SMTL ID : 1iqc.2 (1 other biounit)

Crystal structure of Di-Heme Peroxidase from Nitrosomonas europaea

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: N.67, T.239, P.241 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:P.241, H2O.1, H2O.1, H2O.1, H2O.2 CA.5: 3 residues within 4Å: Chain B: N.67, T.239, P.241 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.239, B:P.241, H2O.9, H2O.11, H2O.11

4 x HEC: HEME C(Non-covalent)

HEC.2: 26 residues within 4Å: Chain A: F.26, I.37, S.38, C.39, C.42, H.43, S.56, I.57, I.66, A.68, P.69, V.71, N.77, Q.80, F.81, W.82, R.85, L.89, Q.92, A.93, P.96, E.102, M.103, I.142, E.146, K.229 25 PLIP interactions: 24 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:F.26, A:I.37, A:I.66, A:A.68, A:P.69, A:V.71, A:F.81, A:F.81, A:L.89, A:Q.92, A:P.96, A:P.96, A:E.102, A:I.142 Hydrogen bonds: A:N.77, A:F.81, A:W.82 Water bridges: A:D.83, A:R.85, A:R.85, A:K.229 Salt bridges: A:R.85, A:K.229 Metal complexes: A:H.43, H2O.8 HEC.3: 22 residues within 4Å: Chain A: W.82, F.178, G.182, C.183, C.186, H.187, Q.198, M.200, V.202, F.228, P.231, L.233, I.236, Y.242, F.243, H.244, A.254, M.258, Q.262, L.263, F.267, I.275 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:W.82, A:F.178, A:Q.198, A:V.202, A:P.231, A:L.233, A:I.236, A:F.243, A:F.243, A:A.254, A:M.258, A:Q.262, A:L.263, A:L.263, A:F.267, A:I.275 Hydrogen bonds: A:F.243, A:H.244 Salt bridges: A:H.244 Metal complexes: A:H.187 HEC.7: 26 residues within 4Å: Chain B: F.26, I.37, S.38, C.39, C.42, H.43, S.56, I.57, I.66, A.68, P.69, V.71, N.77, Q.80, F.81, W.82, R.85, L.89, Q.92, A.93, P.96, E.102, M.103, I.142, E.146, K.229 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:F.26, B:I.37, B:A.68, B:P.69, B:V.71, B:F.81, B:F.81, B:L.89, B:Q.92, B:P.96, B:P.96, B:E.102, B:I.142, B:I.142 Hydrogen bonds: B:Q.80, B:F.81, B:W.82 Salt bridges: B:R.85, B:K.229 Metal complexes: B:H.43 HEC.8: 23 residues within 4Å: Chain B: W.82, F.178, G.182, C.183, Q.185, C.186, H.187, Q.198, M.200, F.228, P.231, L.233, I.236, Y.242, F.243, H.244, V.255, M.258, G.259, Q.262, L.263, F.267, I.275 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:W.82, B:F.178, B:Q.185, B:Q.198, B:L.233, B:I.236, B:F.243, B:V.255, B:M.258, B:L.263, B:L.263, B:F.267, B:I.275 Hydrogen bonds: B:F.243, B:H.244 Salt bridges: B:H.244 Metal complexes: B:H.187

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: Y.197, R.215, T.219 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.215, A:D.224

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 1 residues within 4Å: Chain B: E.207 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimizu, H. et al., Crystal structure of Nitrosomonas europaea cytochrome c peroxidase and the structural basis for ligand switching in bacterial di-heme peroxidases. Biochemistry (2001)

Release Date

2002-01-23

Peptides

di-heme peroxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

di-heme peroxidase

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