T.56, E:T.56, E:K.188, F:E.70, F:E.70, F:R.183 EDO.32: 6 residues within 4Å: Chain F: Y.50, Y.88, Q.102, M.191, V.192, F.193 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Y.50, F:Y.88, F:Y.88 Water bridges: F:F.193 EDO.33: 3 residues within 4Å: Chain E: R.343 Chain F: N.91, Q.94 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:N.91, F:Q.94 Water bridges: F:N.91, E:D.264, E:R.350, E:R.350, E:R.350

3 x IND: INDOLE(Non-covalent)

IND.5: 8 residues within 4Å: Chain A: N.201, F.202, D.205, H.208, H.295, N.297, L.307 Ligands: NO.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.297, A:L.307, A:L.307 Hydrogen bonds: A:N.201 pi-Stacking: A:H.208 IND.17: 8 residues within 4Å: Chain C: N.201, F.202, D.205, H.208, H.295, N.297, L.307 Ligands: NO.18 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:N.297, C:L.307, C:L.307 Hydrogen bonds: C:N.201 pi-Stacking: C:H.208 IND.29: 8 residues within 4Å: Chain E: N.201, F.202, D.205, H.208, H.295, N.297, L.307 Ligands: NO.30 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:N.297, E:L.307, E:L.307 Hydrogen bonds: E:N.201 pi-Stacking: E:H.208

3 x NO: NITRIC OXIDE(Non-covalent)

NO.6: 6 residues within 4Å: Chain A: H.208, H.213, F.352, D.362 Ligands: IND.5, FE.7 No protein-ligand interaction detected (PLIP) NO.18: 6 residues within 4Å: Chain C: H.208, H.213, F.352, D.362 Ligands: IND.17, FE.19 No protein-ligand interaction detected (PLIP) NO.30: 6 residues within 4Å: Chain E: H.208, H.213, F.352, D.362 Ligands: IND.29, FE.31 No protein-ligand interaction detected (PLIP)

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

FE.7: 5 residues within 4Å: Chain A: N.201, H.208, H.213, D.362 Ligands: NO.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.208, A:H.213, A:D.362, A:D.362, NO.6 FE.19: 5 residues within 4Å: Chain C: N.201, H.208, H.213, D.362 Ligands: NO.18 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.208, C:H.213, C:D.362, C:D.362, NO.18 FE.31: 5 residues within 4Å: Chain E: N.201, H.208, H.213, D.362 Ligands: NO.30 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.208, E:H.213, E:D.362, E:D.362

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

SO4.10: 2 residues within 4Å: Chain B: Q.63, Q.65 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.63, B:Q.65 SO4.11: 5 residues within 4Å: Chain B: G.59, S.60, E.61, K.164, K.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.60 Salt bridges: B:K.164 SO4.12: 2 residues within 4Å: Chain B: R.165, R.171 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.165, B:R.165, B:R.171 Salt bridges: B:R.165, B:R.171 SO4.22: 2 residues within 4Å: Chain D: Q.63, Q.65 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.63, D:Q.65 SO4.23: 5 residues within 4Å: Chain D: G.59, S.60, E.61, K.164, K.172 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.60 Salt bridges: D:K.164 SO4.24: 2 residues within 4Å: Chain D: R.165, R.171 5 PLIP interactions: 5 interactions with chain D Water bridges: D:R.165, D:R.165, D:R.171 Salt bridges: D:R.165, D:R.171 SO4.34: 2 residues within 4Å: Chain F: Q.63, Q.65 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.63, F:Q.65 SO4.35: 5 residues within 4Å: Chain F: G.59, S.60, E.61, K.164, K.172 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.60 Salt bridges: F:K.164 SO4.36: 2 residues within 4Å: Chain F: R.165, R.171 5 PLIP interactions: 5 interactions with chain F Water bridges: F:R.165, F:R.165, F:R.171 Salt bridges: F:R.165, F:R.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karlsson, A. et al., No Binding to Naphthalene Dioxygenase. J.Biol.Inorg.Chem. (2005)

Release Date

2005-02-09

Peptides

NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT: ACE
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

NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT

NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT

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