SMTL ID : 1h9y.1

Cytochrome cd1 Nitrite Reductase, reduced form complexed to CN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 22 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, Y.197 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:L.81, A:L.94, A:F.97, A:I.98, A:M.106, A:P.107, A:W.109, A:L.115, A:L.127, A:Y.197 Hydrogen bonds: A:S.102 Salt bridges: A:K.79, A:K.79 pi-Stacking: A:H.69, 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, M.123, L.127 17 PLIP interactions: 17 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:F.97, B:M.106, B:P.107, B:W.109, B:M.123, B:L.127 Hydrogen bonds: B:Y.93, B:S.102 Salt bridges: B:K.79, B:K.79 Metal complexes: B:H.69

2 x DHE: HEME D(Non-covalent)

DHE.2: 22 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, L.443, F.444, Q.507, W.522, T.554, G.555, F.557 Ligands: CYN.3 34 PLIP interactions: 34 interactions with chain A, Hydrophobic interactions: A:I.201, A:R.243, A:R.243, A:A.302, A:L.443, A:F.444, A:F.444, A:T.554, A:F.557 Hydrogen bonds: A:R.174, A:I.245, A:Y.263, A:I.303, A:Q.507, A:T.554 Water bridges: A:R.203, A:R.203, A:R.203, A:R.203, A:R.216, A:R.391, A:K.446, A:K.446, A:G.555 Salt bridges: A:R.174, 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: 22 residues within 4Å: Chain B: 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 32 PLIP interactions: 32 interactions with chain B, Hydrophobic interactions: B:R.243, B:R.243, B:A.302, B:L.443, B:F.444, B:F.444, B:T.554, B:F.557 Hydrogen bonds: B:R.174, B:I.245, B:I.303, B:Q.507, B:T.554 Water bridges: B:R.203, B:R.203, B:R.216, B:R.216, B:K.446, B:K.446, B:K.446, B:G.555 Salt bridges: B:R.174, 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-Cation interactions: B:R.216 Metal complexes: B:H.200

2 x CYN: CYANIDE ION(Non-covalent)

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

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 8 residues within 4Å: Chain A: H.69, G.70, V.71, L.72, R.73, K.74, G.75, E.241 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.70, A:V.71, A:L.72, A:K.74, A:G.75 SO4.8: 1 residues within 4Å: Chain B: K.79 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.79, B:K.79, B:K.79 SO4.9: 1 residues within 4Å: Chain B: P.103 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sjogren, T. et al., The Structure of an Alternative Form of Paracoccus Pantotrophus Cytochrome Cd1 Nitrite Reductase. J.Biol.Chem. (2001)

Release Date

2001-08-09

Peptides

CYTOCHROME CD1 NITRITE REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CYTOCHROME CD1 NITRITE REDUCTASE

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