SMTL ID : 4hjl.1

Naphthalene 1,2-Dioxygenase bound to 1-chloronaphthalene

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-oligomer

Ligands

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

FES.1: 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.16: 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.31: 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 FE: FE (III) ION(Non-covalent)

FE.2: 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.7 FE.17: 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.39 FE.32: 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.72

3 x 15O: 1-CHLORONAPHTHALENE(Non-covalent)

15O.3: 9 residues within 4Å: Chain A: N.201, F.202, D.205, H.208, V.209, V.260, H.295, N.297, L.307 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.209, A:N.297, A:L.307 pi-Stacking: A:H.208 15O.18: 9 residues within 4Å: Chain C: N.201, F.202, D.205, H.208, V.209, V.260, H.295, N.297, L.307 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.209, C:N.297, C:L.307 pi-Stacking: C:H.208 15O.33: 9 residues within 4Å: Chain E: N.201, F.202, D.205, H.208, V.209, V.260, H.295, N.297, L.307 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:V.209, E:N.297, E:L.307 pi-Stacking: E:H.208

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

EDO.4: 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 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: H.18, S.381, D.382, L.383 Chain E: V.80, C.81, R.82 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: T.56, E.92, P.186, K.188, W.327 Chain B: E.68, R.181 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: P.49, A.50, D.53 Chain B: R.76, Y.77, K.78, L.79 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: P.118, F.119 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain B: Y.48, Y.86, Q.100, M.189, V.190, F.191 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain B: R.136, A.156, E.158, F.175, V.176, D.177 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain B: E.81, A.82, N.84 Ligand excluded by PLIP EDO.19: 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 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain A: V.80, C.81, R.82 Chain C: H.18, S.381, D.382, L.383 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain C: T.56, E.92, P.186, K.188, W.327 Chain D: E.68, R.181 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain C: P.49, A.50, D.53 Chain D: R.76, Y.77, K.78, L.79 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain C: P.118, F.119 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain D: Y.48, Y.86, Q.100, M.189, V.190, F.191 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain D: R.136, A.156, E.158, F.175, V.176, D.177 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain D: E.81, A.82, N.84 Ligand excluded by PLIP EDO.34: 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 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain C: V.80, C.81, R.82 Chain E: H.18, S.381, D.382, L.383 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain E: T.56, E.92, P.186, K.188, W.327 Chain F: E.68, R.181 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain E: P.49, A.50, D.53 Chain F: R.76, Y.77, K.78, L.79 Ligand excluded by PLIP EDO.39: 2 residues within 4Å: Chain E: P.118, F.119 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain F: Y.48, Y.86, Q.100, M.189, V.190, F.191 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain F: R.136, A.156, E.158, F.175, V.176, D.177 Ligand excluded by PLIP EDO.45: 3 residues within 4Å: Chain F: E.81, A.82, N.84 Ligand excluded by PLIP

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

SO4.6: 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:K.130, A:K.131 Water bridges: A:E.126, A:E.126, A:N.129, A:K.130 Salt bridges: A:K.130 SO4.10: 3 residues within 4Å: Chain A: K.245, W.439, H.440 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.439 Water bridges: A:W.439 Salt bridges: A:K.245 SO4.13: 2 residues within 4Å: Chain B: Q.61, Q.63 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.61, B:Q.63 Water bridges: B:Q.61, B:Q.63 SO4.14: 6 residues within 4Å: Chain B: G.57, S.58, E.59, G.164, E.165, K.170 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.58, B:E.165, B:E.165 Water bridges: B:S.58, B:S.58, B:E.165, B:E.165 Salt bridges: B:K.170 SO4.21: 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:K.130, C:K.131 Water bridges: C:E.126, C:E.126, C:N.129, C:K.130 Salt bridges: C:K.130 SO4.25: 3 residues within 4Å: Chain C: K.245, W.439, H.440 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.439 Water bridges: C:W.439 Salt bridges: C:K.245 SO4.28: 2 residues within 4Å: Chain D: Q.61, Q.63 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.61, D:Q.63 Water bridges: D:Q.61, D:Q.63 SO4.29: 6 residues within 4Å: Chain D: G.57, S.58, E.59, G.164, E.165, K.170 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.58, D:E.165, D:E.165 Water bridges: D:S.58, D:S.58, D:E.165, D:E.165 Salt bridges: D:K.170 SO4.36: 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:K.130, E:K.131 Water bridges: E:E.126, E:E.126, E:N.129, E:K.130 Salt bridges: E:K.130 SO4.40: 3 residues within 4Å: Chain E: K.245, W.439, H.440 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:W.439 Water bridges: E:W.439 Salt bridges: E:K.245 SO4.43: 2 residues within 4Å: Chain F: Q.61, Q.63 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.61, F:Q.63 Water bridges: F:Q.61, F:Q.63 SO4.44: 6 residues within 4Å: Chain F: G.57, S.58, E.59, G.164, E.165, K.170 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:S.58, F:E.165, F:E.165 Water bridges: F:S.58, F:S.58, F:E.165, F:E.165 Salt bridges: F:K.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferraro, D.J. et al., Naphthalene 1,2-Dioxygenase bound to 1-chloronaphthalene. TO BE PUBLISHED

Release Date

2013-10-16

Peptides

Naphthalene 1,2-dioxygenase subunit alpha: ACE
Naphthalene 1,2-dioxygenase subunit beta: 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 subunit alpha

Naphthalene 1,2-dioxygenase subunit beta