SMTL ID : 3car.2 (1 other biounit)

REDUCED STRUCTURE OF THE ACIDIC CYTOCHROME C3 FROM DESULFOVIBRIO AFRICANUS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

16 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.6, V.21, N.103 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.6, H2O.1 ZN.2: 1 residues within 4Å: Chain A: D.53 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.53, A:D.53 ZN.3: 4 residues within 4Å: Chain A: E.87 Ligands: ARS.10, ARS.11, ARS.22 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.87, A:E.87 ZN.4: 6 residues within 4Å: Chain A: E.29 Chain D: E.26, E.29 Ligands: ARS.9, ZN.37, ARS.42 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:E.26, D:E.29, A:E.29, A:E.29, H2O.21 ZN.12: 3 residues within 4Å: Chain B: H.6, V.21, N.103 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.6, H2O.7 ZN.13: 1 residues within 4Å: Chain B: D.53 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.53, B:D.53 ZN.14: 4 residues within 4Å: Chain B: E.87 Ligands: ARS.11, ARS.21, ARS.22 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.87, B:E.87 ZN.15: 6 residues within 4Å: Chain B: E.29 Chain C: E.26, E.29 Ligands: ARS.20, ZN.26, ARS.31 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:E.26, C:E.29, B:E.29, B:E.29, H2O.15 ZN.23: 3 residues within 4Å: Chain C: H.6, V.21, N.103 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.6, H2O.13 ZN.24: 1 residues within 4Å: Chain C: D.53 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.53, C:D.53 ZN.25: 4 residues within 4Å: Chain C: E.87 Ligands: ARS.32, ARS.33, ARS.44 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.87, C:E.87 ZN.26: 6 residues within 4Å: Chain B: E.26, E.29 Chain C: E.29 Ligands: ZN.15, ARS.20, ARS.31 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:E.29, C:E.29, B:E.26, B:E.29, H2O.9 ZN.34: 3 residues within 4Å: Chain D: H.6, V.21, N.103 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.6, H2O.19 ZN.35: 1 residues within 4Å: Chain D: D.53 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.53, D:D.53 ZN.36: 4 residues within 4Å: Chain D: E.87 Ligands: ARS.33, ARS.43, ARS.44 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.87, D:E.87 ZN.37: 6 residues within 4Å: Chain A: E.26, E.29 Chain D: E.29 Ligands: ZN.4, ARS.9, ARS.42 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:E.26, A:E.29, D:E.29, D:E.29, H2O.3

