SMTL ID : 1n2n.1 (1 other biounit)

Crystal structure of cyanide complex of the oxygenase domain of inducible nitric oxide synthase.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x CYN: CYANIDE ION(Non-covalent)

CYN.1: 3 residues within 4Å: Chain A: F.287 Ligands: HEM.3, ARG.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Water bridges: A:G.289 Hydrogen bonds: R.5 CYN.6: 3 residues within 4Å: Chain B: F.287 Ligands: HEM.8, ARG.10 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain B Hydrogen bonds: R.10 Water bridges: B:G.289

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.28, C.33 Chain B: C.28, C.33 Ligands: ZN.7 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:C.28, A:C.33, B:C.28, B:C.33 ZN.7: 5 residues within 4Å: Chain A: C.28, C.33 Chain B: C.28, C.33 Ligands: ZN.2 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:C.28, A:C.33, B:C.28, B:C.33

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.3: 21 residues within 4Å: Chain A: W.112, R.117, C.118, I.119, G.120, Q.123, L.127, S.160, M.273, F.287, N.288, G.289, W.290, E.295, M.352, W.381, Y.407, Y.409 Ligands: CYN.1, H4B.4, ARG.5 22 PLIP interactions: 19 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:W.112, A:W.112, A:W.112, A:Q.123, A:L.127, A:L.127, A:F.287, A:F.287, A:F.287, A:W.290, A:W.290, A:Y.407, A:Y.407, R.5 Water bridges: A:R.117, A:R.117, A:R.299, A:R.299 pi-Stacking: A:W.112 Metal complexes: A:C.118 Hydrogen bonds: R.5 pi-Cation interactions: R.5 HEM.8: 21 residues within 4Å: Chain B: W.112, R.117, C.118, I.119, G.120, Q.123, L.127, S.160, M.273, F.287, N.288, G.289, W.290, E.295, M.352, W.381, Y.407, Y.409 Ligands: CYN.6, H4B.9, ARG.10 23 PLIP interactions: 20 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:W.112, B:W.112, B:W.112, B:Q.123, B:L.127, B:L.127, B:F.287, B:F.287, B:F.287, B:W.290, B:W.290, B:Y.407, B:Y.407, R.10 Hydrogen bonds: B:Y.409, R.10 Water bridges: B:R.117, B:R.117, B:R.299, B:R.299 pi-Stacking: B:W.112 Metal complexes: B:C.118 pi-Cation interactions: R.10

2 x H4B: 5,6,7,8-TETRAHYDROBIOPTERIN(Non-covalent)

H4B.4: 11 residues within 4Å: Chain A: S.36, M.38, R.299, I.380, W.381 Chain B: W.379, F.394, H.395, Q.396, E.397 Ligands: HEM.3 13 PLIP interactions: 10 interactions with chain A, 2 Ligand-Ligand interactions, 1 interactions with chain B Hydrogen bonds: A:R.299, A:R.299, A:I.380, A:W.381 Water bridges: A:S.36, A:W.381, R.5, R.5 pi-Stacking: A:W.381, A:W.381 pi-Cation interactions: A:W.381, A:W.381 Hydrophobic interactions: B:E.397 H4B.9: 11 residues within 4Å: Chain A: W.379, F.394, H.395, Q.396, E.397 Chain B: S.36, M.38, R.299, I.380, W.381 Ligands: HEM.8 14 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: B:R.299, B:R.299, B:I.380, B:W.381 Water bridges: B:S.36, B:W.381, A:H.395, R.10, R.10 pi-Stacking: B:W.381, B:W.381 pi-Cation interactions: B:W.381, B:W.381 Hydrophobic interactions: A:E.397

2 x ARG: ARGININE(Non-covalent)

ARG.5: 8 residues within 4Å: Chain A: Q.181, P.268, W.290, Y.291, E.295, D.300 Ligands: CYN.1, HEM.3 10 PLIP interactions: 9 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.291 Hydrogen bonds: A:G.289, A:W.290, A:W.290, A:Y.291, A:E.295 Water bridges: A:Y.265, A:E.295, R.5 Salt bridges: A:E.295 ARG.10: 8 residues within 4Å: Chain B: Q.181, P.268, W.290, Y.291, E.295, D.300 Ligands: CYN.6, HEM.8 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.291 Hydrogen bonds: B:G.289, B:W.290, B:W.290 Water bridges: B:E.295, B:R.306, R.10 Salt bridges: B:E.295

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Fedorov, R. et al., Crystal structures of cyanide complexes of P450cam and the oxygenase domain of inducible nitric oxide synthase-structural models of the short-lived oxygen complexes. Arch.Biochem.Biophys. (2003)

Release Date

2003-02-11

Peptides

Inducible Nitric Oxide Synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Inducible Nitric Oxide Synthase

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