- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.40 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x HEC: HEME C(Covalent)
- 2 x DHE: HEME D(Non-covalent)
DHE.2: 26 residues within 4Å:- Chain A: S.25, P.27, S.28, M.106, W.109, R.174, H.200, I.201, R.203, R.216, R.243, S.244, I.245, Y.263, A.301, A.302, I.303, H.345, R.391, F.444, Q.507, W.522, T.554, G.555, F.557
- Ligands: SO4.3
36 PLIP interactions:36 interactions with chain A,- Hydrophobic interactions: A:W.109, A:I.201, A:I.201, A:R.243, A:R.243, A:F.444, A:F.444, A:W.522, A:T.554, A:F.557
- Hydrogen bonds: A:S.28, A:I.245, A:Y.263, A:Y.263, A:I.303, A:Q.507
- Water bridges: A:R.174, A:R.174, A:R.203, A:R.203, A:R.203, A:R.203, A:K.446, A:K.446, A:K.446, A:G.555
- Salt bridges: A:R.174, A:H.200, A:H.200, A:R.203, A:R.203, A:R.216, A:R.243, A:R.391, A:K.446
- Metal complexes: A:H.200
DHE.9: 27 residues within 4Å:- Chain B: S.25, E.26, P.27, S.28, M.106, W.109, R.174, H.200, I.201, R.203, R.216, R.243, S.244, I.245, Y.263, A.301, A.302, I.303, H.345, R.391, F.444, Q.507, W.522, T.554, G.555, F.557
- Ligands: SO4.10
36 PLIP interactions:36 interactions with chain B,- Hydrophobic interactions: B:W.109, B:I.201, B:I.201, B:R.243, B:R.243, B:F.444, B:F.444, B:W.522, B:T.554, B:F.557
- Hydrogen bonds: B:S.28, B:I.245, B:Y.263, B:I.303, B:Q.507, B:T.554
- Water bridges: B:R.174, B:R.174, B:R.203, B:R.203, B:R.203, B:R.203, B:K.446, B:K.446, B:K.446, B:G.555
- Salt bridges: B:R.174, B:H.200, B:H.200, B:R.203, B:R.203, B:R.216, B:R.243, B:R.391, B:K.446
- Metal complexes: B:H.200
- 8 x SO4: SULFATE ION(Non-functional Binders)
SO4.3: 4 residues within 4Å:- Chain A: S.25, H.345, H.388
- Ligands: DHE.2
2 PLIP interactions:2 interactions with chain A- Salt bridges: A:H.345, A:H.388
SO4.6: 6 residues within 4Å:- Chain A: Y.289, D.290, E.291, Q.292
- Chain B: M.139, R.143
3 PLIP interactions:1 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:Q.292, B:R.143
- Water bridges: B:K.279
SO4.7: 3 residues within 4Å:- Chain A: Q.35, K.237, S.240
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:Q.35, A:S.240
- Water bridges: A:S.240, A:S.240, A:S.240
- Salt bridges: A:K.237
SO4.10: 4 residues within 4Å:- Chain B: S.25, H.345, H.388
- Ligands: DHE.9
4 PLIP interactions:4 interactions with chain B- Water bridges: B:S.25, B:D.346
- Salt bridges: B:H.345, B:H.388
SO4.12: 3 residues within 4Å:- Chain B: Y.308, R.354, K.372
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:Y.308, B:Y.308
- Water bridges: B:R.354, B:R.354, B:R.354
- Salt bridges: B:R.354, B:K.372
SO4.13: 4 residues within 4Å:- Chain B: N.31, Q.35, K.237, S.240
8 PLIP interactions:8 interactions with chain B- Hydrogen bonds: B:N.31, B:Q.35, B:S.240
- Water bridges: B:N.31, B:Q.34, B:S.240, B:S.240
- Salt bridges: B:K.237
SO4.14: 3 residues within 4Å:- Chain B: F.395, V.396, P.449
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:V.396
- Water bridges: B:P.449
SO4.15: 4 residues within 4Å:- Chain B: G.439, G.440, N.461, I.466
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:G.440, B:N.461
- Water bridges: B:D.412
- 3 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 13 residues within 4Å:- Chain A: N.23, R.24, S.25, E.26, P.27, S.28, E.63, R.64, P.103, A.104, G.105, T.111
- Ligands: HEC.1
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:N.23, A:E.26, A:E.26
- Water bridges: A:S.28, A:G.67, A:M.106
GOL.5: 5 residues within 4Å:- Chain A: F.395, V.396, P.449, S.451, I.475
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:V.396, A:P.449
GOL.11: 12 residues within 4Å:- Chain B: N.23, R.24, S.25, E.26, P.27, E.63, R.64, P.103, A.104, G.105, T.111
- Ligands: HEC.8
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:N.23, B:E.26, B:E.26
- Water bridges: B:S.28, B:M.106
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gordon, E.H.J. et al., Structure and Kinetic Properties of Paracoccus Pantotrophus Cytochrome Cd1 Nitrite Reductase with the D1 Heme Active Site Ligand Tyrosine 25 Replaced by Serine. J.Biol.Chem. (2003)
- Release Date
- 2002-11-28
- Peptides
- CYTOCHROME CD1 NITRITE REDUCTASE: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.40 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x HEC: HEME C(Covalent)
- 2 x DHE: HEME D(Non-covalent)
- 8 x SO4: SULFATE ION(Non-functional Binders)
- 3 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gordon, E.H.J. et al., Structure and Kinetic Properties of Paracoccus Pantotrophus Cytochrome Cd1 Nitrite Reductase with the D1 Heme Active Site Ligand Tyrosine 25 Replaced by Serine. J.Biol.Chem. (2003)
- Release Date
- 2002-11-28
- Peptides
- CYTOCHROME CD1 NITRITE REDUCTASE: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B