16 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.5: 17 residues within 4Å: Chain A: X.1, M.4, P.8, F.22, H.24, H.27, N.28, I.33, S.35, C.36, C.39, H.40, V.55, P.58, C.59, Y.78 Ligands: HEM.7 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:P.8, A:F.22, A:I.33, A:I.33, A:V.55, A:V.55, A:Y.78 Hydrogen bonds: A:C.59, A:Y.78, A:Y.78 Metal complexes: A:H.24, A:H.40 HEM.6: 17 residues within 4Å: Chain A: C.39, H.41, W.43, G.46, S.54, T.57, P.58, C.59, C.62, H.63, D.70, T.71, P.72, A.77, Y.78, Q.80, Q.81 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:W.43, A:W.43, A:W.43, A:T.57, A:T.71, A:P.72, A:A.77, A:Y.78, A:Q.80, A:Q.81 Water bridges: A:Q.81, A:Q.81, A:Q.81 Salt bridges: A:H.41 pi-Cation interactions: A:H.41 Metal complexes: A:H.41, A:H.63 HEM.7: 15 residues within 4Å: Chain A: V.21, F.22, H.27, A.31, I.33, C.39, Q.81, C.82, C.85, H.86, Q.89, K.91, G.92, P.93 Ligands: HEM.5 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:F.22, A:A.31, A:I.33, A:K.91, A:P.93 Salt bridges: A:K.30 pi-Stacking: A:H.86 Metal complexes: A:H.27, A:H.86 HEM.8: 19 residues within 4Å: Chain A: V.7, P.8, T.9, F.12, L.15, E.16, R.17, A.19, A.20, Q.75, Y.78, H.79, C.82, W.83, H.86, M.95, C.96, C.99, H.100 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:V.7, A:V.7, A:F.12, A:F.12, A:L.15, A:R.17, A:A.20, A:Q.75, A:Y.78, A:Y.78, A:W.83, A:W.83, A:W.83 Hydrogen bonds: A:E.16, A:R.17, A:R.17, A:A.20 Salt bridges: A:H.100 pi-Stacking: A:H.100 Metal complexes: A:H.79, A:H.100 HEM.16: 17 residues within 4Å: Chain B: X.1, M.4, P.8, F.22, H.24, H.27, N.28, I.33, S.35, C.36, C.39, H.40, V.55, P.58, C.59, Y.78 Ligands: HEM.18 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:P.8, B:F.22, B:I.33, B:I.33, B:V.55, B:V.55, B:Y.78 Hydrogen bonds: B:C.59, B:Y.78, B:Y.78 Metal complexes: B:H.24, B:H.40 HEM.17: 17 residues within 4Å: Chain B: C.39, H.41, W.43, G.46, S.54, T.57, P.58, C.59, C.62, H.63, D.70, T.71, P.72, A.77, Y.78, Q.80, Q.81 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:W.43, B:W.43, B:W.43, B:T.57, B:T.71, B:P.72, B:A.77, B:Y.78, B:Q.80, B:Q.81 Water bridges: B:Q.81, B:Q.81, B:Q.81 Salt bridges: B:H.41 pi-Cation interactions: B:H.41 Metal complexes: B:H.41, B:H.63 HEM.18: 15 residues within 4Å: Chain B: V.21, F.22, H.27, A.31, I.33, C.39, Q.81, C.82, C.85, H.86, Q.89, K.91, G.92, P.93 Ligands: HEM.16 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:F.22, B:A.31, B:I.33, B:K.91, B:P.93 Salt bridges: B:K.30 pi-Stacking: B:H.86 Metal complexes: B:H.27, B:H.86 HEM.19: 19 residues within 4Å: Chain B: V.7, P.8, T.9, F.12, L.15, E.16, R.17, A.19, A.20, Q.75, Y.78, H.79, C.82, W.83, H.86, M.95, C.96, C.99, H.100 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:V.7, B:V.7, B:F.12, B:F.12, B:L.15, B:R.17, B:A.20, B:Q.75, B:Y.78, B:Y.78, B:W.83, B:W.83, B:W.83 Hydrogen bonds: B:E.16, B:R.17, B:R.17, B:A.20 Salt bridges: B:H.100 pi-Stacking: B:H.100 Metal complexes: B:H.79, B:H.100 HEM.27: 17 residues within 4Å: Chain C: X.1, M.4, P.8, F.22, H.24, H.27, N.28, I.33, S.35, C.36, C.39, H.40, V.55, P.58, C.59, Y.78 Ligands: HEM.29 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:P.8, C:F.22, C:I.33, C:I.33, C:V.55, C:V.55, C:Y.78 Hydrogen bonds: C:C.59, C:Y.78, C:Y.78 Metal complexes: C:H.24, C:H.40 HEM.28: 17 residues within 4Å: Chain C: C.39, H.41, W.43, G.46, S.54, T.57, P.58, C.59, C.62, H.63, D.70, T.71, P.72, A.77, Y.78, Q.80, Q.81 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:W.43, C:W.43, C:W.43, C:T.57, C:T.71, C:P.72, C:A.77, C:Y.78, C:Q.80, C:Q.81 Water bridges: C:Q.81, C:Q.81, C:Q.81 Salt bridges: C:H.41 pi-Cation interactions: C:H.41 Metal complexes: C:H.41, C:H.63 HEM.29: 15 residues within 4Å: Chain C: V.21, F.22, H.27, A.31, I.33, C.39, Q.81, C.82, C.85, H.86, Q.89, K.91, G.92, P.93 Ligands: HEM.27 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:F.22, C:A.31, C:I.33, C:K.91, C:P.93 Salt bridges: C:K.30 pi-Stacking: C:H.86 Metal complexes: C:H.27, C:H.86 HEM.30: 19 residues within 4Å: Chain C: V.7, P.8, T.9, F.12, L.15, E.16, R.17, A.19, A.20, Q.75, Y.78, H.79, C.82, W.83, H.86, M.95, C.96, C.99, H.100 23 PLIP interactions: 23 interactions with chain C, Hydrophobic interactions: C:V.7, C:V.7, C:F.12, C:F.12, C:L.15, C:R.17, C:A.20, C:Q.75, C:Y.78, C:Y.78, C:W.83, C:W.83, C:W.83 Hydrogen bonds: C:E.16, C:R.17, C:R.17, C:A.20 Water bridges: C:H.100, C:H.100 Salt bridges: C:H.100 pi-Stacking: C:H.100 Metal complexes: C:H.79, C:H.100 HEM.38: 17 residues within 4Å: Chain D: X.1, M.4, P.8, F.22, H.24, H.27, N.28, I.33, S.35, C.36, C.39, H.40, V.55, P.58, C.59, Y.78 Ligands: HEM.40 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:P.8, D:F.22, D:I.33, D:I.33, D:V.55, D:V.55, D:Y.78 Hydrogen bonds: D:C.59, D:Y.78, D:Y.78 Metal complexes: D:H.24, D:H.40 HEM.39: 17 residues within 4Å: Chain D: C.39, H.41, W.43, G.46, S.54, T.57, P.58, C.59, C.62, H.63, D.70, T.71, P.72, A.77, Y.78, Q.80, Q.81 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:W.43, D:W.43, D:W.43, D:T.57, D:T.71, D:P.72, D:A.77, D:Y.78, D:Q.80, D:Q.81 Water bridges: D:Q.81, D:Q.81, D:Q.81 Salt bridges: D:H.41 pi-Cation interactions: D:H.41 Metal complexes: D:H.41, D:H.63 HEM.40: 15 residues within 4Å: Chain D: V.21, F.22, H.27, A.31, I.33, C.39, Q.81, C.82, C.85, H.86, Q.89, K.91, G.92, P.93 Ligands: HEM.38 9 PLIP interactions: 9 interactions with chain D, Hydrophobic interactions: D:F.22, D:A.31, D:I.33, D:K.91, D:P.93 Salt bridges: D:K.30 pi-Stacking: D:H.86 Metal complexes: D:H.27, D:H.86 HEM.41: 19 residues within 4Å: Chain D: V.7, P.8, T.9, F.12, L.15, E.16, R.17, A.19, A.20, Q.75, Y.78, H.79, C.82, W.83, H.86, M.95, C.96, C.99, H.100 23 PLIP interactions: 23 interactions with chain D, Hydrophobic interactions: D:V.7, D:V.7, D:F.12, D:F.12, D:L.15, D:R.17, D:A.20, D:Q.75, D:Y.78, D:Y.78, D:W.83, D:W.83, D:W.83 Hydrogen bonds: D:E.16, D:R.17, D:R.17, D:A.20 Water bridges: D:H.100, D:H.100 Salt bridges: D:H.100 pi-Stacking: D:H.100 Metal complexes: D:H.79, D:H.100

