SMTL ID : 1o7p.1

NAPHTHALENE 1,2-DIOXYGENASE, PRODUCT COMPLEX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-3-3-mer

Ligands

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

EDO.1: 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.2: 8 residues within 4Å: Chain A: H.18, S.381, D.382, L.383 Chain E: V.80, C.81, R.82, G.85 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain B: Y.50, Y.88, Q.102, M.191, V.192, F.193 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain B: N.91, Q.94 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain B: R.138, A.158, E.160, F.177, V.178, D.179 Ligand excluded by PLIP EDO.10: 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.13: 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.14: 8 residues within 4Å: Chain A: V.80, C.81, R.82, G.85 Chain C: H.18, S.381, D.382, L.383 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain D: Y.50, Y.88, Q.102, M.191, V.192, F.193 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain D: N.91, Q.94 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain D: R.138, A.158, E.160, F.177, V.178, D.179 Ligand excluded by PLIP EDO.22: 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.25: 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.26: 8 residues within 4Å: Chain C: V.80, C.81, R.82, G.85 Chain E: H.18, S.381, D.382, L.383 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain F: Y.50, Y.88, Q.102, M.191, V.192, F.193 Ligand excluded by PLIP EDO.32: 2 residues within 4Å: Chain F: N.91, Q.94 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain F: R.138, A.158, E.160, F.177, V.178, D.179 Ligand excluded by PLIP EDO.34: 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

3 x NDH: (1R, 2S)-CIS 1,2 DIHYDROXY-1,2-DIHYDRONAPHTHALENE(Non-covalent)

NDH.3: 12 residues within 4Å: Chain A: N.201, F.202, D.205, H.208, V.209, H.213, L.253, H.295, N.297, F.352, D.362 Ligands: FE.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.209, A:L.253, A:N.297 Hydrogen bonds: A:N.201, A:D.362 NDH.15: 12 residues within 4Å: Chain C: N.201, F.202, D.205, H.208, V.209, H.213, L.253, H.295, N.297, F.352, D.362 Ligands: FE.18 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.209, C:L.253, C:N.297 Hydrogen bonds: C:N.201, C:D.362 NDH.27: 12 residues within 4Å: Chain E: N.201, F.202, D.205, H.208, V.209, H.213, L.253, H.295, N.297, F.352, D.362 Ligands: FE.30 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:V.209, E:L.253, E:N.297 Hydrogen bonds: E:N.201, E:D.362

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

SO4.4: 4 residues within 4Å: Chain A: L.128, N.129, K.130, K.131 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.128, A:K.130, A:K.131 Salt bridges: A:K.130 SO4.11: 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 SO4.12: 5 residues within 4Å: Chain B: G.59, S.60, E.61, 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 SO4.16: 4 residues within 4Å: Chain C: L.128, N.129, K.130, K.131 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.128, C:K.130, C:K.131 Salt bridges: C:K.130 SO4.23: 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 SO4.24: 5 residues within 4Å: Chain D: G.59, S.60, E.61, 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 SO4.28: 4 residues within 4Å: Chain E: L.128, N.129, K.130, K.131 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:L.128, E:K.130, E:K.131 Salt bridges: E:K.130 SO4.35: 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 SO4.36: 5 residues within 4Å: Chain F: G.59, S.60, E.61, 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

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.17: 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.29: 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.6: 5 residues within 4Å: Chain A: N.201, H.208, H.213, D.362 Ligands: NDH.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.208, A:H.213, A:D.362, A:D.362 FE.18: 5 residues within 4Å: Chain C: N.201, H.208, H.213, D.362 Ligands: NDH.15 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.208, C:H.213, C:D.362, C:D.362 FE.30: 5 residues within 4Å: Chain E: N.201, H.208, H.213, D.362 Ligands: NDH.27 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.208, E:H.213, E:D.362, E:D.362

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karlsson, A. et al., Crystal Structure of Naphthalene Dioxygenase: Side-on Binding of Dioxygen to Iron. Science (2003)

Release Date

2003-02-20

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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