SMTL ID : 1qks.1

CYTOCHROME CD1 NITRITE REDUCTASE, OXIDISED FORM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 18 residues within 4Å: Chain A: D.16, H.17, N.23, 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.127 Ligands: GOL.3 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:D.16, A:N.23, A:L.81, A:L.81, A:L.94, A:F.97, A:P.103, A:L.127 Hydrogen bonds: A:K.79 Water bridges: A:K.79, A:K.79 Salt bridges: A:K.79 Metal complexes: A:H.17, A:H.69 HEC.9: 19 residues within 4Å: Chain B: D.16, H.17, N.23, 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, M.123 Ligands: GOL.11 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:D.16, B:N.23, B:L.81, B:L.81, B:L.94, B:F.97, B:I.98, B:P.103, B:P.103 Hydrogen bonds: B:K.79, B:Y.93 Water bridges: B:K.79, B:K.79, B:K.79, B:K.79, B:A.80 Salt bridges: B:K.79 Metal complexes: B:H.17, B:H.69

2 x DHE: HEME D(Covalent)

DHE.2: 26 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 38 PLIP interactions: 38 interactions with chain A, Hydrophobic interactions: A:Y.25, A:Y.25, A:W.109, A:I.201, A:I.201, A:R.243, A:R.243, A:F.444, A:F.444, A:W.522, A:T.554, A:F.557 Hydrogen bonds: A:S.28, A:I.245, A:Y.263, 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 Metal complexes: A:Y.25, A:H.200 DHE.10: 26 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 38 PLIP interactions: 38 interactions with chain B, Hydrophobic interactions: B:Y.25, B:Y.25, B:W.109, B:I.201, B:I.201, 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:Y.263, B:I.303, B:Q.507, B:T.554 Water bridges: 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 Metal complexes: B:Y.25, B:H.200

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 12 residues within 4Å: Chain A: N.23, R.24, Y.25, E.26, P.27, E.63, R.64, P.103, A.104, G.105, T.111 Ligands: HEC.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.23, A:E.26 Water bridges: A:S.28, A:E.63, A:G.67, A:M.106 GOL.4: 6 residues within 4Å: Chain A: V.396, H.397, P.398, T.399, G.401, H.424 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.397 Water bridges: A:T.399 GOL.5: 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.6: 2 residues within 4Å: Chain A: P.135, E.136 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:K.74, B:K.74, B:K.74 Hydrogen bonds: A:E.136 GOL.11: 11 residues within 4Å: Chain B: N.23, R.24, Y.25, E.26, P.27, E.63, R.64, A.104, G.105, T.111 Ligands: HEC.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.23, B:E.26 Water bridges: B:S.28, B:S.28, B:M.106 GOL.12: 6 residues within 4Å: Chain B: K.488, T.489, L.490, P.491, W.495, L.539 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.539 Water bridges: B:K.488, B:K.488, B:T.489, B:T.489, B:W.495 GOL.13: 7 residues within 4Å: Chain B: E.465, G.468, S.469, P.491, I.492, A.493, E.494 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.465, B:E.465, B:E.465, B:G.468, B:A.493, B:E.494 Water bridges: B:S.469

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

SO4.7: 6 residues within 4Å: Chain A: Y.289, D.290, E.291, Q.292 Chain B: M.139, R.143 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.143, A:Q.292 Water bridges: B:K.279 SO4.8: 4 residues within 4Å: Chain A: N.31, Q.35, K.237, S.240 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.31, A:Q.35, A:S.240 Water bridges: A:S.240, A:S.240 Salt bridges: A:K.237 SO4.14: 7 residues within 4Å: Chain A: M.139, R.143, K.279 Chain B: Y.289, D.290, E.291, Q.292 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.143 Hydrogen bonds: B:Y.289, B:Q.292 SO4.15: 4 residues within 4Å: Chain B: N.31, Q.35, K.237, S.240 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.31, B:Q.35, B:S.240 Water bridges: B:Q.34, B:Q.35, B:S.240, B:S.240 Salt bridges: B:K.237 SO4.16: 3 residues within 4Å: Chain B: F.395, V.396, P.449 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.396 SO4.17: 4 residues within 4Å: Chain B: G.439, G.440, N.461, I.466 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.440, B:N.461 Water bridges: B:D.412, B:D.412

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fulop, V. et al., The anatomy of a bifunctional enzyme: structural basis for reduction of oxygen to water and synthesis of nitric oxide by cytochrome cd1. Cell(Cambridge,Mass.) (1995)

Release Date

1999-08-18

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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