- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.50 Å
- Oligo State
- homo-dimer
- Ligands
- 6 x ACT: ACETATE ION(Non-functional Binders)
- 4 x SO4: SULFATE ION(Non-functional Binders)
SO4.4: 9 residues within 4Å:- Chain A: T.263, G.264, I.265, H.383, A.384, P.385, E.386, E.387
- Chain B: R.325
9 PLIP interactions:7 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:I.265, A:H.383, A:E.386, A:E.387
- Water bridges: A:Q.268, A:Q.268, A:E.386, B:K.322
- Salt bridges: B:R.325
SO4.5: 3 residues within 4Å:- Chain A: S.311, E.312
- Ligands: Y1.9
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.312
- Water bridges: A:S.311, A:Q.313
SO4.19: 9 residues within 4Å:- Chain A: R.325
- Chain B: T.263, G.264, I.265, H.383, A.384, P.385, E.386, E.387
9 PLIP interactions:6 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:I.265, B:H.383, B:E.386, B:E.387
- Water bridges: B:Q.268, B:Q.268, A:K.322, A:K.322
- Salt bridges: A:R.325
SO4.20: 3 residues within 4Å:- Chain B: S.311, E.312
- Ligands: Y1.24
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:E.312
- Water bridges: B:S.311, B:Q.313
- 2 x CA: CALCIUM ION(Non-covalent)
CA.6: 5 residues within 4Å:- Chain A: E.195, F.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:F.196, A:K.252, H2O.4, H2O.8
CA.21: 5 residues within 4Å:- Chain B: E.195, F.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:F.196, B:K.252, H2O.29, H2O.33
- 8 x Y1: YTTRIUM ION(Non-covalent)
Y1.7: 2 residues within 4Å:- Chain A: E.30
- Ligands: ACT.1
No protein-ligand interaction detected (PLIP)Y1.8: 3 residues within 4Å:- Chain A: P.77
- Ligands: HEM.13, HEM.14
No protein-ligand interaction detected (PLIP)Y1.9: 3 residues within 4Å:- Chain A: D.301, E.312
- Ligands: SO4.5
No protein-ligand interaction detected (PLIP)Y1.10: 5 residues within 4Å:- Chain A: E.386
- Chain B: E.386
- Ligands: HEM.15, Y1.25, HEM.30
No protein-ligand interaction detected (PLIP)Y1.22: 2 residues within 4Å:- Chain B: E.30
- Ligands: ACT.16
No protein-ligand interaction detected (PLIP)Y1.23: 3 residues within 4Å:- Chain B: P.77
- Ligands: HEM.28, HEM.29
No protein-ligand interaction detected (PLIP)Y1.24: 3 residues within 4Å:- Chain B: D.301, E.312
- Ligands: SO4.20
No protein-ligand interaction detected (PLIP)Y1.25: 5 residues within 4Å:- Chain A: E.386
- Chain B: E.386
- Ligands: Y1.10, HEM.15, HEM.30
No protein-ligand interaction detected (PLIP)- 10 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)(Non-covalent)
HEM.11: 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, F.196, F.198, V.216, H.255, A.376, H.378
- Ligands: HEM.13
18 PLIP interactions:17 interactions with chain A, 1 Ligand-Water interactions- Hydrophobic interactions: A:P.77, A:T.90, A:T.93, A:L.104, A:F.196, A:F.196, A:F.198, A:V.216, A:H.255
- Hydrogen bonds: A:N.75
- Water bridges: A:R.92, A:D.257, A:A.376
- Salt bridges: A:R.92, A:H.255, A:H.378
- pi-Stacking: A:H.255
- Metal complexes: H2O.21
HEM.12: 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, V.188, M.278, Y.280, Y.288, S.289, H.291
- Ligands: HEM.13
20 PLIP interactions:20 interactions with chain A,- Hydrophobic interactions: A:W.31, A:Y.35, A:Y.35, A:Q.38, A:Q.38, A:F.39, A:W.42, A:L.157, A:L.157, A:V.188
- Hydrogen bonds: A:Q.38, A:Y.280, A:S.289
- Water bridges: A:K.287
- Salt bridges: A:H.181, A:R.185, A:K.287, A:H.291
- Metal complexes: A:H.150, A:H.291
HEM.13: 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, C.149, V.188, C.189, C.192, H.193, C.273, H.277, M.278, V.293, G.294
- Ligands: Y1.8, HEM.11, HEM.12, HEM.14
10 PLIP interactions:10 interactions with chain A,- Hydrophobic interactions: A:P.77, A:K.112, A:I.144, A:H.277
