SMTL ID : 1hj5.1

Cytochrome cd1 Nitrite Reductase, reoxidised enzyme

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 20 residues within 4Å: Chain A: D.16, H.17, N.23, 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, P.103, L.127 Ligands: GOL.3 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:D.16, A:N.23, A:K.79, A:L.81, A:L.89, A:L.94, A:F.97, A:I.98, A:L.127 Hydrogen bonds: A:K.79 Salt bridges: A:K.79 Metal complexes: A:H.17, A:H.69 HEC.8: 18 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 Ligands: GOL.10 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:D.16, B:N.23, B:K.79, B:L.81, B:L.89, B:L.94, B:F.97, B:F.97, B:I.98, B:P.103 Hydrogen bonds: B:K.79 Salt bridges: B:K.79 pi-Cation interactions: B:H.69 Metal complexes: B:H.17, B:H.69

2 x DHE: HEME D(Covalent)(Non-covalent)

DHE.2: 26 residues within 4Å: Chain A: Y.25, P.27, S.28, M.106, W.109, R.174, V.199, 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 39 PLIP interactions: 39 interactions with chain A, Hydrophobic interactions: A:Y.25, A:Y.25, 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.174, A:R.203, A:R.203, A:R.203, A:R.203, A:R.216, 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:Y.25, A:H.200 DHE.9: 25 residues within 4Å: Chain B: Y.25, 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 37 PLIP interactions: 37 interactions with chain B, Hydrophobic interactions: B:Y.25, B:Y.25, 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:I.245, B:Y.263, B:I.303, B:Q.507, B:T.554 Water bridges: B:R.174, 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 Metal complexes: B:Y.25, B:H.200

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 13 residues within 4Å: Chain A: N.23, R.24, Y.25, E.26, P.27, S.28, E.63, R.64, P.103, A.104, G.105, T.111 Ligands: HEC.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.23, A:E.26 Water bridges: A:S.28, A:E.63 GOL.4: 6 residues within 4Å: Chain A: V.396, H.397, P.398, T.399, G.401, H.424 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.399 GOL.5: 5 residues within 4Å: Chain A: F.395, V.396, P.449, S.451, I.475 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.396, A:P.449 Water bridges: A:S.451 GOL.10: 12 residues within 4Å: Chain B: N.23, R.24, E.26, P.27, S.28, E.63, R.64, P.103, A.104, G.105, T.111 Ligands: HEC.8 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:L.29

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

SO4.6: 6 residues within 4Å: Chain A: Y.289, D.290, E.291, Q.292 Chain B: M.139, R.143 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.292, B:R.143 SO4.7: 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 SO4.11: 4 residues within 4Å: Chain B: N.31, Q.35, K.237, S.240 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.31, B:Q.35, B:S.240 Water bridges: B:N.31, B:Q.35, B:S.240 Salt bridges: B:K.237 SO4.12: 3 residues within 4Å: Chain B: Y.308, R.354, K.372 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.308 Water bridges: B:S.352, B:S.352, B:R.354, B:R.354, B:R.354 Salt bridges: B:R.354, B:K.372 SO4.13: 4 residues within 4Å: Chain B: G.439, G.440, N.461, I.466 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.440, B:N.461 Water bridges: B:D.412

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sjogren, T. et al., Structure of the bound dioxygen species in the cytochrome oxidase reaction of cytochrome cd1 nitrite reductase. J. Biol. Chem. (2001)

Release Date

2001-01-16

Peptides

Nitrite reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitrite reductase

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