SMTL ID : 1h9x.1

Cytochrome cd1 Nitrite Reductase, reduced form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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.127, Y.197, A.198 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:K.79, A:L.81, A:L.94, A:F.97, A:I.98, A:I.98, A:M.106, A:W.109, 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.3: 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.127, Y.197 21 PLIP interactions: 21 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:I.98, B:I.98, B:M.106, B:W.109, B:W.109, B:L.127, B:Y.197 Hydrogen bonds: B:Y.93, B:S.102 Water bridges: B:A.104 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: 22 residues within 4Å: Chain A: T.77, 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 38 PLIP interactions: 38 interactions with chain A, Hydrophobic interactions: A:I.201, A:I.201, A:R.243, A:R.243, A:L.443, A:F.444, A:F.444, A:W.522, A:T.554, A:F.557 Hydrogen bonds: A:R.174, A:I.245, A:Y.263, 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.216, A:R.243, A:K.446, A:K.446, A:K.446, A:G.555 Salt bridges: A:R.174, A:R.203, A:R.203, A:R.216, A:R.216, A:R.243, A:R.391, A:K.446 pi-Cation interactions: A:H.200 Metal complexes: A:H.200 DHE.4: 21 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 33 PLIP interactions: 33 interactions with chain B, Hydrophobic interactions: B:I.201, B:I.201, B:R.243, B:R.243, B:L.443, B:F.444, B:F.444, B:F.557, B:F.557 Hydrogen bonds: B:T.77, B:I.245, B:Y.263, B:I.303, B:Q.507, B:T.554 Water bridges: B:R.174, 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:R.203, B:R.203, B:R.216, B:R.216, B:R.243, B:R.391, B:K.446 Metal complexes: B:H.200

1 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.5: 7 residues within 4Å: Chain B: N.108, S.112, E.114, A.176, G.177, D.194, Y.197 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.197 Hydrogen bonds: B:N.108, B:N.108, B:Y.197 Water bridges: B:N.108

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

SO4.6: 1 residues within 4Å: Chain B: K.79 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.79 SO4.7: 6 residues within 4Å: Chain B: G.70, V.71, L.72, R.73, K.74, E.241 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.71, B:L.72, B:K.74, B:E.241 Salt bridges: B:K.74 SO4.8: 5 residues within 4Å: Chain B: G.423, H.424, P.425, D.426, N.427 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.424, B:D.426, B:N.427

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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