SMTL ID : 1e2r.1

CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED AND CYANIDE BOUND

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 21 residues within 4Å: Chain A: R.64, C.65, C.68, H.69, T.77, G.78, K.79, L.81, L.89, Y.93, L.94, F.97, I.98, S.102, A.104, G.105, M.106, P.107, W.109, L.115, L.127 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:L.81, A:L.81, A:L.94, A:F.97, A:F.97, A:F.97, A:I.98, A:A.104, A:M.106, A:P.107, A:W.109, A:L.115 Hydrogen bonds: A:Y.93, A:S.102, A:S.102, A:A.104 Salt bridges: A:K.79, A:K.79 pi-Cation interactions: A:H.69 Metal complexes: A:H.69 HEC.5: 21 residues within 4Å: Chain B: R.64, C.65, C.68, H.69, T.77, G.78, K.79, L.81, L.89, Y.93, L.94, F.97, I.98, S.102, A.104, G.105, M.106, P.107, W.109, L.115, L.127 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:L.81, B:L.81, B:L.94, B:F.97, B:F.97, B:F.97, B:I.98, B:I.98, B:A.104, B:M.106, B:W.109, B:L.115, B:L.127 Hydrogen bonds: B:S.102, B:S.102 Salt bridges: B:K.79, B:K.79 pi-Stacking: B:H.69 Metal complexes: B:H.69

2 x DHE: HEME D(Non-covalent)

DHE.2: 20 residues within 4Å: Chain A: 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, G.555, F.557 Ligands: CYN.3 38 PLIP interactions: 38 interactions with chain A, Hydrophobic interactions: A:I.201, A:R.243, A:R.243, A:A.301, A:A.302, A:F.444, A:F.444, A:W.522, A:W.522, A:F.557 Hydrogen bonds: A:I.245, A:Y.263, A:I.303, A:Q.507 Water bridges: A:R.174, A:R.203, A:R.203, A:R.203, A:R.203, A:R.216, A:R.216, A:R.216, A:R.299, A:R.299, A:K.446, A:K.446, A:K.446 Salt bridges: A:R.174, A:H.200, A:H.200, A:R.203, A:R.203, A:R.216, A:R.216, A:R.243, A:R.391, A:K.446 Metal complexes: A:H.200 DHE.6: 27 residues within 4Å: Chain B: Y.25, E.26, P.27, S.28, 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, L.443, F.444, Q.507, W.522, T.554, G.555, F.557 Ligands: CYN.7, GOL.8 38 PLIP interactions: 38 interactions with chain B, Hydrophobic interactions: B:Y.25, B:Y.25, B:I.201, B:R.243, B:R.243, B:L.443, B:F.444, B:F.444, B:W.522, B:W.522, B:T.554, B:F.557 Hydrogen bonds: B:S.28, B:I.245, B:I.303, B:Q.507, B:T.554 Water bridges: B:R.203, B:R.203, B:R.203, B:R.203, B:R.216, 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.216, B:R.243, B:R.391, B:K.446 pi-Stacking: B:H.345 Metal complexes: B:H.200

2 x CYN: CYANIDE ION(Non-covalent)

CYN.3: 4 residues within 4Å: Chain A: H.200, H.345, H.388 Ligands: DHE.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.388 CYN.7: 5 residues within 4Å: Chain B: Y.25, H.200, H.345, H.388 Ligands: DHE.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.25 Water bridges: B:D.346

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: F.395, V.396, P.449, S.451, I.475 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.396, A:P.449 GOL.8: 7 residues within 4Å: Chain B: Y.25, K.317, H.345, N.361, H.388, M.409 Ligands: DHE.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.361, B:N.361

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jafferji, A. et al., X-Ray Crystallographic Study of Cyanide Binding Provides Insights Into the Structure-Function Relationship for Cytochrome Cd1 Nitrite Reductase from Paracoccus Pantotrophus. J.Biol.Chem. (2000)

Release Date

2000-05-30

Peptides

NITRITE REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NITRITE REDUCTASE