SMTL ID : 1ary.1

CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: SUGAR (2-MER)(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain A: A.82, R.104, I.108, G.111, V.112, F.114, N.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.104 Water bridges: A:I.108

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.57, G.75, D.77, S.79 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.57, A:D.77, A:S.79, H2O.2072, H2O.2072 CA.3: 5 residues within 4Å: Chain A: S.185, D.202, T.204, V.207, D.209 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.202, A:D.202, A:T.204, A:V.207, A:D.209

7 x IOD: IODIDE ION(Non-functional Binders)

IOD.4: 4 residues within 4Å: Chain A: A.92 Ligands: IOD.5, IOD.8, HEM.12 Ligand excluded by PLIP IOD.5: 6 residues within 4Å: Chain A: R.52, H.56, A.92 Ligands: IOD.4, IOD.6, HEM.12 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: R.52, H.56 Ligands: IOD.5, HEM.12 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: G.191, L.192 Ligands: IOD.8 Ligand excluded by PLIP IOD.8: 4 residues within 4Å: Chain A: F.230 Ligands: IOD.4, IOD.7, IOD.9 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Ligands: IOD.8, IOD.10 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: G.155 Ligands: IOD.9 Ligand excluded by PLIP

1 x K: POTASSIUM ION(Non-covalent)

K.11: 1 residues within 4Å: Chain A: Q.271 No protein-ligand interaction detected (PLIP)

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

HEM.12: 26 residues within 4Å: Chain A: R.48, K.49, L.51, R.52, F.55, P.154, G.155, P.156, I.163, L.180, L.181, A.183, H.184, L.186, A.187, S.188, Q.189, E.190, G.191, L.192, M.243, S.245, M.277 Ligands: IOD.4, IOD.5, IOD.6 28 PLIP interactions: 28 interactions with chain A, Hydrophobic interactions: A:R.48, A:L.51, A:R.52, A:F.55, A:F.55, A:F.55, A:F.55, A:P.156, A:I.163, A:L.180, A:L.181, A:A.183, A:A.187, A:Q.189, A:L.192 Hydrogen bonds: A:S.188, A:E.190, A:G.191, A:L.192 Salt bridges: A:R.48, A:K.49, A:R.52 Water bridges: A:R.48, A:K.49, A:R.52, A:R.52, A:R.52 Metal complexes: A:H.184

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Fukuyama, K. et al., Crystal structures of cyanide- and triiodide-bound forms of Arthromyces ramosus peroxidase at different pH values. Perturbations of active site residues and their implication in enzyme catalysis. J.Biol.Chem. (1995)

Peptides

PEROXIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PEROXIDASE

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