SMTL ID : 1j0p.1

Three dimensional Structure of the Y43L mutant of Tetraheme Cytochrome c3 from Desulfovibrio vulgaris Miyazaki F

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.91 Å

Oligo State

monomer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: K.102, G.103 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.103 Water bridges: A:K.102, A:K.102, A:K.102 Salt bridges: A:K.102 SO4.2: 2 residues within 4Å: Chain A: K.58 Ligands: EOH.18 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.58 Salt bridges: A:K.58

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.3: 21 residues within 4Å: Chain A: M.12, D.13, K.14, T.15, Q.17, P.18, V.19, Y.66, Y.67, M.70, H.71, C.80, V.81, H.84, L.98, T.99, G.100, C.101, C.106, H.107 Ligands: EOH.9 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:T.15, A:Q.17, A:V.19, A:V.19, A:Y.66, A:Y.67, A:V.81 Hydrogen bonds: A:K.14, A:T.15, A:Q.17 Water bridges: A:K.16, A:K.16, A:M.56, A:M.56, A:Y.66 pi-Stacking: A:Y.67 Metal complexes: A:H.71, A:H.107 HEM.4: 19 residues within 4Å: Chain A: C.34, H.35, H.36, V.38, D.43, Q.45, K.46, C.47, C.52, H.53, A.63, H.68, A.69, M.70, T.75, K.76, F.77 Ligands: EOH.7, EOH.12 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:V.38, A:Q.45, A:A.63, A:T.75, A:F.77 Hydrogen bonds: A:K.76 Salt bridges: A:H.68, A:K.76 pi-Stacking: A:F.77 Metal complexes: A:H.36, A:H.53 HEM.5: 19 residues within 4Å: Chain A: P.3, K.4, A.5, P.6, L.10, M.12, F.21, H.23, H.26, V.29, K.30, C.31, C.34, H.35, L.44, K.46, C.47 Ligands: HEM.6, EOH.23 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:P.6, A:L.10, A:L.10, A:F.21, A:F.21, A:F.21, A:V.29, A:L.44 Hydrogen bonds: A:C.47 Water bridges: A:K.46, A:A.48 Salt bridges: A:K.46 Metal complexes: A:H.23, A:H.35 HEM.6: 20 residues within 4Å: Chain A: M.12, V.19, F.21, N.22, T.25, H.26, V.29, S.79, C.80, C.83, H.84, T.87, K.94, L.98, K.105, C.106 Ligands: HEM.5, EOH.14, EOH.15, EOH.22 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:V.19, A:T.25, A:V.29, A:T.87, A:L.98, A:K.105, A:K.105 Hydrogen bonds: A:N.22, A:T.25 Water bridges: A:N.22, A:K.94, A:K.94 Salt bridges: A:K.94 pi-Stacking: A:F.21 Metal complexes: A:H.26, A:H.84

17 x EOH: ETHANOL(Non-functional Binders)

EOH.7: 4 residues within 4Å: Chain A: G.51, C.52, K.64 Ligands: HEM.4 Ligand excluded by PLIP EOH.8: 2 residues within 4Å: Chain A: H.71, K.73 Ligand excluded by PLIP EOH.9: 5 residues within 4Å: Chain A: Q.17, C.101, K.102, H.107 Ligands: HEM.3 Ligand excluded by PLIP EOH.10: 1 residues within 4Å: Chain A: K.16 Ligand excluded by PLIP EOH.11: 2 residues within 4Å: Chain A: A.5, P.6 Ligand excluded by PLIP EOH.12: 2 residues within 4Å: Chain A: G.51 Ligands: HEM.4 Ligand excluded by PLIP EOH.13: 2 residues within 4Å: Chain A: E.86, T.87 Ligand excluded by PLIP EOH.14: 4 residues within 4Å: Chain A: V.20, N.22, K.105 Ligands: HEM.6 Ligand excluded by PLIP EOH.15: 3 residues within 4Å: Chain A: A.28 Ligands: HEM.6, EOH.21 Ligand excluded by PLIP EOH.16: 1 residues within 4Å: Chain A: Y.67 Ligand excluded by PLIP EOH.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EOH.18: 2 residues within 4Å: Chain A: K.59 Ligands: SO4.2 Ligand excluded by PLIP EOH.19: 2 residues within 4Å: Chain A: K.61, S.62 Ligand excluded by PLIP EOH.20: 1 residues within 4Å: Chain A: K.64 Ligand excluded by PLIP EOH.21: 6 residues within 4Å: Chain A: T.25, H.26, K.27, A.28, V.29 Ligands: EOH.15 Ligand excluded by PLIP EOH.22: 2 residues within 4Å: Chain A: D.33 Ligands: HEM.6 Ligand excluded by PLIP EOH.23: 5 residues within 4Å: Chain A: L.10, K.11, M.12, K.46 Ligands: HEM.5 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ozawa, K. et al., Role of the aromatic ring of Tyr43 in tetraheme cytochrome c(3) from Desulfovibrio vulgaris Miyazaki F. Biophys.J. (2003)

Release Date

2003-11-19

Peptides

Cytochrome c3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytochrome c3