- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.30 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, F.196, Q.254, H.255
- Ligands: HEM.10
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.92, A:H.255
SO3.16: 6 residues within 4Å:- Chain B: F.70, R.92, F.196, Q.254, H.255
- Ligands: HEM.24
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:R.92, B:H.255, B:H.255
- Water bridges: B:Q.254
- 2 x SO4: SULFATE ION(Non-functional Binders)
SO4.3: 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:5 interactions with chain A, 4 interactions with chain B- Hydrogen bonds: A:I.265, A:H.383, A:E.386, A:E.387
- Water bridges: A:H.266, B:R.325, B:R.325, B:R.325
- Salt bridges: B:R.325
SO4.17: 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:4 interactions with chain A, 5 interactions with chain B- Water bridges: A:R.325, A:R.325, A:R.325, B:H.266
- Salt bridges: A:R.325
- Hydrogen bonds: B:I.265, B:H.383, B:E.386, B:E.387
- 6 x Y1: YTTRIUM ION(Non-covalent)
Y1.4: 1 residues within 4Å:- Chain A: E.30
No protein-ligand interaction detected (PLIP)Y1.5: 3 residues within 4Å:- Chain A: P.77
- Ligands: HEM.12, HEM.13
No protein-ligand interaction detected (PLIP)Y1.6: 5 residues within 4Å:- Chain A: E.386
- Chain B: E.386
- Ligands: HEM.14, Y1.20, HEM.28
No protein-ligand interaction detected (PLIP)Y1.18: 1 residues within 4Å:- Chain B: E.30
No protein-ligand interaction detected (PLIP)Y1.19: 3 residues within 4Å:- Chain B: P.77
- Ligands: HEM.26, HEM.27
No protein-ligand interaction detected (PLIP)Y1.20: 5 residues within 4Å:- Chain A: E.386
- Chain B: E.386
- Ligands: Y1.6, HEM.14, HEM.28
No protein-ligand interaction detected (PLIP)- 6 x ACT: ACETATE ION(Non-functional Binders)
ACT.7: 2 residues within 4Å:- Chain A: E.125, R.166
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:R.166
ACT.8: 4 residues within 4Å:- Chain A: G.21, I.22, E.23, Y.34
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:E.23, A:Y.34
- Water bridges: A:E.23, A:E.23, A:E.23
ACT.9: 5 residues within 4Å:- Chain A: A.170, A.171, S.221, K.222, G.223
1 PLIP interactions:1 interactions with chain A- Water bridges: A:A.171
ACT.21: 2 residues within 4Å:- Chain B: E.125, R.166
1 PLIP interactions:1 interactions with chain B- Salt bridges: B:R.166
ACT.22: 4 residues within 4Å:- Chain B: G.21, I.22, E.23, Y.34
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:E.23, B:Y.34
- Water bridges: B:E.23, B:E.23, B:E.23
ACT.23: 5 residues within 4Å:- Chain B: A.170, A.171, S.221, K.222, G.223
1 PLIP interactions:1 interactions with chain B- Water bridges: B:A.171
- 10 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)(Non-covalent)
HEM.10: 25 residues within 4Å:- Chain A: Y.74, N.75, P.77, D.86, N.87, T.90, R.92, T.93, L.104, A.107, 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: SO3.2, HEM.12
16 PLIP interactions:16 interactions with chain A,- 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, A:A.376
- Water bridges: A:R.92
- Salt bridges: A:R.92, A:H.255, A:H.378
- pi-Stacking: A:H.255
HEM.11: 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.12
19 PLIP interactions:19 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, A:V.188, A:A.274
- 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
HEM.12: 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: Y1.5, HEM.10, HEM.11, HEM.13
13 PLIP interactions:13 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:Y.82, A:D.86
- Water bridges: A:S.48, A:V.293, A:N.295
- Metal complexes: A:H.80, A:H.193
HEM.13: 22 residues within 4Å:- Chain A: P.77, C.189, H.193, D.257, 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.382, H.383
- Ligands: Y1.5, HEM.12, HEM.14
16 PLIP interactions:16 interactions with chain A,- Hydrophobic interactions: A:H.193, A:D.257, A:W.258, A:Y.261, A:Y.261, A:Y.261, A:Y.261, A:H.266, A:V.271, A:L.297, A:H.378, A:F.382, A:F.382
- Hydrogen bonds: A:N.295
- Metal complexes: A:H.277, A:H.383
HEM.14: 23 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: Y1.6, HEM.13, Y1.20, HEM.28
18 PLIP interactions:16 interactions with chain A, 2 interactions with chain B,- Hydrophobic interactions: A:I.265, A:I.265, A:K.269, A:V.271, A:V.271, A:P.296, A:L.315, A:L.315, A:L.315, A:I.318, A:V.319, A:F.382
- Salt bridges: A:K.269, A:K.322, B:H.308
- Metal complexes: A:H.266, A:H.308
- Water bridges: B:R.309
HEM.24: 25 residues within 4Å:- Chain B: Y.74, N.75, P.77, D.86, N.87, T.90, R.92, T.93, L.104, A.107, 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: SO3.16, HEM.26
16 PLIP interactions:16 interactions with chain B,- 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, B:A.376
- Water bridges: B:R.92
- Salt bridges: B:R.92, B:H.255, B:H.378
- pi-Stacking: B:H.255
HEM.25: 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.26
19 PLIP interactions:19 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, B:V.188, B:A.274
- 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
HEM.26: 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: Y1.19, HEM.24, HEM.25, HEM.27
12 PLIP interactions:12 interactions with chain B,- Hydrophobic interactions: B:K.112, B:I.144, B:H.277, B:V.293
- Hydrogen bonds: B:S.48, 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.27: 22 residues within 4Å:- Chain B: P.77, C.189, H.193, D.257, 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.382, H.383
- Ligands: Y1.19, HEM.26, HEM.28
16 PLIP interactions:16 interactions with chain B,- Hydrophobic interactions: B:H.193, B:D.257, B:W.258, B:Y.261, B:Y.261, B:Y.261, B:Y.261, B:H.266, B:V.271, B:L.297, B:H.378, B:F.382, B:F.382
- Hydrogen bonds: B:N.295
- Metal complexes: B:H.277, B:H.383
HEM.28: 23 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: Y1.6, HEM.14, Y1.20, HEM.27
18 PLIP interactions:16 interactions with chain B, 2 interactions with chain A,- Hydrophobic interactions: B:I.265, B:I.265, B:K.269, B:V.271, B:V.271, B:P.296, B:L.315, B:L.315, B:L.315, B:I.318, B:V.319, B:F.382
- Salt bridges: B:K.269, B:K.322, A:H.308
- Metal complexes: B:H.266, B:H.308
- Water bridges: A:R.309
- 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 1.30 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x CA: CALCIUM ION(Non-covalent)
- 2 x SO3: SULFITE ION(Non-covalent)
- 2 x SO4: SULFATE ION(Non-functional Binders)
- 6 x Y1: YTTRIUM ION(Non-covalent)
- 6 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