12 x ARS: ARSENIC(Non-covalent)

ARS.9: 6 residues within 4Å: Chain A: E.26, E.29 Chain D: E.26 Ligands: ZN.4, ZN.37, ARS.42 No protein-ligand interaction detected (PLIP) ARS.10: 2 residues within 4Å: Chain A: E.87 Ligands: ZN.3 No protein-ligand interaction detected (PLIP) ARS.11: 5 residues within 4Å: Chain A: E.87 Chain B: E.87 Ligands: ZN.3, ZN.14, ARS.22 No protein-ligand interaction detected (PLIP) ARS.20: 6 residues within 4Å: Chain B: E.26, E.29 Chain C: E.26 Ligands: ZN.15, ZN.26, ARS.31 No protein-ligand interaction detected (PLIP) ARS.21: 2 residues within 4Å: Chain B: E.87 Ligands: ZN.14 No protein-ligand interaction detected (PLIP) ARS.22: 5 residues within 4Å: Chain A: E.87 Chain B: E.87 Ligands: ZN.3, ARS.11, ZN.14 No protein-ligand interaction detected (PLIP) ARS.31: 6 residues within 4Å: Chain B: E.26 Chain C: E.26, E.29 Ligands: ZN.15, ARS.20, ZN.26 No protein-ligand interaction detected (PLIP) ARS.32: 2 residues within 4Å: Chain C: E.87 Ligands: ZN.25 No protein-ligand interaction detected (PLIP) ARS.33: 5 residues within 4Å: Chain C: E.87 Chain D: E.87 Ligands: ZN.25, ZN.36, ARS.44 No protein-ligand interaction detected (PLIP) ARS.42: 6 residues within 4Å: Chain A: E.26 Chain D: E.26, E.29 Ligands: ZN.4, ARS.9, ZN.37 No protein-ligand interaction detected (PLIP) ARS.43: 2 residues within 4Å: Chain D: E.87 Ligands: ZN.36 No protein-ligand interaction detected (PLIP) ARS.44: 5 residues within 4Å: Chain C: E.87 Chain D: E.87 Ligands: ZN.25, ARS.33, ZN.36 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Norager, S. et al., Crystal structure of the oxidised and reduced acidic cytochrome c3from Desulfovibrio africanus. J.Mol.Biol. (1999)

Release Date

2000-07-23

Peptides

CYTOCHROME C3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

CYTOCHROME C3

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