Sodium in PDB 5ksk: Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate

All present enzymatic activity of Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate:
1.11.1.21;

The structure of Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate, PDB code: 5ksk was solved by P.C.Loewen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.39 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.703, 115.480, 174.966, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 18

The structure of Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate (pdb code 5ksk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate, PDB code: 5ksk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:19.2 occ:1.00 O A:GLY124 2.3 16.6 1.0 O A:HOH1495 2.3 23.1 1.0 O A:SER494 2.4 19.6 1.0 O A:GLY122 2.4 17.3 1.0 O A:HOH1045 2.4 20.9 1.0 C A:SER494 3.3 16.9 1.0 C A:GLY124 3.4 17.2 1.0 C A:GLY122 3.5 17.2 1.0 N A:GLY124 3.6 16.5 1.0 C A:ARG123 3.6 18.0 1.0 CA A:ARG123 3.6 17.6 1.0 O A:HOH1559 3.8 22.3 1.0 OD2 A:ASP427 4.0 21.1 1.0 CA A:SER494 4.0 17.6 1.0 O A:HOH1278 4.0 30.6 1.0 N A:ARG123 4.1 17.1 1.0 CB A:ASP427 4.1 20.1 1.0 CA A:GLY124 4.1 17.5 1.0 CB A:SER494 4.2 18.1 1.0 N A:ASP495 4.2 16.6 1.0 O A:ARG123 4.2 16.8 1.0 CA A:ASP495 4.5 18.5 1.0 N A:GLY125 4.5 16.9 1.0 CL A:CL803 4.6 30.9 1.0 CG A:ASP427 4.6 22.0 1.0 CD1 A:TYR117 4.6 17.8 1.0 CB A:ASP495 4.7 17.3 1.0 CA A:GLY122 4.8 19.6 1.0 CA A:GLY125 4.8 17.1 1.0 CE1 A:TYR117 4.9 17.6 1.0 CB A:ARG123 4.9 20.1 1.0 O A:HOH1011 5.0 43.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:20.6 occ:1.00 O B:GLY122 2.3 17.5 1.0 O B:HOH1015 2.4 23.1 1.0 O B:HOH1488 2.4 26.5 1.0 O B:GLY124 2.4 18.3 1.0 O B:SER494 2.4 22.0 1.0 C B:SER494 3.3 20.2 1.0 C B:GLY122 3.5 17.6 1.0 C B:GLY124 3.6 17.8 1.0 N B:GLY124 3.6 18.2 1.0 C B:ARG123 3.6 18.3 1.0 CA B:ARG123 3.6 17.0 1.0 O B:HOH1537 3.9 24.1 1.0 CA B:SER494 4.0 19.2 1.0 O B:HOH1115 4.0 32.4 1.0 OD2 B:ASP427 4.0 22.2 1.0 N B:ARG123 4.1 15.5 1.0 CB B:SER494 4.1 19.0 1.0 N B:ASP495 4.1 17.8 1.0 CB B:ASP427 4.2 21.2 1.0 CA B:GLY124 4.2 17.8 1.0 O B:ARG123 4.2 17.4 1.0 CA B:ASP495 4.4 18.6 1.0 CB B:ASP495 4.6 17.9 1.0 CD1 B:TYR117 4.6 19.7 1.0 CL B:CL803 4.7 32.6 1.0 N B:GLY125 4.7 16.7 1.0 CG B:ASP427 4.7 22.4 1.0 CA B:GLY122 4.8 17.4 1.0 CE1 B:TYR117 4.8 17.1 1.0 CA B:GLY125 4.9 17.3 1.0 CB B:ARG123 4.9 17.5 1.0 OG B:SER494 5.0 17.8 1.0

M.Machuqueiro, B.Victor, J.Switala, J.Villanueva, C.Rovira, I.Fita, P.C.Loewen. The Catalase Activity of Catalase-Peroxidases Is Modulated By Changes in the Pka of the Distal Histidine. Biochemistry V. 56 2271 2017.
ISSN: ISSN 1520-4995
PubMed: 28409923
DOI: 10.1021/ACS.BIOCHEM.6B01276