SMTL ID : 2hml.1

Crystal Structure of the Naphthalene 1,2-Dioxygenase F352V Mutant Bound to Phenanthrene.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-3-3-mer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: N.201, H.208, H.213, D.362 Ligands: PEY.5 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.2 FE.26: 5 residues within 4Å: Chain C: N.201, H.208, H.213, D.362 Ligands: PEY.30 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.23 FE.51: 5 residues within 4Å: Chain E: N.201, H.208, H.213, D.362 Ligands: PEY.55 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.44

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

SO4.2: 4 residues within 4Å: Chain A: L.128, N.129, K.130, K.131 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.130, A:K.131 Water bridges: A:E.120, A:L.128 Salt bridges: A:K.130 SO4.3: 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:Y.394 Salt bridges: A:K.245 SO4.16: 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 SO4.17: 6 residues within 4Å: Chain B: G.59, S.60, E.61, G.166, E.167, K.172 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.60, B:E.167, B:E.167 Water bridges: B:K.172 Salt bridges: B:K.172 SO4.18: 5 residues within 4Å: Chain A: T.368 Chain B: R.148 Chain E: T.87, V.89, S.90 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain B Water bridges: E:N.79, E:T.87, B:R.148, B:R.148, B:R.148 Salt bridges: B:R.148 SO4.27: 4 residues within 4Å: Chain C: L.128, N.129, K.130, K.131 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.130, C:K.131 Water bridges: C:E.120, C:L.128 Salt bridges: C:K.130 SO4.28: 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:Y.394 Salt bridges: C:K.245 SO4.41: 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 SO4.42: 6 residues within 4Å: Chain D: G.59, S.60, E.61, G.166, E.167, K.172 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.60, D:E.167, D:E.167 Water bridges: D:K.172 Salt bridges: D:K.172 SO4.43: 5 residues within 4Å: Chain A: T.87, V.89, S.90 Chain C: T.368 Chain D: R.148 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain D Water bridges: A:N.79, A:T.87, D:R.148, D:R.148, D:R.148 Salt bridges: D:R.148 SO4.52: 4 residues within 4Å: Chain E: L.128, N.129, K.130, K.131 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:K.130, E:K.131 Water bridges: E:E.120, E:L.128 Salt bridges: E:K.130 SO4.53: 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:Y.394 Salt bridges: E:K.245 SO4.66: 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 SO4.67: 6 residues within 4Å: Chain F: G.59, S.60, E.61, G.166, E.167, K.172 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.60, F:E.167, F:E.167 Water bridges: F:K.172 Salt bridges: F:K.172 SO4.68: 5 residues within 4Å: Chain C: T.87, V.89, S.90 Chain E: T.368 Chain F: R.148 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain C Water bridges: F:R.148, F:R.148, F:R.148, C:N.79, C:T.87 Salt bridges: F:R.148

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

FES.4: 9 residues within 4Å: Chain A: C.81, H.83, R.84, 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.29: 9 residues within 4Å: Chain C: C.81, H.83, R.84, 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.54: 9 residues within 4Å: Chain E: C.81, H.83, R.84, 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 PEY: PHENANTHRENE(Non-covalent)

PEY.5: 13 residues within 4Å: Chain A: N.201, F.202, D.205, H.208, V.209, H.213, L.253, H.295, N.297, L.307, W.358, D.362 Ligands: FE.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.202, A:V.209, A:L.253, A:N.297, A:L.307, A:W.358 pi-Stacking: A:H.208 PEY.30: 13 residues within 4Å: Chain C: N.201, F.202, D.205, H.208, V.209, H.213, L.253, H.295, N.297, L.307, W.358, D.362 Ligands: FE.26 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.202, C:V.209, C:L.253, C:N.297, C:L.307, C:W.358 pi-Stacking: C:H.208 PEY.55: 13 residues within 4Å: Chain E: N.201, F.202, D.205, H.208, V.209, H.213, L.253, H.295, N.297, L.307, W.358, D.362 Ligands: FE.51 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:F.202, E:V.209, E:L.253, E:N.297, E:L.307, E:W.358 pi-Stacking: E:H.208

