Sodium in PDB 5kq2: Crystal Structure of the A357D Variant of Catalase-Peroxidase From B. Pseudomallei

All present enzymatic activity of Crystal Structure of the A357D Variant of Catalase-Peroxidase From B. Pseudomallei:
1.11.1.21;

The structure of Crystal Structure of the A357D Variant of Catalase-Peroxidase From B. Pseudomallei, PDB code: 5kq2 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)	47.78 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.827, 114.130, 174.989, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 19.1

The structure of Crystal Structure of the A357D 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 A357D Variant of Catalase-Peroxidase From B. Pseudomallei (pdb code 5kq2). 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 A357D Variant of Catalase-Peroxidase From B. Pseudomallei, PDB code: 5kq2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the A357D 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 A357D Variant of Catalase-Peroxidase From B. Pseudomallei within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:20.5 occ:1.00 O A:GLY124 2.3 17.9 1.0 O A:GLY122 2.3 20.2 1.0 O A:HOH1432 2.3 23.0 1.0 O A:SER494 2.3 20.5 1.0 O A:HOH1174 2.5 27.6 1.0 C A:SER494 3.3 19.8 1.0 C A:GLY124 3.4 18.0 1.0 C A:GLY122 3.5 19.1 1.0 N A:GLY124 3.5 18.3 1.0 C A:ARG123 3.6 19.8 1.0 CA A:ARG123 3.6 18.3 1.0 N A:ARG123 4.0 18.9 1.0 O A:HOH1494 4.0 23.6 1.0 O A:HOH980 4.0 29.9 1.0 CA A:SER494 4.0 19.2 1.0 CA A:GLY124 4.1 18.7 1.0 OD2 A:ASP427 4.1 25.1 1.0 CB A:ASP427 4.1 24.5 1.0 O A:ARG123 4.2 19.3 1.0 N A:ASP495 4.2 19.3 1.0 CB A:SER494 4.2 19.3 1.0 CA A:ASP495 4.5 19.6 1.0 N A:GLY125 4.5 18.4 1.0 CG A:ASP427 4.6 26.0 1.0 CB A:ASP495 4.6 19.6 1.0 CD1 A:TYR117 4.6 19.1 1.0 CL A:CL803 4.7 44.1 1.0 CA A:GLY122 4.8 19.7 1.0 CB A:ARG123 4.8 19.3 1.0 CA A:GLY125 4.9 17.8 1.0 OE2 A:GLU128 4.9 38.8 1.0 CE1 A:TYR117 4.9 19.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the A357D 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 A357D Variant of Catalase-Peroxidase From B. Pseudomallei within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:22.1 occ:1.00 O B:HOH1442 2.3 22.4 1.0 O B:GLY122 2.3 20.8 1.0 O B:GLY124 2.3 21.8 1.0 O B:SER494 2.3 23.2 1.0 O B:HOH1063 2.4 23.4 1.0 C B:SER494 3.2 19.9 1.0 C B:GLY122 3.4 18.5 1.0 C B:GLY124 3.5 18.9 1.0 C B:ARG123 3.6 19.8 1.0 N B:GLY124 3.6 18.9 1.0 CA B:ARG123 3.6 18.4 1.0 O B:HOH1478 4.0 25.1 1.0 CA B:SER494 4.0 19.5 1.0 N B:ARG123 4.0 19.5 1.0 N B:ASP495 4.1 20.6 1.0 O B:HOH1103 4.1 37.7 1.0 OD2 B:ASP427 4.1 24.3 1.0 CA B:GLY124 4.1 19.8 1.0 CB B:ASP427 4.2 22.4 1.0 CB B:SER494 4.2 19.1 1.0 O B:ARG123 4.2 16.9 1.0 CA B:ASP495 4.4 20.4 1.0 CB B:ASP495 4.6 20.7 1.0 N B:GLY125 4.6 19.6 1.0 CD1 B:TYR117 4.6 19.4 1.0 CG B:ASP427 4.7 21.9 1.0 CA B:GLY122 4.7 18.7 1.0 CL B:CL803 4.8 39.9 1.0 CE1 B:TYR117 4.9 20.0 1.0 CB B:ARG123 4.9 20.5 1.0 OE2 B:GLU128 4.9 39.8 1.0 CA B:GLY125 5.0 19.2 1.0 OG B:SER494 5.0 18.9 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