SMTL ID : 4uqr.1

Structure of Bacillus subtilis Nitric Oxide Synthase in complex with N-omega-Nitro-L-Arginine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: W.60, S.63, R.65, C.66, I.67, G.68, L.75, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: H4B.2, NRG.3 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:W.60, A:W.60, A:W.60, A:I.67, A:L.75, A:F.235, A:F.235, A:F.235, A:F.235, A:W.238, A:W.238, A:E.243, A:V.300, A:W.329, A:W.329, A:Y.355, A:Y.355 Water bridges: A:Y.357 Salt bridges: A:R.65 pi-Stacking: A:W.60 Metal complexes: A:C.66 HEM.12: 19 residues within 4Å: Chain B: W.60, S.63, R.65, C.66, I.67, G.68, L.75, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: H4B.13, NRG.14 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:W.60, B:W.60, B:W.60, B:I.67, B:L.75, B:F.235, B:F.235, B:F.235, B:F.235, B:W.238, B:W.238, B:E.243, B:V.300, B:W.329, B:W.329, B:Y.355, B:Y.355 Water bridges: B:Y.357 Salt bridges: B:R.65 pi-Stacking: B:W.60 Metal complexes: B:C.66

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

H4B.2: 9 residues within 4Å: Chain A: R.247, T.328, W.329 Chain B: W.327, F.342, H.343, R.344 Ligands: HEM.1, PEG.8 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:W.327, A:R.247, A:R.247, A:T.328, A:W.329 pi-Stacking: A:W.329, A:W.329 pi-Cation interactions: A:W.329, A:W.329 H4B.13: 9 residues within 4Å: Chain A: W.327, F.342, H.343, R.344 Chain B: R.247, T.328, W.329 Ligands: HEM.12, PEG.19 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.247, B:R.247, B:T.328, B:W.329, A:W.327 pi-Stacking: B:W.329, B:W.329 pi-Cation interactions: B:W.329, B:W.329

2 x NRG: N-OMEGA-NITRO-L-ARGININE(Non-covalent)

NRG.3: 13 residues within 4Å: Chain A: Q.129, R.132, Y.213, P.216, I.218, F.235, N.236, G.237, W.238, Y.239, E.243, N.248 Ligands: HEM.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.129, A:Q.129, A:Y.213, A:Y.239, A:E.243, A:N.248 Water bridges: A:R.132, A:R.254 Salt bridges: A:R.132, A:E.243 NRG.14: 13 residues within 4Å: Chain B: Q.129, R.132, Y.213, P.216, I.218, F.235, N.236, G.237, W.238, Y.239, E.243, N.248 Ligands: HEM.12 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.129, B:Q.129, B:Y.213, B:Y.239, B:E.243, B:N.248 Water bridges: B:R.132, B:R.254 Salt bridges: B:R.132, B:E.243

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: E.156, G.159, W.160, R.161 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.156, A:G.159 GOL.5: 3 residues within 4Å: Chain A: V.183, W.184, Y.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.184 Water bridges: A:E.186 GOL.6: 3 residues within 4Å: Chain A: C.149, S.150, A.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.149 Water bridges: A:S.150 GOL.7: 5 residues within 4Å: Chain A: K.310, E.313, H.340, H.343, R.344 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.340 Water bridges: A:H.343 GOL.11: 8 residues within 4Å: Chain A: D.251, E.252, K.253 Chain B: A.338, T.339, H.340, H.343 Ligands: PEG.8 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.252, A:K.253, B:H.343 Water bridges: A:D.251, B:A.337 GOL.15: 4 residues within 4Å: Chain B: E.156, G.159, W.160, R.161 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.156, B:G.159 GOL.16: 3 residues within 4Å: Chain B: V.183, W.184, Y.185 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.184 Water bridges: B:E.186 GOL.17: 3 residues within 4Å: Chain B: C.149, S.150, A.153 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.149 Water bridges: B:S.150 GOL.18: 5 residues within 4Å: Chain B: K.310, E.313, H.340, H.343, R.344 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.340 Water bridges: B:H.343 GOL.22: 8 residues within 4Å: Chain A: A.338, T.339, H.340, H.343 Chain B: D.251, E.252, K.253 Ligands: PEG.19 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.252, B:K.253, A:H.343 Water bridges: B:D.251, A:A.337

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 6 residues within 4Å: Chain A: R.247, D.251, K.253 Chain B: H.343 Ligands: H4B.2, GOL.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.247, A:R.247 PEG.9: 2 residues within 4Å: Chain A: N.73, S.74 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.73 PEG.19: 6 residues within 4Å: Chain A: H.343 Chain B: R.247, D.251, K.253 Ligands: H4B.13, GOL.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.247, B:R.247 PEG.20: 2 residues within 4Å: Chain B: N.73, S.74 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.73

2 x POL: N-PROPANOL(Non-covalent)

POL.10: 6 residues within 4Å: Chain A: R.142, G.144, D.166, R.254, Y.255, K.257 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.255 Hydrogen bonds: A:R.142 Water bridges: A:R.254 POL.21: 6 residues within 4Å: Chain B: R.142, G.144, D.166, R.254, Y.255, K.257 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.255 Hydrogen bonds: B:R.142 Water bridges: B:R.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holden, J.K. et al., Identification of Redox Partners and Development of a Novel Chimeric Bacterial Nitric Oxide Synthase for Structure Activity Analyses. J.Biol.Chem. (2014)

Release Date

2014-09-17

Peptides

NITRIC OXIDE SYNTHASE OXYGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NITRIC OXIDE SYNTHASE OXYGENASE

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