- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x CA: CALCIUM ION(Non-covalent)
- 4 x EU: EUROPIUM ION(Non-covalent)(Non-functional Binders)
EU.2: 3 residues within 4Å:- Chain A: P.65
- Ligands: HEC.5, HEC.6
5 PLIP interactions:1 interactions with chain A, 4 Ligand-Water interactions- Metal complexes: A:P.65, H2O.6, H2O.9, H2O.10, H2O.20
EU.8: 2 residues within 4Å:- Ligands: HEC.7, HEC.16
No protein-ligand interaction detected (PLIP)EU.9: 3 residues within 4Å:- Chain B: E.370
- Ligands: HEC.7, HEC.16
No protein-ligand interaction detected (PLIP)EU.11: 3 residues within 4Å:- Chain B: P.65
- Ligands: HEC.14, HEC.15
5 PLIP interactions:1 interactions with chain B, 4 Ligand-Water interactions- Metal complexes: B:P.65, H2O.26, H2O.27, H2O.29, H2O.29
- 10 x HEC: HEME C(Covalent)(Non-covalent)
HEC.3: 22 residues within 4Å:- Chain A: Y.62, N.63, P.65, D.74, V.75, T.78, R.80, T.81, L.92, C.96, C.99, K.100, C.186, H.187, V.188, Y.190, F.192, V.199, H.238, A.360, H.362
- Ligands: HEC.5
22 PLIP interactions:21 interactions with chain A, 1 Ligand-Water interactions- Hydrophobic interactions: A:P.65, A:V.75, A:T.78, A:T.81, A:L.92, A:V.188, A:Y.190, A:Y.190, A:Y.190, A:F.192, A:V.199, A:H.238
- Hydrogen bonds: A:N.63, A:N.63, A:A.360
- Water bridges: A:R.80, A:H.362
- Salt bridges: A:R.80, A:H.238, A:H.362
- pi-Stacking: A:H.238
- Metal complexes: H2O.15
HEC.4: 25 residues within 4Å:- Chain A: F.19, H.23, Q.26, Y.27, W.30, H.68, L.132, G.133, C.134, C.137, H.138, F.145, G.148, P.150, L.152, R.175, Q.179, I.257, M.261, K.263, Y.272, T.273, H.275, I.277
- Ligands: HEC.5
22 PLIP interactions:22 interactions with chain A,- Hydrophobic interactions: A:F.19, A:H.23, A:Q.26, A:Q.26, A:Y.27, A:W.30, A:L.132, A:F.145, A:P.150, A:L.152, A:L.152, A:I.257, A:I.277
- Hydrogen bonds: A:Q.179, A:T.273
- Water bridges: A:R.175, A:K.263
- Salt bridges: A:R.175, A:K.263, A:K.263
- Metal complexes: A:H.138, A:H.275
HEC.5: 28 residues within 4Å:- Chain A: Q.36, P.65, R.66, G.67, H.68, F.70, A.71, D.74, C.99, K.100, L.132, D.136, C.137, R.156, V.182, C.183, C.186, H.187, C.256, I.257, H.260, M.261, I.277, G.278
- Ligands: EU.2, HEC.3, HEC.4, HEC.6
14 PLIP interactions:14 interactions with chain A,- Hydrophobic interactions: A:P.65, A:A.71, A:K.100, A:L.132, A:L.132, A:I.257, A:H.260, A:I.277, A:I.277
- Hydrogen bonds: A:Q.36, A:F.70, A:D.74
- Metal complexes: A:H.68, A:H.187
HEC.6: 23 residues within 4Å:- Chain A: P.65, C.183, H.187, E.240, Y.241, W.244, H.249, V.254, T.255, C.256, C.259, H.260, P.280, F.281, V.303, H.362, G.363, H.365, M.366, H.367
- Ligands: EU.2, HEC.5, HEC.7
14 PLIP interactions:14 interactions with chain A,- Hydrophobic interactions: A:H.187, A:E.240, A:W.244, A:W.244, A:H.249, A:V.254, A:P.280, A:F.281, A:H.362
- Water bridges: A:N.279, A:H.362
- Salt bridges: A:H.365
- Metal complexes: A:H.260, A:H.367
HEC.7: 23 residues within 4Å:- Chain A: I.248, H.249, N.252, V.254, D.258, C.259, P.280, F.281, T.287, C.288, C.291, H.292, L.299, V.302, R.306, M.366
- Chain B: I.248, H.292, Q.294
- Ligands: HEC.6, EU.8, EU.9, HEC.16
15 PLIP interactions:3 interactions with chain B, 12 interactions with chain A,- Hydrophobic interactions: B:I.248, A:N.252, A:V.254, A:D.258, A:P.280, A:F.281, A:L.299, A:V.302
- Hydrogen bonds: B:Q.294
- Salt bridges: B:H.292, A:R.306
- Water bridges: A:I.248, A:R.306
