SMTL ID : 2e81.1

Cytochrome c Nitrite Reductase from Wolinella succinogenes with bound intermediate hydroxylamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.195, Y.196, Y.233, K.252, Q.254 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.195, A:Y.196, A:K.252, H2O.4, H2O.9 CA.11: 5 residues within 4Å: Chain B: E.195, Y.196, Y.233, K.252, Q.254 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.195, B:Y.196, B:K.252, H2O.21, H2O.26

6 x YT3: YTTRIUM (III) ION(Non-covalent)

YT3.2: 1 residues within 4Å: Chain A: E.30 No protein-ligand interaction detected (PLIP) YT3.3: 3 residues within 4Å: Chain A: P.77 Ligands: HEM.7, HEM.8 No protein-ligand interaction detected (PLIP) YT3.4: 5 residues within 4Å: Chain A: E.386 Chain B: E.386 Ligands: HEM.9, YT3.14, HEM.19 No protein-ligand interaction detected (PLIP) YT3.12: 1 residues within 4Å: Chain B: E.30 No protein-ligand interaction detected (PLIP) YT3.13: 3 residues within 4Å: Chain B: P.77 Ligands: HEM.17, HEM.18 No protein-ligand interaction detected (PLIP) YT3.14: 5 residues within 4Å: Chain A: E.386 Chain B: E.386 Ligands: YT3.4, HEM.9, HEM.19 No protein-ligand interaction detected (PLIP)

