Sodium in PDB 5v4o: Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei

All present enzymatic activity of Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei:
1.11.1.21;

The structure of Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei, PDB code: 5v4o 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)	46.20 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.828, 115.454, 175.577, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 18.1

The structure of Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei (pdb code 5v4o). 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/N240D Variant of Catalase- Peroxidase From B. Pseudomallei, PDB code: 5v4o:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the D141A/Q233E/N240D 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/N240D Variant of Catalase- Peroxidase From B. Pseudomallei within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:26.2 occ:1.00 O A:GLY124 2.4 23.9 1.0 O A:HOH1293 2.4 29.3 1.0 O A:SER494 2.4 23.7 1.0 O A:HOH1017 2.4 28.9 1.0 O A:GLY122 2.5 24.4 1.0 C A:SER494 3.3 23.4 1.0 C A:GLY124 3.5 23.0 1.0 N A:GLY124 3.6 25.1 1.0 C A:ARG123 3.6 24.2 1.0 C A:GLY122 3.6 24.0 1.0 CA A:ARG123 3.6 24.6 1.0 O A:HOH1008 3.8 46.6 1.0 O A:HOH1225 3.9 30.5 1.0 OD2 A:ASP427 4.0 28.2 1.0 CA A:SER494 4.0 21.9 1.0 N A:ARG123 4.1 23.5 1.0 CB A:ASP427 4.1 26.4 1.0 CA A:GLY124 4.1 24.6 1.0 O A:ARG123 4.1 22.2 1.0 N A:ASP495 4.2 22.8 1.0 CB A:SER494 4.3 24.1 1.0 CA A:ASP495 4.5 25.0 1.0 OE1 A:GLU198 4.6 34.7 1.0 N A:GLY125 4.6 22.3 1.0 CG A:ASP427 4.6 29.2 1.0 CD1 A:TYR117 4.7 24.7 1.0 CB A:ASP495 4.7 24.6 1.0 CA A:GLY122 4.9 23.7 1.0 OE2 A:GLU128 4.9 45.5 1.0 CB A:ARG123 4.9 24.8 1.0 CE1 A:TYR117 4.9 23.8 1.0 CA A:GLY125 4.9 22.0 1.0 O A:HOH1103 5.0 47.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the D141A/Q233E/N240D 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/N240D Variant of Catalase- Peroxidase From B. Pseudomallei within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:28.2 occ:1.00 O B:HOH914 2.2 27.9 1.0 O B:GLY124 2.4 22.7 1.0 O B:HOH943 2.4 31.1 1.0 O B:GLY122 2.4 20.7 1.0 O B:SER494 2.5 24.1 1.0 C B:SER494 3.3 23.8 1.0 N B:GLY124 3.6 22.6 1.0 C B:GLY124 3.6 23.3 1.0 C B:GLY122 3.6 21.7 1.0 C B:ARG123 3.6 23.4 1.0 CA B:ARG123 3.7 22.6 1.0 O B:HOH1243 3.9 28.8 1.0 CA B:SER494 4.0 23.4 1.0 O B:HOH1161 4.0 46.3 1.0 N B:ARG123 4.1 19.9 1.0 OD2 B:ASP427 4.1 29.8 1.0 N B:ASP495 4.1 22.9 1.0 CA B:GLY124 4.2 22.7 1.0 O B:ARG123 4.2 23.3 1.0 CB B:ASP427 4.2 27.4 1.0 CB B:SER494 4.2 22.7 1.0 OE2 B:GLU198 4.5 49.4 1.0 CA B:ASP495 4.5 23.5 1.0 CD1 B:TYR117 4.6 24.3 1.0 CB B:ASP495 4.6 23.3 1.0 N B:GLY125 4.7 21.1 1.0 CG B:ASP427 4.7 28.5 1.0 OE1 B:GLU198 4.8 36.3 1.0 CA B:GLY122 4.8 21.7 1.0 CE1 B:TYR117 4.9 24.6 1.0 OE2 B:GLU128 4.9 52.4 1.0 CB B:ARG123 4.9 20.3 1.0 CA B:GLY125 4.9 20.8 1.0 OG B:SER494 5.0 24.4 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