- Hydrogen bonds: A:S.48, A:Y.82, A:D.86
- Water bridges: A:N.87
- Metal complexes: A:H.80, A:H.193
HEM.14: 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: Y1.8, HEM.13, HEM.15
15 PLIP interactions:15 interactions with chain A,- Hydrophobic interactions: A:H.193, A:Y.261, A:Y.261, 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.15: 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, V.319, K.322, F.382, P.385
- Chain B: I.265, H.308, E.310, E.386
- Ligands: Y1.10, HEM.14, Y1.25, HEM.30
16 PLIP interactions:15 interactions with chain A, 1 interactions with chain B,- Hydrophobic interactions: A:I.265, A:K.269, A:V.271, A:P.296, A:L.315, A:L.315, A:I.318, A:V.319, A:F.382
- Water bridges: A:K.269, A:K.322, A:K.322
- Salt bridges: A:K.322, B:H.308
- Metal complexes: A:H.266, A:H.308
HEM.26: 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, F.196, F.198, V.216, H.255, A.376, H.378
- Ligands: HEM.28
18 PLIP interactions:17 interactions with chain B, 1 Ligand-Water interactions- Hydrophobic interactions: B:P.77, B:T.90, B:T.93, B:L.104, B:F.196, B:F.196, B:F.198, B:V.216, B:H.255
- Hydrogen bonds: B:N.75
- Water bridges: B:R.92, B:D.257, B:A.376
- Salt bridges: B:R.92, B:H.255, B:H.378
- pi-Stacking: B:H.255
- Metal complexes: H2O.46
HEM.27: 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, V.188, M.278, Y.280, Y.288, S.289, H.291
- Ligands: HEM.28
20 PLIP interactions:20 interactions with chain B,- Hydrophobic interactions: B:W.31, B:Y.35, B:Y.35, B:Q.38, B:Q.38, B:F.39, B:W.42, B:L.157, B:L.157, B:V.188
- Hydrogen bonds: B:Q.38, B:Y.280, B:S.289
- Water bridges: B:K.287
- Salt bridges: B:H.181, B:R.185, B:K.287, B:H.291
- Metal complexes: B:H.150, B:H.291
HEM.28: 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, C.149, V.188, C.189, C.192, H.193, C.273, H.277, M.278, V.293, G.294
- Ligands: Y1.23, HEM.26, HEM.27, HEM.29
10 PLIP interactions:10 interactions with chain B,- Hydrophobic interactions: B:P.77, B:K.112, B:I.144, B:H.277
- Hydrogen bonds: B:S.48, B:Y.82, B:D.86
- Water bridges: B:N.87
- Metal complexes: B:H.80, B:H.193
HEM.29: 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: Y1.23, HEM.28, HEM.30
15 PLIP interactions:15 interactions with chain B,- Hydrophobic interactions: B:H.193, B:Y.261, B:Y.261, 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.30: 24 residues within 4Å:- Chain A: I.265, H.308, E.310, 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, V.319, K.322, F.382, P.385
- Ligands: Y1.10, HEM.15, Y1.25, HEM.29
16 PLIP interactions:15 interactions with chain B, 1 interactions with chain A,- Hydrophobic interactions: B:I.265, B:K.269, B:V.271, B:P.296, B:L.315, B:L.315, B:I.318, B:V.319, B:F.382
- Water bridges: B:K.269, B:K.322, B:K.322
- Salt bridges: B:K.322, A:H.308
- Metal complexes: B:H.266, B:H.308
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lukat, P. et al., Binding and Reduction of Sulfite by Cytochrome c Nitrite Reductase. Biochemistry (2008)
- Release Date
- 2008-02-26
- Peptides
- Cytochrome c-552: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.50 Å
- Oligo State
- homo-dimer
- Ligands
- 6 x ACT: ACETATE ION(Non-functional Binders)
- 4 x SO4: SULFATE ION(Non-functional Binders)
- 2 x CA: CALCIUM ION(Non-covalent)
- 8 x Y1: YTTRIUM ION(Non-covalent)
- 10 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lukat, P. et al., Binding and Reduction of Sulfite by Cytochrome c Nitrite Reductase. Biochemistry (2008)
- Release Date
- 2008-02-26
- Peptides
- Cytochrome c-552: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A