Iron in PDB 6erc: Peroxidase A From Dictyostelium Discoideum (Ddpoxa)

All present enzymatic activity of Peroxidase A From Dictyostelium Discoideum (Ddpoxa):
1.11.1.7;

The structure of Peroxidase A From Dictyostelium Discoideum (Ddpoxa), PDB code: 6erc was solved by A.Nicolussi, G.Mlynek, P.G.Furtmueller, K.Djinovic-Carugo, C.Obinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.67 / 2.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	128.253, 128.253, 146.015, 90.00, 90.00, 120.00
R / Rfree (%)	22.8 / 25.7

The structure of Peroxidase A From Dictyostelium Discoideum (Ddpoxa) also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Iron atom in the Peroxidase A From Dictyostelium Discoideum (Ddpoxa) (pdb code 6erc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Peroxidase A From Dictyostelium Discoideum (Ddpoxa), PDB code: 6erc:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Peroxidase A From Dictyostelium Discoideum (Ddpoxa)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Peroxidase A From Dictyostelium Discoideum (Ddpoxa) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe604 b:61.9 occ:1.00 FE A:HEM604 0.0 61.9 1.0 ND A:HEM604 2.0 55.1 1.0 NA A:HEM604 2.0 54.1 1.0 NC A:HEM604 2.0 52.8 1.0 NB A:HEM604 2.0 54.6 1.0 NE2 A:HIS325 2.3 57.2 1.0 O A:HOH731 3.0 41.6 1.0 C4D A:HEM604 3.0 54.0 1.0 C1D A:HEM604 3.0 52.1 1.0 C1A A:HEM604 3.0 52.1 1.0 C4C A:HEM604 3.1 51.5 1.0 C4B A:HEM604 3.1 49.5 1.0 C1B A:HEM604 3.1 49.2 1.0 C4A A:HEM604 3.1 49.8 1.0 C1C A:HEM604 3.1 47.7 1.0 CD2 A:HIS325 3.2 56.5 1.0 HD2 A:HIS325 3.3 67.8 1.0 CE1 A:HIS325 3.4 58.2 1.0 CHA A:HEM604 3.4 54.1 1.0 CHD A:HEM604 3.4 52.4 1.0 CHC A:HEM604 3.4 47.8 1.0 CHB A:HEM604 3.5 50.1 1.0 HE1 A:HIS325 3.6 69.8 1.0 HG3 A:GLN97 3.9 61.5 1.0 C3D A:HEM604 4.2 54.2 1.0 C2D A:HEM604 4.2 51.4 1.0 HD21 A:LEU399 4.2 69.7 1.0 C2A A:HEM604 4.3 50.8 1.0 C3A A:HEM604 4.3 49.4 1.0 C2B A:HEM604 4.3 47.7 1.0 C3C A:HEM604 4.3 49.5 1.0 C3B A:HEM604 4.3 48.2 1.0 C2C A:HEM604 4.3 48.1 1.0 HHA A:HEM604 4.4 64.9 1.0 HHD A:HEM604 4.4 62.9 1.0 CG A:HIS325 4.4 57.8 1.0 HHB A:HEM604 4.4 60.1 1.0 HHC A:HEM604 4.4 57.3 1.0 ND1 A:HIS325 4.4 58.2 1.0 HE21 A:GLN97 4.6 63.4 1.0 HG21 A:ILE100 4.7 63.9 1.0 CG A:GLN97 4.8 51.2 1.0 HD11 A:LEU399 4.8 70.3 1.0 NE2 A:GLN97 4.9 52.8 1.0

Iron binding site 2 out of 2 in the Peroxidase A From Dictyostelium Discoideum (Ddpoxa)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Peroxidase A From Dictyostelium Discoideum (Ddpoxa) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe602 b:53.5 occ:1.00 FE B:HEM602 0.0 53.5 1.0 NB B:HEM602 2.0 50.8 1.0 ND B:HEM602 2.1 52.6 1.0 NC B:HEM602 2.1 52.8 1.0 NA B:HEM602 2.1 53.6 1.0 NE2 B:HIS325 2.1 62.5 1.0 C4B B:HEM602 3.1 48.8 1.0 C1B B:HEM602 3.1 50.5 1.0 CD2 B:HIS325 3.1 59.6 1.0 C4A B:HEM602 3.1 52.4 1.0 C4D B:HEM602 3.1 53.1 1.0 C1A B:HEM602 3.1 54.0 1.0 C1C B:HEM602 3.1 49.8 1.0 C1D B:HEM602 3.1 52.2 1.0 C4C B:HEM602 3.1 52.3 1.0 CE1 B:HIS325 3.2 61.1 1.0 HD2 B:HIS325 3.2 71.5 1.0 HE1 B:HIS325 3.4 73.3 1.0 CHC B:HEM602 3.4 49.1 1.0 CHB B:HEM602 3.4 51.8 1.0 CHA B:HEM602 3.4 52.9 1.0 CHD B:HEM602 3.4 51.9 1.0 HG3 B:GLN97 3.9 75.4 1.0 CG B:HIS325 4.2 59.0 1.0 ND1 B:HIS325 4.2 60.6 1.0 C2A B:HEM602 4.3 53.3 1.0 C3A B:HEM602 4.3 52.9 1.0 C2B B:HEM602 4.3 47.3 1.0 C3B B:HEM602 4.3 47.4 1.0 C3D B:HEM602 4.3 53.4 1.0 C2D B:HEM602 4.3 53.0 1.0 C2C B:HEM602 4.3 48.1 1.0 C3C B:HEM602 4.3 48.7 1.0 HD21 B:LEU399 4.3 70.1 1.0 HHC B:HEM602 4.4 58.9 1.0 HHB B:HEM602 4.4 62.2 1.0 HHA B:HEM602 4.4 63.5 1.0 HHD B:HEM602 4.4 62.3 1.0 HD11 B:LEU399 4.5 69.8 1.0 HE21 B:GLN97 4.5 76.2 1.0 CG B:GLN97 4.8 62.8 1.0 NE2 B:GLN97 4.9 63.5 1.0 HE1 B:HIS101 4.9 79.0 1.0 HG21 B:ILE100 4.9 78.7 1.0

A.Nicolussi, J.D.Dunn, G.Mlynek, M.Bellei, M.Zamocky, G.Battistuzzi, K.Djinovic-Carugo, P.G.Furtmuller, T.Soldati, C.Obinger. Secreted Heme Peroxidase From Dictyostelium Discoideum: Insights Into Catalysis, Structure, and Biological Role. J. Biol. Chem. V. 293 1330 2018.
ISSN: ESSN 1083-351X
PubMed: 29242189
DOI: 10.1074/JBC.RA117.000463