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

EDO.6: 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.7: 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.8: 3 residues within 4Å: Chain A: P.118, F.119 Chain C: N.230 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: E.24, K.374 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: T.56, E.92, P.186, K.188, W.327 Chain B: E.70, R.183 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: V.183, R.342, A.345, D.346 Chain B: N.82, N.86 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: Y.376, Q.377, D.380 Chain E: K.136 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: S.73, I.74, V.141, S.143 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: V.9, S.10, E.11, R.418, Q.421, E.442 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: Y.3, H.29, K.32 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: Y.50, Y.88, Q.102, M.191, V.192, F.193 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain B: N.91, Q.94 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: R.138, A.158, E.160, F.177, V.178, D.179 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain A: P.49, A.50, D.53 Chain B: R.78, Y.79, K.80, L.81 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain B: E.83, A.84, N.86 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: V.190, K.192 Chain B: Q.186, T.187, H.188 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: K.9, L.10, V.11, S.12 Chain D: K.113 Ligand excluded by PLIP EDO.31: 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.32: 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.33: 3 residues within 4Å: Chain C: P.118, F.119 Chain E: N.230 Ligand excluded by PLIP EDO.34: 2 residues within 4Å: Chain C: E.24, K.374 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain C: T.56, E.92, P.186, K.188, W.327 Chain D: E.70, R.183 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain C: V.183, R.342, A.345, D.346 Chain D: N.82, N.86 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain A: K.136 Chain C: Y.376, Q.377, D.380 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain C: S.73, I.74, V.141, S.143 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain C: V.9, S.10, E.11, R.418, Q.421, E.442 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain C: Y.3, H.29, K.32 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain D: Y.50, Y.88, Q.102, M.191, V.192, F.193 Ligand excluded by PLIP EDO.45: 2 residues within 4Å: Chain D: N.91, Q.94 Ligand excluded by PLIP EDO.46: 6 residues within 4Å: Chain D: R.138, A.158, E.160, F.177, V.178, D.179 Ligand excluded by PLIP EDO.47: 7 residues within 4Å: Chain C: P.49, A.50, D.53 Chain D: R.78, Y.79, K.80, L.81 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain D: E.83, A.84, N.86 Ligand excluded by PLIP EDO.49: 5 residues within 4Å: Chain C: V.190, K.192 Chain D: Q.186, T.187, H.188 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain D: K.9, L.10, V.11, S.12 Chain F: K.113 Ligand excluded by PLIP EDO.56: 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.57: 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.58: 3 residues within 4Å: Chain A: N.230 Chain E: P.118, F.119 Ligand excluded by PLIP EDO.59: 2 residues within 4Å: Chain E: E.24, K.374 Ligand excluded by PLIP EDO.60: 7 residues within 4Å: Chain E: T.56, E.92, P.186, K.188, W.327 Chain F: E.70, R.183 Ligand excluded by PLIP EDO.61: 6 residues within 4Å: Chain E: V.183, R.342, A.345, D.346 Chain F: N.82, N.86 Ligand excluded by PLIP EDO.62: 4 residues within 4Å: Chain C: K.136 Chain E: Y.376, Q.377, D.380 Ligand excluded by PLIP EDO.63: 4 residues within 4Å: Chain E: S.73, I.74, V.141, S.143 Ligand excluded by PLIP EDO.64: 6 residues within 4Å: Chain E: V.9, S.10, E.11, R.418, Q.421, E.442 Ligand excluded by PLIP EDO.65: 3 residues within 4Å: Chain E: Y.3, H.29, K.32 Ligand excluded by PLIP EDO.69: 6 residues within 4Å: Chain F: Y.50, Y.88, Q.102, M.191, V.192, F.193 Ligand excluded by PLIP EDO.70: 2 residues within 4Å: Chain F: N.91, Q.94 Ligand excluded by PLIP EDO.71: 6 residues within 4Å: Chain F: R.138, A.158, E.160, F.177, V.178, D.179 Ligand excluded by PLIP EDO.72: 7 residues within 4Å: Chain E: P.49, A.50, D.53 Chain F: R.78, Y.79, K.80, L.81 Ligand excluded by PLIP EDO.73: 3 residues within 4Å: Chain F: E.83, A.84, N.86 Ligand excluded by PLIP EDO.74: 5 residues within 4Å: Chain E: V.190, K.192 Chain F: Q.186, T.187, H.188 Ligand excluded by PLIP EDO.75: 5 residues within 4Å: Chain B: K.113 Chain F: K.9, L.10, V.11, S.12 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferraro, D.J. et al., Structural basis for regioselectivity and stereoselectivity of product formation by naphthalene 1,2-dioxygenase. J.Bacteriol. (2006)

Release Date

2006-10-10

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

Related Entries With Identical Sequence