SMTL ID : 2boq.1

CRYSTAL STRUCTURE OF VERSATILE PEROXIDASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 26 residues within 4Å: Chain A: E.36, H.39, E.40, L.42, R.43, T.45, F.46, P.139, E.140, P.141, I.148, L.165, L.166, S.168, H.169, I.171, A.172, A.173, A.174, D.175, K.176, V.177, F.186, L.228, S.230 Ligands: MN.7 28 PLIP interactions: 27 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:L.42, A:L.42, A:R.43, A:F.46, A:F.46, A:F.46, A:F.46, A:P.139, A:P.141, A:I.148, A:L.165, A:L.166, A:L.166, A:A.172, A:A.174, A:V.177, A:F.186, A:F.186, A:L.228 Hydrogen bonds: A:A.173, A:D.175, A:K.176, A:V.177 Water bridges: A:R.43, A:D.175 Salt bridges: A:R.43 Metal complexes: A:H.169, H2O.73

8 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.2: 2 residues within 4Å: Chain A: D.30, E.37 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.30, A:D.30, A:E.37, A:E.37, H2O.376 ZN.3: 1 residues within 4Å: Chain A: D.237 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.237, A:D.237, H2O.377, H2O.378 ZN.4: 4 residues within 4Å: Chain A: H.136, E.140 Ligands: ZN.5, CAC.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.136 ZN.5: 4 residues within 4Å: Chain A: E.140 Ligands: ZN.4, ZN.6, CAC.8 No protein-ligand interaction detected (PLIP) ZN.6: 5 residues within 4Å: Chain A: E.140, F.142, D.143 Ligands: ZN.5, CAC.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.140, A:D.143, A:D.143 ZN.11: 2 residues within 4Å: Chain A: H.293, D.318 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.293, A:D.318, H2O.379, H2O.380 ZN.12: 1 residues within 4Å: Chain A: H.95 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.95, H2O.381 ZN.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.7: 4 residues within 4Å: Chain A: E.36, E.40, D.175 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.36

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.8: 8 residues within 4Å: Chain A: H.136, V.138, E.140, D.143, S.147 Ligands: ZN.4, ZN.5, ZN.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.147 Water bridges: A:H.136

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain A: D.48, G.60, D.62, S.64 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.48, A:D.62, A:S.64, H2O.81, H2O.110 CA.10: 5 residues within 4Å: Chain A: S.170, D.187, T.189, V.192, D.194 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.187, A:D.187, A:T.189, A:V.192, A:D.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perez-Boada, M. et al., Versatile Peroxidase Oxidation of High Redox Potential Aromatic Compounds: Site-Directed Mutagenesis, Spectroscopic and Crystallographic Investigation of Three Long-Range Electron Transfer Pathways. J.Mol.Biol. (2005)

Release Date

2005-11-02

Peptides

VERSATILE PEROXIDASE VPL2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

VERSATILE PEROXIDASE VPL2