- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NO2: NITRITE ION(Non-covalent)
- 6 x ACT: ACETATE ION(Non-functional Binders)
ACT.2: 9 residues within 4Å:- Chain A: I.265, P.385, E.386
- Chain B: K.322, E.386
- Ligands: YT3.8, HEM.13, YT3.21, HEM.26
6 PLIP interactions:4 interactions with chain A, 2 interactions with chain B- Hydrophobic interactions: A:I.265
- Hydrogen bonds: A:E.386
- Water bridges: A:E.387, B:K.322
- Salt bridges: A:K.322, B:K.322
ACT.3: 4 residues within 4Å:- Chain A: A.76, P.77
- Ligands: YT3.7, HEM.12
1 PLIP interactions:1 interactions with chain A- Water bridges: A:N.295
ACT.4: 3 residues within 4Å:- Chain A: R.37, T.281, D.290
4 PLIP interactions:4 interactions with chain A- Water bridges: A:R.37, A:S.41, A:T.281
- Salt bridges: A:R.37
ACT.15: 9 residues within 4Å:- Chain A: K.322, E.386
- Chain B: I.265, P.385, E.386
- Ligands: YT3.8, HEM.13, YT3.21, HEM.26
6 PLIP interactions:4 interactions with chain B, 2 interactions with chain A- Hydrophobic interactions: B:I.265
- Hydrogen bonds: B:E.386
- Water bridges: B:E.387, A:K.322
- Salt bridges: B:K.322, A:K.322
ACT.16: 4 residues within 4Å:- Chain B: A.76, P.77
- Ligands: YT3.20, HEM.25
1 PLIP interactions:1 interactions with chain B- Water bridges: B:N.295
ACT.17: 3 residues within 4Å:- Chain B: R.37, T.281, D.290
4 PLIP interactions:4 interactions with chain B- Water bridges: B:R.37, B:S.41, B:T.281
- Salt bridges: B:R.37
- 2 x CA: CALCIUM ION(Non-covalent)
CA.5: 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.5, H2O.11
CA.18: 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.30, H2O.36
- 6 x YT3: YTTRIUM (III) ION(Non-covalent)
YT3.6: 1 residues within 4Å:- Chain A: E.30
No protein-ligand interaction detected (PLIP)YT3.7: 4 residues within 4Å:- Chain A: P.77
- Ligands: ACT.3, HEM.11, HEM.12
No protein-ligand interaction detected (PLIP)YT3.8: 7 residues within 4Å:- Chain A: E.386
- Chain B: E.386
- Ligands: ACT.2, HEM.13, ACT.15, YT3.21, HEM.26
No protein-ligand interaction detected (PLIP)YT3.19: 1 residues within 4Å:- Chain B: E.30
No protein-ligand interaction detected (PLIP)YT3.20: 4 residues within 4Å:- Chain B: P.77
- Ligands: ACT.16, HEM.24, HEM.25
No protein-ligand interaction detected (PLIP)YT3.21: 7 residues within 4Å:- Chain A: E.386
- Chain B: E.386
- Ligands: ACT.2, YT3.8, HEM.13, ACT.15, HEM.26
No protein-ligand interaction detected (PLIP)- 10 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)
HEM.9: 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: NO2.1, HEM.11
20 PLIP interactions:20 interactions with chain A,- Hydrophobic interactions: A:P.77, A:T.90, A:T.93, A:L.104, A:Y.196, A:Y.196, A:F.198, A:F.198, A:V.216, A:H.255
- Hydrogen bonds: A:N.75, 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-Stacking: A:H.255
HEM.10: 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.11
19 PLIP interactions:19 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
- 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:K.287, A:H.291
- Metal complexes: A:H.150, A:H.291
HEM.11: 25 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, C.192, H.193, C.273, H.277, M.278, V.293, G.294
- Ligands: YT3.7, HEM.9, HEM.10, HEM.12
8 PLIP interactions:8 interactions with chain A,- Hydrophobic interactions: A:P.77, A:K.112, A:H.277
- Hydrogen bonds: A:S.48, A:Y.82, A:D.86
- Metal complexes: A:H.80, A:H.193
HEM.12: 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: ACT.3, YT3.7, HEM.11, HEM.13
11 PLIP interactions:11 interactions with chain A,- Hydrophobic interactions: A:H.193, A:Y.261, A:Y.261, A:V.271, A:P.296, A:H.378, A:F.382, A:F.382
- Hydrogen bonds: A:N.295
- Metal complexes: A:H.277, A:H.383
HEM.13: 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, I.318, V.319, K.322, F.382, P.385
- Chain B: I.265, H.308, E.310, E.386
- Ligands: ACT.2, YT3.8, HEM.12, ACT.15, YT3.21, HEM.26
16 PLIP interactions:4 interactions with chain B, 12 interactions with chain A,- Water bridges: B:C.307, B:H.308, B:R.309
- Salt bridges: B:H.308, A:K.269, A:K.322
- Hydrophobic interactions: A:I.265, A:I.265, A:K.269, A:P.296, A:I.318, A:V.319, A:F.382, A:F.382
- Metal complexes: A:H.266, A:H.308
HEM.22: 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: NO2.14, HEM.24
20 PLIP interactions:20 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:F.198, B:V.216, B:H.255
- Hydrogen bonds: B:N.75, 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-Stacking: B:H.255
HEM.23: 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.24
19 PLIP interactions:19 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
- 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:K.287, B:H.291
- Metal complexes: B:H.150, B:H.291
HEM.24: 25 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, C.192, H.193, C.273, H.277, M.278, V.293, G.294
- Ligands: YT3.20, HEM.22, HEM.23, HEM.25
8 PLIP interactions:8 interactions with chain B,- Hydrophobic interactions: B:P.77, B:K.112, B:H.277
- Hydrogen bonds: B:S.48, B:Y.82, B:D.86
- Metal complexes: B:H.80, B:H.193
HEM.25: 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: ACT.16, YT3.20, HEM.24, HEM.26
11 PLIP interactions:11 interactions with chain B,- Hydrophobic interactions: B:H.193, B:Y.261, B:Y.261, B:V.271, B:P.296, B:H.378, B:F.382, B:F.382
- Hydrogen bonds: B:N.295
- Metal complexes: B:H.277, B:H.383
HEM.26: 25 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, I.318, V.319, K.322, F.382, P.385
- Ligands: ACT.2, YT3.8, HEM.13, ACT.15, YT3.21, HEM.25
16 PLIP interactions:4 interactions with chain A, 12 interactions with chain B,- Water bridges: A:C.307, A:H.308, A:R.309
- Salt bridges: A:H.308, B:K.269, B:K.322
- Hydrophobic interactions: B:I.265, B:I.265, B:K.269, B:P.296, B:I.318, B:V.319, B:F.382, B:F.382
- Metal complexes: B:H.266, B:H.308
- 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
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NO2: NITRITE ION(Non-covalent)
- 6 x ACT: ACETATE ION(Non-functional Binders)
- 2 x CA: CALCIUM ION(Non-covalent)
- 6 x YT3: YTTRIUM (III) ION(Non-covalent)
- 10 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)
- 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
AB
A