SMTL ID : 1aoq.1

CYTOCHROME CD1 NITRITE REDUCTASE WITH SUBSTRATE AND PRODUCT BOUND

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 19 residues within 4Å: Chain A: H.17, N.23, E.26, R.64, C.65, C.68, H.69, G.78, K.79, L.81, L.89, Y.93, L.94, F.97, S.102, P.103, L.115, M.123, L.127 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:N.23, A:E.26, A:L.81, A:L.94, A:F.97, A:F.97, A:P.103, A:L.115, A:L.127 Hydrogen bonds: A:K.79, A:Y.93 Salt bridges: A:K.79 Metal complexes: A:H.17, A:H.69 HEM.4: 18 residues within 4Å: Chain B: D.16, H.17, N.23, E.26, R.64, C.65, C.68, H.69, G.78, K.79, L.81, L.89, Y.93, L.94, F.97, I.98, S.102, P.103 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:D.16, B:N.23, B:E.26, B:L.81, B:L.81, B:L.94, B:F.97, B:I.98, B:P.103 Hydrogen bonds: B:K.79, B:Y.93 Salt bridges: B:K.79 Metal complexes: B:H.17, B:H.69

2 x DHE: HEME D(Non-covalent)

DHE.2: 27 residues within 4Å: Chain A: Y.25, E.26, P.27, S.28, M.106, W.109, R.174, H.200, I.201, R.203, R.216, R.243, S.244, I.245, Y.263, A.301, A.302, I.303, H.345, R.391, F.444, Q.507, W.522, T.554, G.555, F.557 Ligands: 2NO.3 34 PLIP interactions: 34 interactions with chain A, Hydrophobic interactions: A:I.201, A:R.243, A:R.243, A:F.444, A:F.444, A:W.522, A:W.522, A:T.554, A:F.557 Hydrogen bonds: A:S.28, A:I.245, A:Y.263, A:I.303, A:Q.507 Water bridges: A:R.174, A:R.174, A:R.203, A:R.203, A:R.203, A:R.203, A:K.446, A:K.446, A:K.446, A:G.555 Salt bridges: A:R.174, A:H.200, A:H.200, A:R.203, A:R.203, A:R.216, A:R.243, A:R.391, A:K.446 Metal complexes: A:H.200 DHE.5: 27 residues within 4Å: Chain B: Y.25, E.26, P.27, S.28, M.106, W.109, R.174, H.200, I.201, R.203, R.216, R.243, S.244, I.245, Y.263, A.301, A.302, I.303, H.345, R.391, F.444, Q.507, W.522, T.554, G.555, F.557 Ligands: NO.6 34 PLIP interactions: 34 interactions with chain B, Hydrophobic interactions: B:W.109, B:R.243, B:R.243, B:F.444, B:F.444, B:W.522, B:T.554, B:F.557 Hydrogen bonds: B:S.28, B:R.243, B:I.245, B:I.303, B:Q.507, B:T.554 Water bridges: B:R.174, B:R.203, B:R.203, B:R.203, B:R.203, B:K.446, B:K.446, B:K.446, B:G.555 Salt bridges: B:R.174, B:H.200, B:H.200, B:R.203, B:R.203, B:R.216, B:R.243, B:R.391, B:K.446 pi-Cation interactions: B:H.345 Metal complexes: B:H.200

1 x 2NO: NITROGEN DIOXIDE(Non-covalent)

2NO.3: 4 residues within 4Å: Chain A: H.200, H.345, H.388 Ligands: DHE.2 No protein-ligand interaction detected (PLIP)

1 x NO: NITRIC OXIDE(Non-covalent)

NO.6: 3 residues within 4Å: Chain B: H.345, H.388 Ligands: DHE.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.388 Water bridges: B:Y.25, B:H.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, P.A. et al., Haem-ligand switching during catalysis in crystals of a nitrogen-cycle enzyme. Nature (1997)

Release Date

1998-02-04

Peptides

NITRITE REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NITRITE REDUCTASE

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