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

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

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Peroxidase A From Dictyostelium Discoideum (Ddpoxa) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na609 b:57.0 occ:1.00 O A:TYR169 2.3 54.0 1.0 OD1 A:ASN173 2.4 58.1 1.0 O A:ASN102 2.4 56.1 1.0 OD1 A:ASP171 2.5 59.2 1.0 O A:GLY167 2.6 55.9 1.0 CG A:ASP171 3.3 59.0 1.0 CG A:ASN173 3.4 59.2 1.0 C A:GLY167 3.4 56.1 1.0 C A:ASN102 3.4 55.9 1.0 H A:ASP171 3.4 69.0 1.0 HA3 A:GLY167 3.5 68.8 1.0 O A:HOH706 3.5 58.4 1.0 C A:TYR169 3.5 53.0 1.0 OD2 A:ASP171 3.5 60.3 1.0 O A:HOH781 3.6 46.1 1.0 HB3 A:ASN173 3.6 72.3 1.0 HA A:ASN102 3.9 67.3 1.0 HA A:MET103 3.9 66.5 1.0 CA A:GLY167 3.9 57.4 1.0 H A:TYR169 3.9 68.0 1.0 HA A:ILE170 4.0 66.2 1.0 N A:TYR169 4.1 56.7 1.0 CB A:ASN173 4.1 60.2 1.0 H A:GLY167 4.1 71.6 1.0 H A:ASN173 4.1 69.9 1.0 N A:ASP171 4.1 57.5 1.0 CA A:ASN102 4.2 56.1 1.0 HB3 A:ASN102 4.2 68.0 1.0 N A:GLY167 4.2 59.7 1.0 HG A:LEU166 4.3 69.3 1.0 N A:MET103 4.3 57.5 1.0 ND2 A:ASN173 4.3 59.3 1.0 CA A:TYR169 4.4 54.9 1.0 HD21 A:ASN173 4.4 71.2 1.0 N A:SER168 4.4 55.9 1.0 C A:SER168 4.5 54.3 1.0 CB A:ASP171 4.5 59.2 1.0 N A:ILE170 4.5 52.1 1.0 HD23 A:LEU166 4.5 70.4 1.0 CA A:MET103 4.5 55.4 1.0 HB2 A:TYR169 4.6 65.8 1.0 CA A:ILE170 4.7 55.2 1.0 HB2 A:ASN173 4.7 72.3 1.0 HB3 A:ASP171 4.7 71.0 1.0 CB A:ASN102 4.7 56.6 1.0 HA2 A:GLY167 4.8 68.8 1.0 CA A:ASP171 4.8 57.8 1.0 N A:ASN173 4.9 58.3 1.0 CA A:SER168 4.9 54.9 1.0 HA A:SER168 4.9 65.8 1.0 C A:ILE170 4.9 56.5 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Peroxidase A From Dictyostelium Discoideum (Ddpoxa) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na606 b:68.7 occ:1.00 O B:TYR169 2.4 79.2 1.0 O B:ASN102 2.4 76.8 1.0 OD1 B:ASP171 2.4 81.3 1.0 OD1 B:ASN173 2.5 77.4 1.0 O B:GLY167 2.7 80.4 1.0 H B:ASP171 3.1 96.2 1.0 CG B:ASP171 3.1 82.5 1.0 OD2 B:ASP171 3.4 83.9 1.0 C B:ASN102 3.4 76.0 1.0 C B:GLY167 3.4 80.7 1.0 HA3 B:GLY167 3.5 98.2 1.0 CG B:ASN173 3.5 77.3 1.0 C B:TYR169 3.6 79.0 1.0 HB3 B:ASN173 3.7 94.1 1.0 HA B:MET103 3.8 92.0 1.0 CA B:GLY167 3.8 81.8 1.0 H B:GLY167 3.9 97.0 1.0 H B:ASN173 3.9 93.8 1.0 N B:ASP171 3.9 80.1 1.0 HA B:ASN102 3.9 89.9 1.0 HA B:ILE170 4.0 91.6 1.0 H B:TYR169 4.1 95.6 1.0 HB3 B:ASN102 4.1 90.6 1.0 N B:GLY167 4.2 80.8 1.0 N B:TYR169 4.2 79.7 1.0 CB B:ASN173 4.2 78.5 1.0 CA B:ASN102 4.2 74.9 1.0 N B:MET103 4.3 75.7 1.0 CB B:ASP171 4.4 81.8 1.0 HB3 B:LEU166 4.4 90.5 1.0 CA B:TYR169 4.5 79.8 1.0 N B:SER168 4.5 79.7 1.0 N B:ILE170 4.5 77.1 1.0 CA B:MET103 4.5 76.7 1.0 ND2 B:ASN173 4.6 76.2 1.0 C B:SER168 4.6 78.4 1.0 HB2 B:TYR169 4.6 95.5 1.0 CA B:ILE170 4.6 76.3 1.0 HB3 B:ASP171 4.6 98.2 1.0 HD21 B:ASN173 4.7 91.4 1.0 CA B:ASP171 4.7 80.9 1.0 HD22 B:LEU166 4.7 90.7 1.0 CB B:ASN102 4.7 75.5 1.0 N B:ASN173 4.7 78.2 1.0 H B:GLY172 4.7 92.4 1.0 HA2 B:GLY167 4.8 98.2 1.0 C B:ILE170 4.8 77.6 1.0 HB2 B:ASN173 4.8 94.1 1.0 HA B:SER168 4.9 94.9 1.0 CA B:SER168 4.9 79.1 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