SMTL ID : 7dvo.2 (1 other biounit)

Structure of Reaction Intermediate of Cytochrome P450 NO Reductase (P450nor) Determined by XFEL

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

HEM.1: 28 residues within 4Å: Chain A: F.86, V.87, H.94, R.98, I.153, L.236, A.239, G.240, T.243, M.244, M.247, S.286, A.289, I.290, N.315, G.344, F.345, G.346, F.347, H.350, R.351, C.352, I.353, A.354, A.358, L.362 Ligands: NO.2, GOL.3 25 PLIP interactions: 24 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:F.86, A:F.86, A:V.87, A:I.153, A:T.243, A:A.289, A:F.345, A:F.345, A:I.353, A:A.354, A:A.358, A:L.362 Hydrogen bonds: A:F.347 Water bridges: A:K.62, A:R.292, A:R.292, A:R.292, A:H.350 Salt bridges: A:K.62, A:K.62, A:H.94, A:R.98, A:H.350 Metal complexes: A:C.352, H2O.4

1 x NO: NITRIC OXIDE(Non-covalent)

NO.2: 5 residues within 4Å: Chain A: A.239, G.240, T.243 Ligands: HEM.1, GOL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.243, A:T.243 Water bridges: A:A.239

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: V.87, A.239, S.286, A.289 Ligands: HEM.1, NO.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.286, A:S.286 Water bridges: A:A.289 GOL.4: 10 residues within 4Å: Chain A: A.55, T.56, S.57, K.62, M.89, D.90, P.91, R.292, D.349, H.350 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.55, A:D.90, A:R.292, A:D.349, A:H.350 Water bridges: A:D.349, A:H.350 GOL.5: 5 residues within 4Å: Chain A: Q.127, K.142, E.143, P.147, Y.151 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.143 Water bridges: A:Q.127, A:E.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nomura, T. et al., Short-lived intermediate in N 2 O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-05-19

Peptides

NADP nitrous oxide-forming nitric oxide reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

NADP nitrous oxide-forming nitric oxide reductase

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