SMTL ID : 1o7h.1

NAPHTHALENE 1,2-DIOXYGENASE WITH OXIDIZED RIESKE IRON SULPHUR CENTER SITE.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-3-3-mer

Ligands

12 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 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.2: 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.3: 2 residues within 4Å: Chain A: E.24, K.374 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.374, A:K.374, A:K.374 EDO.8: 3 residues within 4Å: Chain B: D.46, R.115, F.116 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain B Water bridges: F:R.138, F:A.158, F:D.179, B:Q.48 Hydrogen bonds: B:R.115, B:F.116, B:F.116 EDO.11: 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.12: 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.13: 2 residues within 4Å: Chain C: E.24, K.374 3 PLIP interactions: 3 interactions with chain C Water bridges: C:K.374, C:K.374, C:K.374 EDO.18: 3 residues within 4Å: Chain D: D.46, R.115, F.116 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain D Water bridges: B:R.138, B:A.158, B:D.179, D:Q.48 Hydrogen bonds: D:R.115, D:F.116, D:F.116 EDO.21: 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.22: 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.23: 2 residues within 4Å: Chain E: E.24, K.374 3 PLIP interactions: 3 interactions with chain E Water bridges: E:K.374, E:K.374, E:K.374 EDO.28: 3 residues within 4Å: Chain F: D.46, R.115, F.116 7 PLIP interactions: 4 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:R.115, F:F.116, F:F.116 Water bridges: F:Q.48, D:R.138, D:A.158, D:D.179

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.6 FE.14: 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.20 FE.24: 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.33

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

SO4.5: 3 residues within 4Å: Chain A: K.245, Y.394, W.439 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.439 Water bridges: A:Y.394, A:Y.394, A:Y.394 Salt bridges: A:K.245 SO4.6: 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 SO4.9: 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 SO4.10: 5 residues within 4Å: Chain B: G.59, S.60, G.166, E.167, K.172 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.60, B:E.167, B:E.167 Water bridges: B:E.61, B:K.172 Salt bridges: B:K.172 SO4.15: 3 residues within 4Å: Chain C: K.245, Y.394, W.439 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:W.439 Water bridges: C:Y.394, C:Y.394, C:Y.394 Salt bridges: C:K.245 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 SO4.19: 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 SO4.20: 5 residues within 4Å: Chain D: G.59, S.60, G.166, E.167, K.172 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.60, D:E.167, D:E.167 Water bridges: D:E.61, D:K.172 Salt bridges: D:K.172 SO4.25: 3 residues within 4Å: Chain E: K.245, Y.394, W.439 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:W.439 Water bridges: E:Y.394, E:Y.394, E:Y.394 Salt bridges: E:K.245 SO4.26: 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 SO4.29: 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 SO4.30: 5 residues within 4Å: Chain F: G.59, S.60, G.166, E.167, K.172 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:S.60, F:E.167, F:E.167 Water bridges: F:E.61, F:K.172 Salt bridges: F:K.172

3 x FES: FE2/S2 (INORGANIC) CLUSTER(Covalent)

FES.7: 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.17: 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.27: 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

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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