Sodium in PDB 5txq: Crystal Structure of the A143D Variant of Catalase-Peroxidase From B. Pseudomallei

All present enzymatic activity of Crystal Structure of the A143D Variant of Catalase-Peroxidase From B. Pseudomallei:
1.11.1.21;

The structure of Crystal Structure of the A143D Variant of Catalase-Peroxidase From B. Pseudomallei, PDB code: 5txq 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)	96.13 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.670, 115.117, 174.738, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 19.1

The structure of Crystal Structure of the A143D 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 A143D Variant of Catalase-Peroxidase From B. Pseudomallei (pdb code 5txq). 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 A143D Variant of Catalase-Peroxidase From B. Pseudomallei, PDB code: 5txq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the A143D 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 A143D Variant of Catalase-Peroxidase From B. Pseudomallei within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:19.1 occ:1.00 O A:GLY124 2.3 16.2 1.0 O A:HOH990 2.3 20.6 1.0 O A:SER494 2.4 19.1 1.0 O A:GLY122 2.4 17.6 1.0 O A:HOH1102 2.4 23.1 1.0 C A:SER494 3.3 17.6 1.0 C A:GLY124 3.4 16.2 1.0 C A:GLY122 3.5 17.3 1.0 N A:GLY124 3.5 17.5 1.0 C A:ARG123 3.6 17.4 1.0 CA A:ARG123 3.6 17.7 1.0 O A:HOH1319 3.9 20.1 1.0 CA A:SER494 4.0 18.0 1.0 N A:ARG123 4.0 18.0 1.0 OD2 A:ASP427 4.0 19.9 1.0 O A:HOH1043 4.1 24.7 1.0 CB A:ASP427 4.1 20.3 1.0 N A:ASP495 4.1 19.3 1.0 CA A:GLY124 4.1 16.6 1.0 O A:ARG123 4.1 19.1 1.0 CB A:SER494 4.2 18.1 1.0 CA A:ASP495 4.5 18.1 1.0 N A:GLY125 4.5 16.2 1.0 CG A:ASP427 4.6 22.4 1.0 CB A:ASP495 4.6 18.6 1.0 CD1 A:TYR117 4.6 20.6 1.0 OE1 A:GLU198 4.7 26.6 1.0 OE2 A:GLU198 4.7 43.2 1.0 CA A:GLY122 4.8 19.0 1.0 OE2 A:GLU128 4.8 34.2 1.0 CA A:GLY125 4.9 16.6 1.0 CB A:ARG123 4.9 18.3 1.0 CE1 A:TYR117 4.9 20.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the A143D 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 A143D Variant of Catalase-Peroxidase From B. Pseudomallei within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:20.3 occ:1.00 O B:HOH920 2.3 24.3 1.0 O B:GLY122 2.3 18.0 1.0 O B:GLY124 2.4 19.6 1.0 O B:SER494 2.4 22.1 1.0 O B:HOH1182 2.5 26.2 1.0 C B:SER494 3.3 20.0 1.0 C B:GLY122 3.4 17.8 1.0 C B:GLY124 3.5 19.4 1.0 N B:GLY124 3.5 20.4 1.0 C B:ARG123 3.5 20.4 1.0 CA B:ARG123 3.6 18.9 1.0 O B:HOH1313 4.0 23.5 1.0 CA B:SER494 4.0 20.8 1.0 N B:ARG123 4.0 17.1 1.0 O B:HOH1175 4.1 35.2 1.0 CA B:GLY124 4.1 19.4 1.0 N B:ASP495 4.1 19.9 1.0 O B:ARG123 4.1 19.4 1.0 CB B:SER494 4.2 19.6 1.0 OD2 B:ASP427 4.2 21.4 1.0 CB B:ASP427 4.2 21.5 1.0 OE1 B:GLU198 4.4 38.2 1.0 CA B:ASP495 4.5 19.7 1.0 CD1 B:TYR117 4.6 20.2 1.0 N B:GLY125 4.6 18.7 1.0 CB B:ASP495 4.7 19.6 1.0 CG B:ASP427 4.7 21.9 1.0 CA B:GLY122 4.7 18.8 1.0 CB B:ARG123 4.8 19.2 1.0 OE2 B:GLU198 4.8 25.5 1.0 OE2 B:GLU128 4.9 36.6 1.0 CE1 B:TYR117 4.9 19.9 1.0 OG B:SER494 5.0 19.8 1.0 CA B:GLY125 5.0 18.6 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