SMTL ID : 2o0c.3 (2 other biounits)

Crystal structure of the H-NOX domain from Nostoc sp. PCC 7120 complexed to NO

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: M.1, Y.2, V.5, W.74, T.78, Y.83, L.87, F.97, L.101, L.104, H.105, V.108, L.115, R.116, P.118, F.120, Y.134, S.136, R.138, L.141, M.144, V.145, L.148 Ligands: NO.2 33 PLIP interactions: 32 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:V.5, A:W.74, A:T.78, A:Y.83, A:Y.83, A:L.87, A:L.87, A:F.97, A:L.101, A:L.101, A:L.104, A:V.108, A:L.115, A:P.118, A:F.120, A:Y.134, A:L.141, A:V.145, A:L.148 Hydrogen bonds: A:Y.2, A:R.116, A:R.116, A:R.116, A:S.136 Water bridges: A:R.138, A:R.138 Salt bridges: A:R.138, A:R.138 pi-Stacking: A:W.74, A:W.74, A:W.74 Metal complexes: A:H.105, NO.2 HEM.3: 24 residues within 4Å: Chain B: M.1, Y.2, V.5, W.74, T.78, Y.83, L.87, F.97, L.101, L.104, H.105, V.108, L.115, R.116, P.118, F.120, Y.134, S.136, R.138, L.141, M.144, V.145, L.148 Ligands: NO.4 34 PLIP interactions: 33 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:V.5, B:W.74, B:T.78, B:Y.83, B:L.87, B:F.97, B:L.101, B:L.101, B:L.104, B:L.104, B:V.108, B:L.115, B:P.118, B:F.120, B:L.141, B:V.145, B:L.148, B:L.148 Hydrogen bonds: B:Y.2, B:R.116, B:R.116, B:R.116, B:Y.134 Water bridges: B:T.137, B:T.137, B:R.138, B:R.138 Salt bridges: B:R.138, B:R.138 pi-Stacking: B:W.74, B:W.74, B:W.74 Metal complexes: B:H.105, NO.4 HEM.5: 24 residues within 4Å: Chain C: M.1, Y.2, V.5, W.74, T.78, Y.83, L.87, F.97, L.101, L.104, H.105, V.108, L.115, R.116, P.118, F.120, Y.134, S.136, R.138, L.141, M.144, V.145, L.148 Ligands: NO.6 34 PLIP interactions: 33 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:V.5, C:W.74, C:T.78, C:Y.83, C:Y.83, C:L.87, C:L.87, C:F.97, C:L.101, C:L.101, C:L.104, C:V.108, C:L.115, C:P.118, C:F.120, C:Y.134, C:L.141, C:V.145, C:L.148 Hydrogen bonds: C:Y.2, C:R.116, C:R.116, C:R.116, C:Y.134, C:S.136 Water bridges: C:R.138, C:R.138 Salt bridges: C:R.138, C:R.138 pi-Stacking: C:W.74, C:W.74, C:W.74 Metal complexes: C:H.105, NO.6 HEM.7: 24 residues within 4Å: Chain D: M.1, Y.2, V.5, W.74, T.78, Y.83, L.87, F.97, L.101, L.104, H.105, V.108, L.115, R.116, P.118, F.120, Y.134, S.136, R.138, L.141, M.144, V.145, L.148 Ligands: NO.8 34 PLIP interactions: 33 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:V.5, D:W.74, D:T.78, D:Y.83, D:L.87, D:F.97, D:L.101, D:L.101, D:L.104, D:L.104, D:V.108, D:L.115, D:P.118, D:F.120, D:L.141, D:V.145, D:L.148, D:L.148 Hydrogen bonds: D:Y.2, D:R.116, D:R.116, D:R.116, D:Y.134 Water bridges: D:T.137, D:T.137, D:R.138, D:R.138 Salt bridges: D:R.138, D:R.138 pi-Stacking: D:W.74, D:W.74, D:W.74 Metal complexes: D:H.105, NO.8 HEM.9: 24 residues within 4Å: Chain E: M.1, Y.2, V.5, W.74, T.78, Y.83, L.87, F.97, L.101, L.104, H.105, V.108, L.115, R.116, P.118, F.120, Y.134, S.136, R.138, L.141, M.144, V.145, L.148 Ligands: NO.10 33 PLIP interactions: 32 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: E:V.5, E:W.74, E:T.78, E:Y.83, E:Y.83, E:L.87, E:L.87, E:F.97, E:L.101, E:L.101, E:L.104, E:V.108, E:L.115, E:P.118, E:F.120, E:Y.134, E:L.141, E:V.145, E:L.148 Hydrogen bonds: E:Y.2, E:R.116, E:R.116, E:R.116, E:S.136 Water bridges: E:R.138, E:R.138 Salt bridges: E:R.138, E:R.138 pi-Stacking: E:W.74, E:W.74, E:W.74 Metal complexes: E:H.105, NO.10 HEM.11: 24 residues within 4Å: Chain F: M.1, Y.2, V.5, W.74, T.78, Y.83, L.87, F.97, L.101, L.104, H.105, V.108, L.115, R.116, P.118, F.120, Y.134, S.136, R.138, L.141, M.144, V.145, L.148 Ligands: NO.12 33 PLIP interactions: 32 interactions with chain F, 1 Ligand-Ligand interactions Hydrophobic interactions: F:V.5, F:W.74, F:T.78, F:Y.83, F:L.87, F:F.97, F:L.101, F:L.101, F:L.104, F:L.104, F:V.108, F:L.115, F:P.118, F:F.120, F:L.141, F:V.145, F:L.148, F:L.148 Hydrogen bonds: F:Y.2, F:R.116, F:R.116, F:R.116 Water bridges: F:T.137, F:T.137, F:R.138, F:R.138 Salt bridges: F:R.138, F:R.138 pi-Stacking: F:W.74, F:W.74, F:W.74 Metal complexes: F:H.105, NO.12

6 x NO: NITRIC OXIDE(Non-covalent)

NO.2: 3 residues within 4Å: Chain A: W.74, H.105 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) NO.4: 3 residues within 4Å: Chain B: W.74, H.105 Ligands: HEM.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.74 NO.6: 3 residues within 4Å: Chain C: W.74, H.105 Ligands: HEM.5 No protein-ligand interaction detected (PLIP) NO.8: 3 residues within 4Å: Chain D: W.74, H.105 Ligands: HEM.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.74 NO.10: 3 residues within 4Å: Chain E: W.74, H.105 Ligands: HEM.9 No protein-ligand interaction detected (PLIP) NO.12: 3 residues within 4Å: Chain F: W.74, H.105 Ligands: HEM.11 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:W.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, X. et al., NO and CO differentially activate soluble guanylyl cyclase via a heme pivot-bend mechanism. Embo J. (2007)

Release Date

2007-01-30

Peptides

Alr2278 protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Alr2278 protein

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