SMTL ID : 6p73.1

Cytochrome-C-nitrite reductase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

10 x HEC: HEME C(Covalent)(Non-covalent)

HEC.1: 24 residues within 4Å: Chain A: Y.54, K.55, P.57, D.66, V.67, T.70, R.72, T.73, L.84, A.87, C.88, C.91, K.92, C.171, H.172, V.173, Y.175, F.177, V.187, F.189, H.226, A.348, H.350 Ligands: HEC.3 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:P.57, A:V.67, A:T.70, A:T.73, A:L.84, A:V.173, A:Y.175, A:Y.175, A:Y.175, A:F.177, A:F.177, A:V.187, A:F.189, A:H.226 Hydrogen bonds: A:K.55, A:A.348 Water bridges: A:R.72 Salt bridges: A:R.72, A:H.226, A:H.350 pi-Stacking: A:H.226 Metal complexes: H2O.13 HEC.2: 19 residues within 4Å: Chain A: F.15, Q.18, Y.19, W.22, G.125, C.126, C.129, H.130, P.135, L.137, K.160, E.164, V.245, M.249, K.251, F.260, T.261, H.263 Ligands: HEC.3 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:F.15, A:F.15, A:Q.18, A:Q.18, A:Y.19, A:W.22, A:P.135, A:L.137, A:V.245, A:T.261 Hydrogen bonds: A:Q.18, A:E.164, A:T.261 Water bridges: A:T.261, A:T.261 Salt bridges: A:K.160, A:K.251, A:K.251 Metal complexes: A:H.130, A:H.263 HEC.3: 24 residues within 4Å: Chain A: S.28, P.57, R.58, G.59, H.60, Y.62, A.63, D.66, C.91, K.92, I.124, D.128, R.141, V.167, C.168, C.171, H.172, H.248, M.249, V.265, G.266 Ligands: HEC.1, HEC.2, HEC.4 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:P.57, A:K.92, A:I.124, A:I.124, A:H.248, A:V.265 Hydrogen bonds: A:S.28, A:R.58, A:Y.62, A:D.66 Water bridges: A:S.28, A:K.264, A:K.264, A:V.265 Metal complexes: A:H.60, A:H.172 HEC.4: 22 residues within 4Å: Chain A: P.57, C.168, H.172, E.228, Y.229, W.232, H.237, V.242, S.243, C.244, C.247, H.248, N.267, P.268, F.269, K.295, H.350, G.351, A.354, H.355 Ligands: HEC.3, HEC.5 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:H.172, A:E.228, A:E.228, A:W.232, A:H.237, A:F.269, A:H.350, A:A.354 Hydrogen bonds: A:N.267, A:N.267 Water bridges: A:S.28 Salt bridges: A:K.295 Metal complexes: A:H.248, A:H.355 HEC.5: 18 residues within 4Å: Chain A: I.236, H.237, N.240, V.242, D.246, P.268, F.269, T.275, C.276, T.278, C.279, H.280, R.294 Chain B: I.236, H.280, Q.282 Ligands: HEC.4, HEC.11 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:I.236, A:I.236, A:P.268, A:F.269, B:I.236 Water bridges: A:N.240 Salt bridges: A:R.294, B:H.280 Metal complexes: A:H.237, A:H.280 Hydrogen bonds: B:Q.282 HEC.7: 22 residues within 4Å: Chain B: Y.54, K.55, P.57, D.66, V.67, T.70, R.72, T.73, L.84, C.88, C.91, K.92, C.171, H.172, V.173, Y.175, F.177, V.187, F.189, H.226, H.350 Ligands: HEC.9 21 PLIP interactions: 20 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:P.57, B:V.67, B:T.70, B:T.73, B:L.84, B:V.173, B:Y.175, B:Y.175, B:Y.175, B:F.177, B:V.187, B:F.189, B:H.226 Hydrogen bonds: B:K.55, B:A.348 Water bridges: B:R.72 Salt bridges: B:R.72, B:H.226, B:H.350 pi-Stacking: B:H.226 Metal complexes: H2O.34 HEC.8: 18 residues within 4Å: Chain B: F.15, Q.18, Y.19, W.22, G.125, C.126, C.129, H.130, P.135, L.137, K.160, V.245, M.249, K.251, F.260, T.261, H.263 Ligands: HEC.9 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:F.15, B:F.15, B:Q.18, B:Q.18, B:Y.19, B:W.22, B:P.135, B:L.137, B:V.245 Hydrogen bonds: B:Q.18, B:T.261 Water bridges: B:E.164 Salt bridges: B:K.160, B:K.251, B:K.251 Metal complexes: B:H.130, B:H.263 HEC.9: 25 residues within 4Å: Chain B: S.28, P.57, R.58, G.59, H.60, Y.62, A.63, D.66, C.91, K.92, I.124, D.128, R.141, V.167, C.168, C.171, H.172, C.244, H.248, M.249, V.265, G.266 Ligands: HEC.7, HEC.8, HEC.10 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:P.57, B:K.92, B:I.124, B:H.248 Hydrogen bonds: B:S.28, B:R.58, B:Y.62, B:D.66, B:V.265 Water bridges: B:K.264, B:K.264, B:K.264 Metal complexes: B:H.60, B:H.172 HEC.10: 21 residues within 4Å: Chain B: P.57, H.172, E.228, Y.229, W.232, H.237, V.242, S.243, C.244, C.247, H.248, N.267, P.268, F.269, K.295, H.350, G.351, A.354, H.355 Ligands: HEC.9, HEC.11 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:H.172, B:E.228, B:E.228, B:W.232, B:H.237, B:V.242, B:F.269, B:H.350, B:A.354 Hydrogen bonds: B:N.267, B:N.267 Salt bridges: B:K.295 Metal complexes: B:H.248, B:H.355 HEC.11: 19 residues within 4Å: Chain A: I.236, H.280, Q.282 Chain B: I.236, H.237, N.240, V.242, D.246, C.247, P.268, F.269, T.275, C.276, C.279, H.280, V.290, R.294 Ligands: HEC.5, HEC.10 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:I.236, B:I.236, B:N.240, B:P.268, B:F.269, B:V.290 Water bridges: B:N.240 Salt bridges: B:R.294, A:H.280 Metal complexes: B:H.237, B:H.280 Hydrogen bonds: A:Q.282

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: E.174, Y.175, Y.204, K.223, Q.225 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.174, A:Y.175, A:K.223, H2O.4, H2O.10 CA.12: 5 residues within 4Å: Chain B: E.174, Y.175, Y.204, K.223, Q.225 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.174, B:Y.175, B:K.223, H2O.27, H2O.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ali, M. et al., Trapping of a Putative Intermediate in the CytochromecNitrite Reductase (ccNiR)-Catalyzed Reduction of Nitrite: Implications for the ccNiR Reaction Mechanism. J.Am.Chem.Soc. (2019)

Release Date

2020-04-01

Peptides

Cytochrome c-552: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytochrome c-552

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