Sodium in PDB 5sx3: Crystal Structure of the Catalase-Peroxidase Katg of B. Pseudomaallei at pH 4.5

All present enzymatic activity of Crystal Structure of the Catalase-Peroxidase Katg of B. Pseudomaallei at pH 4.5:
1.11.1.21;

The structure of Crystal Structure of the Catalase-Peroxidase Katg of B. Pseudomaallei at pH 4.5, PDB code: 5sx3 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)	20.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.049, 114.847, 174.704, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 19.6

The structure of Crystal Structure of the Catalase-Peroxidase Katg of B. Pseudomaallei at pH 4.5 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 Catalase-Peroxidase Katg of B. Pseudomaallei at pH 4.5 (pdb code 5sx3). 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 Catalase-Peroxidase Katg of B. Pseudomaallei at pH 4.5, PDB code: 5sx3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Catalase-Peroxidase Katg of B. Pseudomaallei at pH 4.5


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 Catalase-Peroxidase Katg of B. Pseudomaallei at pH 4.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:28.8 occ:1.00 O A:GLY124 2.3 24.1 1.0 O A:HOH1397 2.3 33.5 1.0 O A:SER494 2.4 27.3 1.0 O A:GLY122 2.4 26.5 1.0 O A:HOH1249 2.6 31.1 1.0 C A:SER494 3.2 24.3 1.0 C A:GLY124 3.5 24.5 1.0 C A:GLY122 3.5 25.0 1.0 C A:ARG123 3.6 23.8 1.0 CA A:ARG123 3.6 24.8 1.0 N A:GLY124 3.6 23.6 1.0 O A:HOH1447 4.0 29.1 1.0 N A:ARG123 4.0 24.2 1.0 CA A:SER494 4.0 23.8 1.0 O A:HOH1152 4.0 33.3 1.0 OD2 A:ASP427 4.0 29.6 1.0 N A:ASP495 4.1 24.4 1.0 CB A:ASP427 4.1 30.9 1.0 O A:ARG123 4.1 26.3 1.0 CA A:GLY124 4.2 24.1 1.0 CB A:SER494 4.3 23.8 1.0 CA A:ASP495 4.4 24.9 1.0 CL A:CL803 4.5 46.1 1.0 N A:GLY125 4.5 26.1 1.0 CB A:ASP495 4.6 24.5 1.0 CG A:ASP427 4.6 32.0 1.0 CD1 A:TYR117 4.7 26.3 1.0 CA A:GLY122 4.8 26.1 1.0 CA A:GLY125 4.8 24.3 1.0 CB A:ARG123 4.9 25.4 1.0 CE1 A:TYR117 4.9 25.8 1.0 O A:HOH1370 4.9 54.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Catalase-Peroxidase Katg of B. Pseudomaallei at pH 4.5


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 Catalase-Peroxidase Katg of B. Pseudomaallei at pH 4.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:26.1 occ:1.00 O B:GLY124 2.3 24.5 1.0 O B:GLY122 2.3 23.0 1.0 O B:HOH1446 2.4 28.4 1.0 O B:SER494 2.4 27.1 1.0 O B:HOH1091 2.4 27.1 1.0 C B:SER494 3.2 25.4 1.0 C B:GLY122 3.5 21.8 1.0 C B:GLY124 3.5 23.8 1.0 C B:ARG123 3.6 24.3 1.0 CA B:ARG123 3.6 22.2 1.0 N B:GLY124 3.7 23.9 1.0 O B:HOH1470 3.8 28.1 1.0 O B:HOH987 3.9 40.9 1.0 CA B:SER494 3.9 24.3 1.0 OD2 B:ASP427 4.0 28.4 1.0 N B:ARG123 4.0 21.7 1.0 N B:ASP495 4.1 24.7 1.0 CB B:ASP427 4.1 28.9 1.0 O B:ARG123 4.2 24.5 1.0 CB B:SER494 4.2 23.2 1.0 CA B:GLY124 4.3 23.7 1.0 CA B:ASP495 4.5 23.9 1.0 CG B:ASP427 4.6 31.2 1.0 N B:GLY125 4.6 22.9 1.0 CL B:CL803 4.7 42.8 1.0 CB B:ASP495 4.7 23.7 1.0 CD1 B:TYR117 4.7 23.9 1.0 CA B:GLY122 4.8 21.7 1.0 CA B:GLY125 4.9 23.7 1.0 CB B:ARG123 4.9 22.4 1.0 CE1 B:TYR117 4.9 24.6 1.0

X.Carpena, B.Wiseman, T.Deemagarn, B.Herguedas, A.Ivancich, R.Singh, P.C.Loewen, I.Fita. Roles For ARG426 and TRP111 in the Modulation of Nadh Oxidase Activity of the Catalase-Peroxidase Katg From Burkholderia Pseudomallei Inferred From pH-Induced Structural Changes. Biochemistry V. 45 5171 2006.
ISSN: ISSN 0006-2960
PubMed: 16618106