- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.70 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x CA: CALCIUM ION(Non-covalent)
- 2 x SO3: SULFITE ION(Non-covalent)
SO3.2: 6 residues within 4Å:- Chain A: F.70, R.92, Y.196, Q.254, H.255
- Ligands: HEM.8
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.92, A:Y.196
SO3.14: 6 residues within 4Å:- Chain B: F.70, R.92, Y.196, Q.254, H.255
- Ligands: HEM.20
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:R.92, B:Y.196
- 6 x Y1: YTTRIUM ION(Non-covalent)
Y1.3: 2 residues within 4Å:- Chain A: E.30
- Ligands: ACT.7
No protein-ligand interaction detected (PLIP)Y1.4: 3 residues within 4Å:- Chain A: P.77
- Ligands: HEM.10, HEM.11
No protein-ligand interaction detected (PLIP)Y1.5: 7 residues within 4Å:- Chain A: E.386
- Chain B: E.386
- Ligands: ACT.6, HEM.12, Y1.17, ACT.18, HEM.24
No protein-ligand interaction detected (PLIP)Y1.15: 2 residues within 4Å:- Chain B: E.30
- Ligands: ACT.19
No protein-ligand interaction detected (PLIP)Y1.16: 3 residues within 4Å:- Chain B: P.77
- Ligands: HEM.22, HEM.23
No protein-ligand interaction detected (PLIP)Y1.17: 7 residues within 4Å:- Chain A: E.386
- Chain B: E.386
- Ligands: Y1.5, ACT.6, HEM.12, ACT.18, HEM.24
No protein-ligand interaction detected (PLIP)- 4 x ACT: ACETATE ION(Non-functional Binders)
ACT.6: 9 residues within 4Å:- Chain A: G.264, I.265, P.385, E.386
- Chain B: E.386
- Ligands: Y1.5, HEM.12, Y1.17, HEM.24
5 PLIP interactions:4 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:E.386
- Water bridges: A:A.384, A:E.387
- Salt bridges: A:K.322, B:K.322
ACT.7: 5 residues within 4Å:- Chain A: G.21, I.22, E.23, Y.34
- Ligands: Y1.3
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:G.21, A:E.23, A:Y.34
- Water bridges: A:E.23
ACT.18: 9 residues within 4Å:- Chain A: E.386
- Chain B: G.264, I.265, P.385, E.386
- Ligands: Y1.5, HEM.12, Y1.17, HEM.24
5 PLIP interactions:4 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:E.386
- Water bridges: B:A.384, B:E.387
- Salt bridges: B:K.322, A:K.322
ACT.19: 5 residues within 4Å:- Chain B: G.21, I.22, E.23, Y.34
- Ligands: Y1.15
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:G.21, B:E.23, B:Y.34
- Water bridges: B:E.23
- 10 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)(Non-covalent)
HEM.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, C.192, H.193, Y.196, F.198, V.216, H.255, A.376, H.378
- Ligands: SO3.2, HEM.10
17 PLIP interactions:17 interactions with chain A,- Hydrophobic interactions: A:T.90, A:T.93, A:L.104, A:Y.196, 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
- pi-Stacking: A:H.255
HEM.9: 20 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, A.274, M.278, Y.280, Y.288, S.289, H.291
- Ligands: HEM.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:V.188, A:A.274
- Hydrogen bonds: A:Q.38, 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
HEM.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, V.188, C.189, Q.191, C.192, H.193, C.273, H.277, M.278, V.293, G.294, N.295
- Ligands: Y1.4, HEM.8, HEM.9, HEM.11
11 PLIP interactions:11 interactions with chain A,- Hydrophobic interactions: A:P.77, A:K.112, A:I.144, A:H.277, A:V.293
- Hydrogen bonds: A:S.48, A:R.78, A:Y.82, A:D.86
- Metal complexes: A:H.80, A:H.193
HEM.11: 21 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, H.378, G.379, F.381, F.382, H.383
- Ligands: Y1.4, HEM.10, HEM.12
13 PLIP interactions:13 interactions with chain A,- Hydrophobic interactions: A:H.193, A:Y.261, A:Y.261, A:H.266, A:V.271, A:P.296, A:H.378, A:F.381, A:F.382, A:F.382
- Hydrogen bonds: A:N.295
- Metal complexes: A:H.277, A:H.383
HEM.12: 25 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.386
- Ligands: Y1.5, ACT.6, HEM.11, Y1.17, ACT.18, HEM.24
15 PLIP interactions:14 interactions with chain A, 1 interactions with chain B,- Hydrophobic interactions: A:I.265, A:I.265, 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
- Salt bridges: A:K.269, A:K.322, B:H.308
- Metal complexes: A:H.266, A:H.308
HEM.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, C.192, H.193, Y.196, F.198, V.216, H.255, A.376, H.378
- Ligands: SO3.14, HEM.22
17 PLIP interactions:17 interactions with chain B,- Hydrophobic interactions: B:T.90, B:T.93, B:L.104, B:Y.196, 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
- pi-Stacking: B:H.255
HEM.21: 20 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, A.274, M.278, Y.280, Y.288, S.289, H.291
- Ligands: HEM.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:V.188, B:A.274
- Hydrogen bonds: B:Q.38, 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
HEM.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, V.188, C.189, Q.191, C.192, H.193, C.273, H.277, M.278, V.293, G.294, N.295
- Ligands: Y1.16, HEM.20, HEM.21, HEM.23
11 PLIP interactions:11 interactions with chain B,- Hydrophobic interactions: B:P.77, 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
- Metal complexes: B:H.80, B:H.193
HEM.23: 21 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, H.378, G.379, F.381, F.382, H.383
- Ligands: Y1.16, HEM.22, HEM.24
13 PLIP interactions:13 interactions with chain B,- Hydrophobic interactions: B:H.193, B:Y.261, B:Y.261, B:H.266, B:V.271, B:P.296, B:H.378, B:F.381, B:F.382, B:F.382
- Hydrogen bonds: B:N.295
- Metal complexes: B:H.277, B:H.383
HEM.24: 25 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, V.319, K.322, F.382, P.385
- Ligands: Y1.5, ACT.6, HEM.12, Y1.17, ACT.18, HEM.23
15 PLIP interactions:14 interactions with chain B, 1 interactions with chain A,- Hydrophobic interactions: B:I.265, B:I.265, 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
- Salt bridges: B:K.269, 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 1.70 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x CA: CALCIUM ION(Non-covalent)
- 2 x SO3: SULFITE ION(Non-covalent)
- 6 x Y1: YTTRIUM ION(Non-covalent)
- 4 x ACT: ACETATE ION(Non-functional Binders)
- 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