- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.40 Å
- Oligo State
- hetero-3-3-mer
- Ligands
- 21 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 3 x IND: INDOLE(Non-covalent)
IND.5: 7 residues within 4Å:- Chain A: N.201, D.205, H.208, V.209, H.295, N.297
- Ligands: OXY.6
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:V.209, A:N.297
- Hydrogen bonds: A:N.201, A:N.297
- pi-Stacking: A:H.208
IND.20: 7 residues within 4Å:- Chain C: N.201, D.205, H.208, V.209, H.295, N.297
- Ligands: OXY.21
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:V.209, C:N.297
- Hydrogen bonds: C:N.201, C:N.297
- pi-Stacking: C:H.208
IND.35: 7 residues within 4Å:- Chain E: N.201, D.205, H.208, V.209, H.295, N.297
- Ligands: OXY.36
5 PLIP interactions:5 interactions with chain E- Hydrophobic interactions: E:V.209, E:N.297
- Hydrogen bonds: E:N.201, E:N.297
- pi-Stacking: E:H.208
- 3 x OXY: OXYGEN MOLECULE(Non-covalent)
OXY.6: 7 residues within 4Å:- Chain A: N.201, F.202, H.208, H.213, D.362
- Ligands: IND.5, FE.9
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.201
OXY.21: 7 residues within 4Å:- Chain C: N.201, F.202, H.208, H.213, D.362
- Ligands: IND.20, FE.24
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:N.201
OXY.36: 7 residues within 4Å:- Chain E: N.201, F.202, H.208, H.213, D.362
- Ligands: IND.35, FE.39
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:N.201
- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.7: 4 residues within 4Å:- Chain A: L.128, N.129, K.130, K.131
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:N.129, A:K.130, A:K.131
- Water bridges: A:K.130
- Salt bridges: A:K.130, A:K.131
SO4.12: 2 residues within 4Å:- Chain B: Q.63, Q.65
4 PLIP interactions:1 interactions with chain A, 3 interactions with chain B- Water bridges: A:R.342, B:Q.63
- Hydrogen bonds: B:Q.63, B:Q.65
SO4.13: 5 residues within 4Å:- Chain B: G.59, S.60, E.61, K.164, K.172
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:S.60
- Water bridges: B:K.164, B:K.172
- Salt bridges: B:K.164, B:K.172
SO4.14: 2 residues within 4Å:- Chain B: R.165, R.171
2 PLIP interactions:2 interactions with chain B- Salt bridges: B:R.165, B:R.171
SO4.22: 4 residues within 4Å:- Chain C: L.128, N.129, K.130, K.131
6 PLIP interactions:6 interactions with chain C- Hydrogen bonds: C:N.129, C:K.130, C:K.131
- Water bridges: C:K.130
- Salt bridges: C:K.130, C:K.131
SO4.27: 2 residues within 4Å:- Chain D: Q.63, Q.65
4 PLIP interactions:3 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: D:Q.63, D:Q.65
- Water bridges: D:Q.63, C:R.342
SO4.28: 5 residues within 4Å:- Chain D: G.59, S.60, E.61, K.164, K.172
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:S.60
- Water bridges: D:K.164, D:K.172
- Salt bridges: D:K.164, D:K.172
SO4.29: 2 residues within 4Å:- Chain D: R.165, R.171
2 PLIP interactions:2 interactions with chain D- Salt bridges: D:R.165, D:R.171
SO4.37: 4 residues within 4Å:- Chain E: L.128, N.129, K.130, K.131
6 PLIP interactions:6 interactions with chain E- Hydrogen bonds: E:N.129, E:K.130, E:K.131
- Water bridges: E:K.130
- Salt bridges: E:K.130, E:K.131
SO4.42: 2 residues within 4Å:- Chain F: Q.63, Q.65
4 PLIP interactions:3 interactions with chain F, 1 interactions with chain E- Hydrogen bonds: F:Q.63, F:Q.65
- Water bridges: F:Q.63, E:R.342
SO4.43: 5 residues within 4Å:- Chain F: G.59, S.60, E.61, K.164, K.172
5 PLIP interactions:5 interactions with chain F- Hydrogen bonds: F:S.60
- Water bridges: F:K.164, F:K.172
- Salt bridges: F:K.164, F:K.172
SO4.44: 2 residues within 4Å:- Chain F: R.165, R.171
2 PLIP interactions:2 interactions with chain F- Salt bridges: F:R.165, F:R.171
- 3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
FES.8: 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.23: 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.38: 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.9: 5 residues within 4Å:- Chain A: N.201, H.208, H.213, D.362
- Ligands: OXY.6
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:H.208, A:H.213, A:D.362, A:D.362
FE.24: 5 residues within 4Å:- Chain C: N.201, H.208, H.213, D.362
- Ligands: OXY.21
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:H.208, C:H.213, C:D.362, C:D.362
FE.39: 5 residues within 4Å:- Chain E: N.201, H.208, H.213, D.362
- Ligands: OXY.36
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
AC
AE
AB
BD
BF
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.40 Å
- Oligo State
- hetero-3-3-mer
- Ligands
- 21 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 3 x IND: INDOLE(Non-covalent)
- 3 x OXY: OXYGEN MOLECULE(Non-covalent)
- 12 x SO4: SULFATE ION(Non-functional Binders)
- 3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 3 x FE: FE (III) ION(Non-covalent)
- 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
AC
AE
AB
BD
BF
B