SMTL ID : 2c1v.1

CRYSTAL STRUCTURE OF THE DI-HAEM CYTOCHROME C PEROXIDASE FROM PARACOCCUS PANTOTROPHUS - Mixed VALENCE FORM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 25 residues within 4Å: Chain A: I.63, S.64, C.65, C.68, H.69, S.82, I.83, G.84, R.92, N.93, A.94, P.95, T.96, Q.106, F.107, W.108, R.111, L.115, Q.118, P.122, E.128, M.129, I.170, E.174, R.260 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:I.63, A:P.95, A:F.107, A:F.107, A:L.115, A:Q.118, A:P.122, A:E.128, A:I.170 Hydrogen bonds: A:T.96, A:F.107, A:W.108 Water bridges: A:R.111, A:R.260, A:R.260 Salt bridges: A:R.92, A:R.111, A:R.260 Metal complexes: A:H.69, H2O.20 HEC.2: 23 residues within 4Å: Chain A: W.108, F.206, G.210, C.211, C.214, H.215, H.226, F.228, L.230, F.259, R.260, A.261, A.262, L.264, Y.273, F.274, H.275, L.282, M.289, S.290, Q.293, I.294, I.306 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:W.108, A:F.206, A:H.226, A:F.228, A:L.230, A:L.264, A:L.264, A:F.274, A:L.282, A:M.289, A:Q.293, A:Q.293, A:I.294, A:I.306 Hydrogen bonds: A:F.274, A:H.275 Salt bridges: A:H.275 Metal complexes: A:H.215 HEC.6: 25 residues within 4Å: Chain B: I.63, S.64, C.65, C.68, H.69, S.82, I.83, G.84, R.92, N.93, A.94, P.95, T.96, Q.106, F.107, W.108, R.111, L.115, Q.118, P.122, E.128, M.129, I.170, E.174, R.260 20 PLIP interactions: 19 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:I.63, B:P.95, B:F.107, B:F.107, B:L.115, B:Q.118, B:P.122, B:E.128, B:I.170 Hydrogen bonds: B:T.96, B:F.107, B:W.108 Water bridges: B:R.111, B:R.260, B:R.260 Salt bridges: B:R.92, B:R.111, B:R.260 Metal complexes: B:H.69, H2O.41 HEC.7: 23 residues within 4Å: Chain B: W.108, G.210, C.211, C.214, H.215, H.226, F.228, L.230, F.259, R.260, A.261, A.262, L.264, Y.273, F.274, H.275, L.282, V.286, M.289, S.290, Q.293, I.294, I.306 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:W.108, B:H.226, B:F.228, B:L.230, B:L.264, B:L.264, B:F.274, B:L.282, B:V.286, B:M.289, B:Q.293, B:Q.293, B:I.294, B:I.306 Hydrogen bonds: B:F.274, B:H.275 Salt bridges: B:H.275 Metal complexes: B:H.215

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: N.93, T.270, P.272 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.270, A:P.272, H2O.8, H2O.16, H2O.20 CA.8: 3 residues within 4Å: Chain B: N.93, T.270, P.272 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.270, B:P.272, H2O.28, H2O.37, H2O.41

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: P.91, R.92, E.248 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.111 EDO.5: 5 residues within 4Å: Chain A: E.19, Y.216, G.217, V.218, Q.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.218 EDO.9: 3 residues within 4Å: Chain B: P.91, R.92, E.248 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.111 EDO.10: 6 residues within 4Å: Chain B: M.143, P.144, E.145, P.326, V.327, T.329 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.145 Water bridges: B:V.327, B:V.327

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Echalier, A. et al., Activation and Catalysis of the Di-Heme Cytochrome C Peroxidase from Paracoccus Pantotrophus. Structure (2006)

Release Date

2006-01-13

Peptides

DI-HAEM CYTOCHROME C PEROXIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DI-HAEM CYTOCHROME C PEROXIDASE

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