Sodium in PDB 5syv: Crystal Structure of Burkholderia Pseudomallei Katg N240D Variant

All present enzymatic activity of Crystal Structure of Burkholderia Pseudomallei Katg N240D Variant:
1.11.1.21;

The structure of Crystal Structure of Burkholderia Pseudomallei Katg N240D Variant, PDB code: 5syv 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)	48.00 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.792, 113.296, 174.520, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19

The structure of Crystal Structure of Burkholderia Pseudomallei Katg N240D Variant 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 Burkholderia Pseudomallei Katg N240D Variant (pdb code 5syv). 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 Burkholderia Pseudomallei Katg N240D Variant, PDB code: 5syv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Burkholderia Pseudomallei Katg N240D Variant


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 Burkholderia Pseudomallei Katg N240D Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:12.3 occ:1.00 O A:HOH1080 2.2 16.9 1.0 O A:GLY124 2.3 12.4 1.0 O A:GLY122 2.4 11.7 1.0 O A:HOH1534 2.4 14.6 1.0 O A:SER494 2.4 15.2 1.0 C A:SER494 3.2 14.8 1.0 C A:GLY124 3.5 12.6 1.0 C A:GLY122 3.5 13.2 1.0 N A:GLY124 3.5 12.6 1.0 CA A:ARG123 3.6 12.0 1.0 C A:ARG123 3.6 13.0 1.0 O A:HOH1582 3.9 17.3 1.0 OD2 A:ASP427 4.0 14.3 1.0 CA A:SER494 4.0 14.1 1.0 N A:ARG123 4.0 13.0 1.0 O A:HOH1029 4.0 19.1 1.0 CA A:GLY124 4.1 13.0 1.0 O A:ARG123 4.1 11.6 1.0 N A:ASP495 4.1 13.6 1.0 CB A:ASP427 4.2 14.9 1.0 CB A:SER494 4.2 14.2 1.0 CA A:ASP495 4.5 12.8 1.0 CL A:CL803 4.5 26.2 1.0 CB A:ASP495 4.6 12.8 1.0 CG A:ASP427 4.6 15.5 1.0 N A:GLY125 4.6 11.8 1.0 CD1 A:TYR117 4.7 12.0 1.0 CA A:GLY122 4.8 12.6 1.0 CA A:GLY125 4.9 11.1 1.0 CB A:ARG123 4.9 13.0 1.0 O A:HOH1465 4.9 34.4 1.0 CE1 A:TYR117 5.0 12.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Burkholderia Pseudomallei Katg N240D Variant


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 Burkholderia Pseudomallei Katg N240D Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:12.5 occ:1.00 O B:HOH1460 2.2 17.8 1.0 O B:GLY122 2.3 10.7 1.0 O B:HOH1164 2.3 16.8 1.0 O B:GLY124 2.4 14.7 1.0 O B:SER494 2.4 11.9 1.0 C B:SER494 3.2 12.6 1.0 C B:GLY122 3.4 12.0 1.0 C B:GLY124 3.5 12.5 1.0 N B:GLY124 3.6 11.7 1.0 CA B:ARG123 3.6 10.9 1.0 C B:ARG123 3.6 11.5 1.0 CA B:SER494 3.9 11.8 1.0 N B:ARG123 3.9 12.2 1.0 O B:HOH1539 4.0 17.5 1.0 O B:HOH1023 4.0 20.5 1.0 OD2 B:ASP427 4.1 15.4 1.0 N B:ASP495 4.1 11.9 1.0 O B:ARG123 4.1 11.2 1.0 CB B:SER494 4.1 12.5 1.0 CB B:ASP427 4.1 16.5 1.0 CA B:GLY124 4.1 12.6 1.0 CA B:ASP495 4.4 13.2 1.0 CB B:ASP495 4.5 12.9 1.0 CG B:ASP427 4.6 16.3 1.0 N B:GLY125 4.6 11.8 1.0 CD1 B:TYR117 4.6 12.7 1.0 CL B:CL803 4.7 24.9 1.0 CA B:GLY122 4.7 11.6 1.0 CE1 B:TYR117 4.9 12.5 1.0 O B:HOH1293 4.9 33.5 1.0 CB B:ARG123 4.9 11.7 1.0 CA B:GLY125 4.9 11.3 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