- Metal complexes: A:H.249, A:H.292
HEC.12: 23 residues within 4Å:- Chain B: Y.62, N.63, P.65, D.74, T.78, R.80, T.81, L.92, A.95, C.96, C.99, K.100, Q.185, C.186, H.187, Y.190, F.192, V.199, F.201, H.238, A.360, H.362
- Ligands: HEC.14
24 PLIP interactions:23 interactions with chain B, 1 Ligand-Water interactions- Hydrophobic interactions: B:P.65, B:T.78, B:T.81, B:L.92, B:Y.190, B:Y.190, B:Y.190, B:F.192, B:V.199, B:V.199, B:F.201, B:H.238
- Hydrogen bonds: B:N.63, B:N.63
- Water bridges: B:Y.62, B:Y.62, B:R.80, B:E.240, B:A.360
- Salt bridges: B:R.80, B:H.238, B:H.362
- pi-Stacking: B:H.238
- Metal complexes: H2O.25
HEC.13: 25 residues within 4Å:- Chain B: F.19, H.23, Q.26, Y.27, W.30, H.68, L.132, G.133, C.134, C.137, H.138, F.145, G.148, P.150, L.152, R.175, Q.179, I.257, M.261, K.263, Y.272, T.273, H.275, I.277
- Ligands: HEC.14
23 PLIP interactions:23 interactions with chain B,- Hydrophobic interactions: B:F.19, B:H.23, B:Q.26, B:Q.26, B:Y.27, B:W.30, B:L.132, B:F.145, B:F.145, B:L.152, B:L.152, B:I.257, B:T.273, B:I.277
- Hydrogen bonds: B:Q.179, B:T.273
- Water bridges: B:T.273, B:T.273
- Salt bridges: B:R.175, B:K.263, B:K.263
- Metal complexes: B:H.138, B:H.275
HEC.14: 28 residues within 4Å:- Chain B: Q.36, P.65, R.66, G.67, H.68, F.70, A.71, D.74, C.99, K.100, L.132, D.136, C.137, R.156, V.182, C.183, C.186, H.187, C.256, I.257, H.260, M.261, I.277, G.278
- Ligands: EU.11, HEC.12, HEC.13, HEC.15
13 PLIP interactions:13 interactions with chain B,- Hydrophobic interactions: B:P.65, B:A.71, B:K.100, B:L.132, B:L.132, B:I.257, B:H.260, B:I.277
- Hydrogen bonds: B:Q.36, B:F.70, B:D.74
- Metal complexes: B:H.68, B:H.187
HEC.15: 24 residues within 4Å:- Chain B: P.65, C.183, H.187, E.240, Y.241, W.244, H.249, V.254, T.255, C.256, C.259, H.260, N.279, P.280, F.281, V.303, H.362, G.363, H.365, M.366, H.367
- Ligands: EU.11, HEC.14, HEC.16
14 PLIP interactions:14 interactions with chain B,- Hydrophobic interactions: B:H.187, B:E.240, B:W.244, B:W.244, B:H.249, B:P.280, B:F.281, B:H.362
- Hydrogen bonds: B:N.279
- Water bridges: B:H.362
- Salt bridges: B:K.307, B:H.365
- Metal complexes: B:H.260, B:H.367
HEC.16: 22 residues within 4Å:- Chain A: I.248, H.292, Q.294
- Chain B: I.248, H.249, N.252, V.254, D.258, C.259, P.280, F.281, T.287, C.288, C.291, H.292, V.302, R.306, M.366
- Ligands: HEC.7, EU.8, EU.9, HEC.15
11 PLIP interactions:3 interactions with chain A, 8 interactions with chain B,- Hydrophobic interactions: A:I.248, B:N.252, B:V.254, B:P.280, B:F.281, B:V.302
- Hydrogen bonds: A:Q.294
- Salt bridges: A:H.292, B:R.306
- Metal complexes: B:H.249, B:H.292
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lockwood, C.W. et al., Characterization of the active site and calcium binding in cytochrome c nitrite reductases. Biochem.Soc.Trans. (2011)
- Release Date
- 2011-12-07
- Peptides
- Cytochrome c nitrite reductase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x CA: CALCIUM ION(Non-covalent)
- 4 x EU: EUROPIUM ION(Non-covalent)(Non-functional Binders)
- 10 x HEC: HEME C(Covalent)(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lockwood, C.W. et al., Characterization of the active site and calcium binding in cytochrome c nitrite reductases. Biochem.Soc.Trans. (2011)
- Release Date
- 2011-12-07
- Peptides
- Cytochrome c nitrite reductase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
D