SMTL ID : 1fs7.1

CYTOCHROME C NITRITE REDUCTASE FROM WOLINELLA SUCCINOGENES

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 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.8 CA.13: 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.29, H2O.33

6 x Y1: YTTRIUM ION(Non-covalent)

Y1.2: 1 residues within 4Å: Chain A: E.30 No protein-ligand interaction detected (PLIP) Y1.3: 4 residues within 4Å: Chain A: P.77 Ligands: ACT.6, HEC.10, HEC.11 No protein-ligand interaction detected (PLIP) Y1.4: 7 residues within 4Å: Chain A: E.386 Chain B: E.386 Ligands: ACT.7, HEC.12, Y1.16, ACT.19, HEC.24 No protein-ligand interaction detected (PLIP) Y1.14: 1 residues within 4Å: Chain B: E.30 No protein-ligand interaction detected (PLIP) Y1.15: 4 residues within 4Å: Chain B: P.77 Ligands: ACT.18, HEC.22, HEC.23 No protein-ligand interaction detected (PLIP) Y1.16: 7 residues within 4Å: Chain A: E.386 Chain B: E.386 Ligands: Y1.4, ACT.7, HEC.12, ACT.19, HEC.24 No protein-ligand interaction detected (PLIP)

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 4 residues within 4Å: Chain A: G.21, I.22, E.23, Y.34 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.23, A:Y.34, A:Y.34 Water bridges: A:E.23 ACT.6: 4 residues within 4Å: Chain A: A.76, P.77 Ligands: Y1.3, HEC.11 No protein-ligand interaction detected (PLIP) ACT.7: 10 residues within 4Å: Chain A: G.264, I.265, P.385, E.386 Chain B: K.322, E.386 Ligands: Y1.4, HEC.12, Y1.16, HEC.24 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.265 Hydrogen bonds: A:E.386 Water bridges: A:E.387 Salt bridges: A:K.322, B:K.322 ACT.17: 4 residues within 4Å: Chain B: G.21, I.22, E.23, Y.34 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.23, B:Y.34, B:Y.34 Water bridges: B:E.23 ACT.18: 4 residues within 4Å: Chain B: A.76, P.77 Ligands: Y1.15, HEC.23 No protein-ligand interaction detected (PLIP) ACT.19: 10 residues within 4Å: Chain A: K.322, E.386 Chain B: G.264, I.265, P.385, E.386 Ligands: Y1.4, HEC.12, Y1.16, HEC.24 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:K.322, B:K.322 Hydrophobic interactions: B:I.265 Hydrogen bonds: B:E.386 Water bridges: B:E.387

10 x HEC: HEME C(Covalent)

HEC.8: 23 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: HEC.10 17 PLIP interactions: 16 interactions with chain A, 1 Ligand-Water 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 Salt bridges: A:R.92, A:H.255, A:H.378 Metal complexes: H2O.1 HEC.9: 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: HEC.10 17 PLIP interactions: 17 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:Q.38, A:Y.280, A:S.289 Water bridges: A:R.185 Salt bridges: A:H.181, A:R.185, A:H.291 Metal complexes: A:H.150, A:H.291 HEC.10: 26 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, N.148, V.188, C.189, Q.191, C.192, H.193, C.273, H.277, M.278, V.293, G.294 Ligands: Y1.3, HEC.8, HEC.9, HEC.11 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:P.77, A:A.83, A:K.112, A:I.144, A:H.277 Hydrogen bonds: A:S.48, A:Y.82, A:D.86 Metal complexes: A:H.80, A:H.193 HEC.11: 24 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, V.319, H.378, G.379, F.381, F.382, H.383 Ligands: Y1.3, ACT.6, HEC.10, HEC.12 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:H.193, A:Y.261, A:Y.261, A:Y.261, A:V.271, A:P.296, A:H.378, A:F.381, A:F.382, A:F.382 Hydrogen bonds: A:N.295, A:N.295 Metal complexes: A:H.277, A:H.383 HEC.12: 24 residues within 4Å: Chain A: I.265, H.266, K.269, V.271, C.276, P.296, S.303, C.304, C.307, H.308, L.315, I.318, K.322, F.382, P.385 Chain B: I.265, H.308, E.386 Ligands: Y1.4, ACT.7, HEC.11, Y1.16, ACT.19, HEC.24 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:I.265, A:I.265, A:K.269, A:P.296, A:L.315, A:I.318, A:F.382 Salt bridges: A:K.322, B:H.308 Metal complexes: A:H.266, A:H.308 Water bridges: B:H.308 HEC.20: 23 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: HEC.22 17 PLIP interactions: 16 interactions with chain B, 1 Ligand-Water interactions 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 Salt bridges: B:R.92, B:H.255, B:H.378 Metal complexes: H2O.25 HEC.21: 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: HEC.22 17 PLIP interactions: 17 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:Q.38, B:Y.280, B:S.289 Water bridges: B:R.185 Salt bridges: B:H.181, B:R.185, B:H.291 Metal complexes: B:H.150, B:H.291 HEC.22: 26 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, N.148, V.188, C.189, Q.191, C.192, H.193, C.273, H.277, M.278, V.293, G.294 Ligands: Y1.15, HEC.20, HEC.21, HEC.23 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:P.77, B:A.83, B:K.112, B:I.144, B:H.277 Hydrogen bonds: B:S.48, B:S.48, B:R.78, B:Y.82, B:D.86 Metal complexes: B:H.80, B:H.193 HEC.23: 24 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, V.319, H.378, G.379, F.381, F.382, H.383 Ligands: Y1.15, ACT.18, HEC.22, HEC.24 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:H.193, B:Y.261, B:Y.261, B:Y.261, B:V.271, B:P.296, B:H.378, B:F.381, B:F.382, B:F.382 Hydrogen bonds: B:N.295, B:N.295 Water bridges: B:H.378 Metal complexes: B:H.277, B:H.383 HEC.24: 24 residues within 4Å: Chain A: I.265, H.308, E.386 Chain B: I.265, H.266, K.269, V.271, C.276, P.296, S.303, C.304, C.307, H.308, L.315, I.318, K.322, F.382, P.385 Ligands: Y1.4, ACT.7, HEC.12, Y1.16, ACT.19, HEC.23 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:I.265, B:I.265, B:K.269, B:P.296, B:L.315, B:I.318, B:F.382 Salt bridges: B:K.322, A:H.308 Metal complexes: B:H.266, B:H.308 Water bridges: A:H.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Einsle, O. et al., Cytochrome c nitrite reductase from Wolinella succinogenes. Structure at 1.6 A resolution, inhibitor binding, and heme-packing motifs. J.Biol.Chem. (2000)

Release Date

2001-01-17

Peptides

CYTOCHROME C NITRITE REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CYTOCHROME C NITRITE REDUCTASE

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