10 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.5: 24 residues within 4Å: Chain A: Y.74, N.75, P.77, D.86, N.87, T.90, R.92, T.93, L.104, C.108, C.111, K.112, Y.163, Q.191, C.192, H.193, Y.196, F.198, V.216, H.255, A.376, H.378 Ligands: HEM.7, HOA.10 19 PLIP interactions: 18 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:P.77, A:T.90, A:T.93, A:L.104, A:Y.196, A:Y.196, A:F.198, A:V.216, A:H.255 Hydrogen bonds: A:N.75, A:A.376 Water bridges: A:R.92, A:R.92, A:H.378 Salt bridges: A:R.92, A:H.255, A:H.378 pi-Cation interactions: A:K.112 Metal complexes: HOA.10 HEM.6: 19 residues within 4Å: Chain A: W.31, Y.35, Q.38, F.39, W.42, G.145, C.146, C.149, H.150, L.157, H.181, R.185, M.278, Y.280, K.287, Y.288, S.289, H.291 Ligands: HEM.7 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:W.31, A:Y.35, A:Y.35, A:Q.38, A:F.39, A:W.42, A:L.157, A:L.157 Hydrogen bonds: A:Y.280, A:S.289 Salt bridges: A:H.181, A:R.185, A:H.291 Metal complexes: A:H.150, A:H.291 HEM.7: 24 residues within 4Å: Chain A: S.48, P.77, R.78, G.79, H.80, Y.82, A.83, D.86, C.111, K.112, I.144, V.188, C.189, C.192, H.193, C.273, H.277, M.278, V.293, G.294 Ligands: YT3.3, HEM.5, HEM.6, HEM.8 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:A.83, A:K.112, A:I.144, A:H.277, A:V.293 Hydrogen bonds: A:S.48, A:Y.82, A:D.86 Water bridges: A:N.295 Metal complexes: A:H.80, A:H.193 HEM.8: 22 residues within 4Å: Chain A: P.77, C.189, H.193, W.258, Y.261, H.266, V.271, S.272, C.273, C.276, H.277, N.295, P.296, L.297, H.378, G.379, F.381, F.382, H.383 Ligands: YT3.3, HEM.7, HEM.9 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:H.193, A:W.258, A:Y.261, A:Y.261, A:V.271, A:P.296, A:L.297, A:H.378, A:F.382, A:F.382 Hydrogen bonds: A:N.295, A:N.295 Metal complexes: A:H.277, A:H.383 HEM.9: 19 residues within 4Å: Chain A: I.265, H.266, V.271, C.276, P.296, S.303, C.304, C.307, H.308, L.315, K.322, F.382, P.385 Chain B: H.308, E.386 Ligands: YT3.4, HEM.8, YT3.14, HEM.19 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:I.265, A:I.265, A:P.296, A:L.315 Salt bridges: A:K.322, B:H.308 Metal complexes: A:H.266, A:H.308 HEM.15: 24 residues within 4Å: Chain B: Y.74, N.75, P.77, D.86, N.87, T.90, R.92, T.93, L.104, C.108, C.111, K.112, Y.163, Q.191, C.192, H.193, Y.196, F.198, V.216, H.255, A.376, H.378 Ligands: HEM.17, HOA.20 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:P.77, B:T.90, B:T.93, B:L.104, B:Y.196, B:Y.196, B:F.198, B:V.216, B:H.255 Hydrogen bonds: B:N.75, B:A.376 Water bridges: B:R.92, B:R.92, B:H.378 Salt bridges: B:R.92, B:H.255, B:H.378 pi-Cation interactions: B:K.112 HEM.16: 19 residues within 4Å: Chain B: W.31, Y.35, Q.38, F.39, W.42, G.145, C.146, C.149, H.150, L.157, H.181, R.185, M.278, Y.280, K.287, Y.288, S.289, H.291 Ligands: HEM.17 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:W.31, B:Y.35, B:Y.35, B:Q.38, B:F.39, B:W.42, B:L.157, B:L.157 Hydrogen bonds: B:Y.280, B:S.289 Salt bridges: B:H.181, B:R.185, B:H.291 Metal complexes: B:H.150, B:H.291 HEM.17: 24 residues within 4Å: Chain B: S.48, P.77, R.78, G.79, H.80, Y.82, A.83, D.86, C.111, K.112, I.144, V.188, C.189, C.192, H.193, C.273, H.277, M.278, V.293, G.294 Ligands: YT3.13, HEM.15, HEM.16, HEM.18 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:A.83, B:K.112, B:I.144, B:H.277, B:V.293 Hydrogen bonds: B:S.48, B:R.78, B:Y.82, B:D.86 Water bridges: B:S.48, B:V.293, B:N.295 Metal complexes: B:H.80, B:H.193 HEM.18: 22 residues within 4Å: Chain B: P.77, C.189, H.193, W.258, Y.261, H.266, V.271, S.272, C.273, C.276, H.277, N.295, P.296, L.297, H.378, G.379, F.381, F.382, H.383 Ligands: YT3.13, HEM.17, HEM.19 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:H.193, B:W.258, B:Y.261, B:Y.261, B:V.271, B:P.296, B:L.297, B:H.378, B:F.382, B:F.382 Hydrogen bonds: B:N.295, B:N.295 Metal complexes: B:H.277, B:H.383 HEM.19: 19 residues within 4Å: Chain A: H.308, E.386 Chain B: I.265, H.266, V.271, C.276, P.296, S.303, C.304, C.307, H.308, L.315, K.322, F.382, P.385 Ligands: YT3.4, HEM.9, YT3.14, HEM.18 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B, Water bridges: A:E.386 Salt bridges: A:H.308, B:K.322 Hydrophobic interactions: B:I.265, B:I.265, B:P.296, B:L.315 Metal complexes: B:H.266, B:H.308

2 x HOA: HYDROXYAMINE(Non-covalent)

HOA.10: 4 residues within 4Å: Chain A: R.92, K.112, H.255 Ligands: HEM.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.92, A:H.255 Water bridges: A:R.92 HOA.20: 4 residues within 4Å: Chain B: R.92, K.112, H.255 Ligands: HEM.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.92, B:K.112, B:H.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Einsle, O. et al., Mechanism of the six-electron reduction of nitrite to ammonia by cytochrome c nitrite reductase. J.Am.Chem.Soc. (2002)

Release Date

2007-01-30

Peptides

Cytochrome c-552: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome c-552

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