Sodium in PDB 5kq3: Crystal Structure of the D141A/Q233E Variant of Catalase-Peroxidase From B. Pseudomallei

All present enzymatic activity of Crystal Structure of the D141A/Q233E Variant of Catalase-Peroxidase From B. Pseudomallei:
1.11.1.21;

The structure of Crystal Structure of the D141A/Q233E Variant of Catalase-Peroxidase From B. Pseudomallei, PDB code: 5kq3 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)	47.73 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.044, 114.028, 174.505, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19.5

The structure of Crystal Structure of the D141A/Q233E Variant of Catalase-Peroxidase From B. Pseudomallei 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 D141A/Q233E Variant of Catalase-Peroxidase From B. Pseudomallei (pdb code 5kq3). 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 D141A/Q233E Variant of Catalase-Peroxidase From B. Pseudomallei, PDB code: 5kq3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the D141A/Q233E Variant of Catalase-Peroxidase From B. Pseudomallei


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 D141A/Q233E Variant of Catalase-Peroxidase From B. Pseudomallei within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:20.8 occ:1.00 O A:GLY124 2.3 19.9 1.0 O A:GLY122 2.3 21.2 1.0 O A:SER494 2.4 23.3 1.0 O A:HOH1384 2.4 23.8 1.0 O A:HOH949 2.4 28.7 1.0 C A:SER494 3.3 21.1 1.0 C A:GLY124 3.4 19.2 1.0 C A:GLY122 3.5 19.6 1.0 C A:ARG123 3.5 20.9 1.0 CA A:ARG123 3.6 20.6 1.0 N A:GLY124 3.6 19.6 1.0 O A:HOH1415 3.9 25.2 1.0 OD2 A:ASP427 4.0 20.7 1.0 N A:ARG123 4.0 21.5 1.0 CA A:SER494 4.0 20.0 1.0 O A:HOH1038 4.0 33.7 1.0 CA A:GLY124 4.1 19.2 1.0 O A:ARG123 4.1 21.8 1.0 CB A:ASP427 4.1 24.2 1.0 N A:ASP495 4.2 20.3 1.0 CB A:SER494 4.2 20.8 1.0 CA A:ASP495 4.5 20.1 1.0 CD1 A:TYR117 4.5 18.4 1.0 N A:GLY125 4.5 19.1 1.0 CG A:ASP427 4.6 23.8 1.0 CL A:CL803 4.6 50.5 1.0 CB A:ASP495 4.6 20.1 1.0 CE1 A:TYR117 4.7 18.8 1.0 CA A:GLY122 4.8 20.0 1.0 CA A:GLY125 4.8 17.1 1.0 CB A:ARG123 4.9 22.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the D141A/Q233E Variant of Catalase-Peroxidase From B. Pseudomallei


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 D141A/Q233E Variant of Catalase-Peroxidase From B. Pseudomallei within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:21.8 occ:1.00 O B:HOH1101 2.3 23.0 1.0 O B:GLY124 2.3 21.5 1.0 O B:GLY122 2.3 20.1 1.0 O B:SER494 2.4 23.0 1.0 O B:HOH1138 2.4 28.3 1.0 C B:SER494 3.3 21.0 1.0 C B:GLY124 3.5 19.9 1.0 C B:GLY122 3.5 18.6 1.0 CA B:ARG123 3.6 18.1 1.0 N B:GLY124 3.6 20.1 1.0 C B:ARG123 3.6 18.4 1.0 O B:HOH1352 3.8 27.2 1.0 CA B:SER494 4.0 20.6 1.0 N B:ARG123 4.0 19.4 1.0 O B:HOH978 4.0 35.2 1.0 OD2 B:ASP427 4.1 27.8 1.0 CA B:GLY124 4.1 20.0 1.0 CB B:SER494 4.1 22.3 1.0 O B:ARG123 4.1 17.3 1.0 N B:ASP495 4.2 18.7 1.0 CB B:ASP427 4.2 23.6 1.0 CL B:CL803 4.5 33.9 0.5 CA B:ASP495 4.5 19.8 1.0 N B:GLY125 4.6 20.9 1.0 CG B:ASP427 4.6 25.2 1.0 CD1 B:TYR117 4.6 19.5 1.0 CB B:ASP495 4.7 20.3 1.0 OE2 B:GLU198 4.8 31.0 0.5 CA B:GLY122 4.8 18.3 1.0 CB B:ARG123 4.8 18.8 1.0 CA B:GLY125 4.9 19.1 1.0 CE1 B:TYR117 4.9 19.6 1.0 OE1 B:GLU198 4.9 30.1 0.5 OE2 B:GLU128 5.0 43.8 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