Calcium 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:

Iron	(Fe)	2 atoms
Chlorine	(Cl)	1 atom
Sodium	(Na)	2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Peroxidase A From Dictyostelium Discoideum (Ddpoxa) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:47.4 occ:1.00 HG A:SER326 2.1 65.7 1.0 OG A:SER326 2.3 54.7 1.0 O A:HOH755 2.3 42.9 1.0 OD1 A:ASP377 2.4 54.5 1.0 O A:TYR379 2.4 56.9 1.0 O A:HOH707 2.4 42.5 1.0 O A:ASN375 2.4 54.6 1.0 O A:SER326 2.5 54.6 1.0 C A:SER326 3.2 54.6 1.0 HA A:SER326 3.3 64.4 1.0 HG3 A:GLU374 3.3 69.2 1.0 H A:ASP377 3.3 69.7 1.0 HB2 A:TYR379 3.4 69.3 1.0 CB A:SER326 3.4 53.5 1.0 CG A:ASP377 3.4 56.4 1.0 C A:TYR379 3.5 56.5 1.0 CA A:SER326 3.5 53.6 1.0 C A:ASN375 3.6 55.1 1.0 H A:TYR379 3.8 69.2 1.0 HG2 A:GLU374 3.8 69.2 1.0 OD2 A:ASP377 3.9 57.5 1.0 HB3 A:SER326 3.9 64.2 1.0 HA A:ILE376 3.9 68.8 1.0 N A:ASP377 4.0 58.1 1.0 CG A:GLU374 4.0 57.7 1.0 HB2 A:SER326 4.1 64.2 1.0 HA A:MET380 4.1 67.7 1.0 CA A:TYR379 4.1 58.1 1.0 HB3 A:GLU374 4.1 65.6 1.0 OE1 A:GLN78 4.1 57.8 1.0 CB A:TYR379 4.2 57.7 1.0 O A:ASP377 4.2 57.7 1.0 N A:TYR379 4.2 57.7 1.0 O A:HOH752 4.3 43.4 1.0 HA A:GLU327 4.3 66.0 1.0 H A:ASN375 4.3 69.3 1.0 HE22 A:GLN78 4.3 68.8 1.0 HB3 A:ASN375 4.3 68.6 1.0 N A:GLU327 4.4 53.0 1.0 N A:ASN375 4.4 57.7 1.0 N A:MET380 4.5 55.8 1.0 N A:ILE376 4.5 56.3 1.0 C A:ASP377 4.5 57.9 1.0 CA A:ASN375 4.5 56.9 1.0 CA A:ILE376 4.6 57.3 1.0 HD2 A:TYR379 4.6 69.4 1.0 CA A:ASP377 4.6 57.9 1.0 CB A:ASP377 4.6 58.1 1.0 CB A:GLU374 4.6 54.7 1.0 HB3 A:TYR379 4.7 69.3 1.0 C A:ILE376 4.7 59.0 1.0 CA A:MET380 4.8 56.4 1.0 CD A:GLN78 4.8 58.0 1.0 NE2 A:GLN78 4.8 57.3 1.0 HD13 A:ILE82 4.8 73.9 1.0 CA A:GLU327 4.9 55.0 1.0 N A:SER326 5.0 52.5 1.0 C A:GLU374 5.0 55.5 1.0 CB A:ASN375 5.0 57.2 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Peroxidase A From Dictyostelium Discoideum (Ddpoxa) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:51.8 occ:1.00 HG B:SER326 2.1 70.0 1.0 OD1 B:ASP377 2.3 59.2 1.0 O B:TYR379 2.3 59.2 1.0 OG B:SER326 2.4 58.3 1.0 O B:SER326 2.4 57.2 1.0 O B:ASN375 2.4 60.5 1.0 O B:HOH724 2.4 46.0 1.0 O B:HOH748 2.5 48.2 1.0 H B:ASP377 3.1 72.7 1.0 C B:SER326 3.3 57.7 1.0 C B:TYR379 3.5 60.5 1.0 CG B:ASP377 3.5 61.0 1.0 HB2 B:TYR379 3.5 75.3 1.0 HA B:SER326 3.5 67.8 1.0 CB B:SER326 3.5 56.5 1.0 HB3 B:GLU374 3.5 74.7 1.0 C B:ASN375 3.7 60.6 1.0 CA B:SER326 3.7 56.5 1.0 H B:TYR379 3.8 74.7 1.0 N B:ASP377 3.9 60.5 1.0 HA B:ILE376 4.0 69.6 1.0 HB3 B:SER326 4.1 67.7 1.0 OD2 B:ASP377 4.1 61.7 1.0 HA B:MET380 4.1 70.0 1.0 HB2 B:SER326 4.2 67.7 1.0 O B:ASP377 4.2 59.5 1.0 CA B:TYR379 4.2 62.6 1.0 N B:TYR379 4.2 62.3 1.0 HA B:GLU327 4.2 71.9 1.0 CB B:TYR379 4.3 62.7 1.0 H B:ASN375 4.3 74.6 1.0 O B:HOH750 4.4 43.0 1.0 N B:ASN375 4.4 62.2 1.0 N B:GLU327 4.4 58.1 1.0 CB B:GLU374 4.4 62.3 1.0 C B:ASP377 4.4 61.0 1.0 HE22 B:GLN78 4.5 76.2 1.0 OE1 B:GLN78 4.5 60.9 1.0 HB2 B:GLU374 4.5 74.7 1.0 N B:MET380 4.5 59.7 1.0 CA B:ASP377 4.5 60.4 1.0 HB3 B:ASN375 4.6 73.8 1.0 N B:ILE376 4.6 59.6 1.0 CA B:ASN375 4.6 61.8 1.0 CA B:ILE376 4.6 58.0 1.0 CB B:ASP377 4.6 61.6 1.0 C B:ILE376 4.7 59.4 1.0 HB3 B:TYR379 4.8 75.3 1.0 HD2 B:TYR379 4.8 78.2 1.0 CA B:MET380 4.8 58.3 1.0 CA B:GLU327 4.8 59.9 1.0 C B:GLU374 4.9 61.2 1.0 NE2 B:GLN78 4.9 63.5 1.0 CD B:GLN78 5.0 63.0 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