SMTL ID : 1dy7.1

Cytochrome cd1 Nitrite Reductase, CO complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x DHE: HEME D(Non-covalent)

DHE.1: 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: CMO.2 32 PLIP interactions: 32 interactions with chain A, Hydrophobic interactions: A:I.201, A:R.243, A:R.243, A:F.444, A:F.444, 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.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 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: 20 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, F.444, Q.507, W.522, G.555, F.557 Ligands: CMO.7 33 PLIP interactions: 32 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:I.201, B:R.243, B:R.243, B:A.302, B:F.444, B:F.444, B:W.522, B:F.557 Hydrogen bonds: B:I.245, B:I.303, B:Q.507 Water bridges: B:R.174, B:R.174, B:R.203, B:R.203, B:R.203, B:R.203, B:R.216, B:K.446, B:K.446, B:K.446 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 Metal complexes: B:H.200, CMO.7

2 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.2: 4 residues within 4Å: Chain A: H.200, H.388, F.444 Ligands: DHE.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.390 CMO.7: 3 residues within 4Å: Chain B: H.388, F.444 Ligands: DHE.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.388 Water bridges: B:D.346

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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: 6 residues within 4Å: Chain B: K.488, T.489, L.490, P.491, W.495, L.539 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.489, B:T.489 GOL.9: 4 residues within 4Å: Chain B: R.174, D.175, Y.197, R.216 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.174, B:R.174, B:D.175, B:Y.197, B:R.216, B:R.216

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

SO4.4: 3 residues within 4Å: Chain A: Y.308, R.354, K.372 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.354, A:K.372 SO4.10: 3 residues within 4Å: Chain B: Y.308, R.354, K.372 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.308 Water bridges: B:R.354, B:R.354, B:R.354, B:R.354, B:K.372, B:K.372 Salt bridges: B:R.354, B:K.372 SO4.11: 4 residues within 4Å: Chain B: G.439, G.440, N.461, E.463 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.440, B:N.461 Water bridges: B:D.412

1 x HEC: HEME C(Covalent)

HEC.5: 22 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, M.123, L.127 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:K.79, 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:L.115, B:M.123, B:L.127 Hydrogen bonds: B:S.102, B:M.106 Salt bridges: B:K.79 pi-Stacking: B:H.69 Metal complexes: B:H.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sjogren, T. et al., Proton-Coupled Structural Changes Upon Binding of Carbon Monoxide to Cytochrome Cd(1): A Combined Flash Photolysis and X-Ray Crystallography Study. Biochemistry (2000)

Release Date

2000-09-24

Peptides

NITRITE REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NITRITE REDUCTASE

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