SMTL ID : 2qfk.1 (2 other biounits)

X-ray Crystal Structure Analysis of the Binding Site in the Ferric and Oxyferrous Forms of the Recombinant Heme Dehaloperoxidase Cloned from Amphitrite ornata

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-dimer

Ligands

3 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.1: 1 residues within 4Å: Chain A: Q.113 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.113, A:Q.113 NH4.2: 3 residues within 4Å: Chain A: D.116, S.117, Q.118 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.116, A:D.116, A:Q.118 Water bridges: A:S.117, A:S.119 NH4.5: 3 residues within 4Å: Chain B: R.109, Q.118, D.121 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.109, B:D.121, B:D.121 Water bridges: B:R.109

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

SO4.3: 3 residues within 4Å: Chain A: R.32, V.39, G.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.40 Water bridges: A:R.32 Salt bridges: A:R.32 SO4.6: 3 residues within 4Å: Chain B: R.32, V.39, G.40 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.40 Salt bridges: B:R.32 SO4.7: 2 residues within 4Å: Chain B: G.95, K.99 5 PLIP interactions: 5 interactions with chain B Water bridges: B:T.93, B:T.94, B:G.95, B:K.99 Salt bridges: B:K.99

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

HEM.4: 18 residues within 4Å: Chain A: F.24, E.31, Y.34, F.35, H.55, K.58, V.59, L.62, M.63, L.83, Q.88, H.89, L.92, N.96, F.97, L.100, F.101, L.127 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:F.24, A:Y.34, A:F.35, A:K.58, A:V.59, A:L.62, A:L.62, A:L.83, A:Q.88, A:L.92, A:L.92, A:F.97, A:L.100, A:F.101, A:L.127 Hydrogen bonds: A:Q.88 pi-Stacking: A:H.55 pi-Cation interactions: A:H.55 Metal complexes: A:H.89, H2O.6 HEM.8: 18 residues within 4Å: Chain B: F.24, E.31, Y.34, F.35, H.55, K.58, V.59, M.63, L.83, M.86, Q.88, H.89, L.92, N.96, F.97, L.100, F.101, L.127 20 PLIP interactions: 19 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:F.24, B:F.35, B:K.58, B:V.59, B:V.59, B:L.83, B:Q.88, B:L.92, B:L.92, B:F.97, B:F.101, B:L.127 Hydrogen bonds: B:Q.88 Water bridges: B:K.51 Salt bridges: B:H.55, B:K.58 pi-Cation interactions: B:H.55, B:H.55 Metal complexes: B:H.89, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Serrano, V.S. et al., X-ray crystal structural analysis of the binding site in the ferric and oxyferrous forms of the recombinant heme dehaloperoxidase cloned from Amphitrite ornata. Acta Crystallogr.,Sect.D (2007)

Release Date

2008-07-08

Peptides

Dehaloperoxidase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dehaloperoxidase A

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