Sodium in PDB 5sx6: Crystal Structure of the Catalase-Peroxidase Katg of B. Pseudomallei at pH 6.5

All present enzymatic activity of Crystal Structure of the Catalase-Peroxidase Katg of B. Pseudomallei at pH 6.5:
1.11.1.21;

The structure of Crystal Structure of the Catalase-Peroxidase Katg of B. Pseudomallei at pH 6.5, PDB code: 5sx6 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 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.529, 114.795, 174.647, 90.00, 90.00, 90.00
R / Rfree (%)	13.9 / 17.2

The structure of Crystal Structure of the Catalase-Peroxidase Katg of B. Pseudomallei at pH 6.5 also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of the Catalase-Peroxidase Katg of B. Pseudomallei at pH 6.5 (pdb code 5sx6). 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. Pseudomallei at pH 6.5, PDB code: 5sx6:
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. Pseudomallei at pH 6.5


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. Pseudomallei at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:24.9 occ:1.00 O A:GLY124 2.4 21.0 1.0 O A:SER494 2.4 20.5 1.0 O A:GLY122 2.4 19.4 1.0 O A:HOH953 2.4 24.5 1.0 O A:HOH1120 2.5 32.0 1.0 C A:SER494 3.2 19.8 1.0 C A:GLY124 3.5 17.2 1.0 C A:GLY122 3.6 18.4 1.0 N A:GLY124 3.6 17.4 1.0 CA A:ARG123 3.6 17.9 1.0 C A:ARG123 3.7 18.2 1.0 O A:HOH1002 3.9 43.7 1.0 OD2 A:ASP427 3.9 25.5 1.0 O A:HOH1066 4.0 24.4 1.0 CA A:SER494 4.0 18.7 1.0 N A:ASP495 4.1 16.5 1.0 CB A:ASP427 4.1 23.1 1.0 N A:ARG123 4.1 17.1 1.0 CB A:SER494 4.1 19.1 1.0 CA A:GLY124 4.2 18.9 1.0 O A:ARG123 4.2 16.2 1.0 CA A:ASP495 4.4 17.6 1.0 CB A:ASP495 4.5 18.1 1.0 CG A:ASP427 4.6 24.9 1.0 N A:GLY125 4.6 16.9 1.0 CD1 A:TYR117 4.6 19.0 1.0 OE2 A:GLU198 4.8 50.5 1.0 CA A:GLY122 4.8 18.3 1.0 CB A:ARG123 4.9 19.6 1.0 CE1 A:TYR117 4.9 20.7 1.0 CA A:GLY125 4.9 16.3 1.0 OG A:SER494 4.9 18.2 1.0 OE1 A:GLU198 5.0 42.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Catalase-Peroxidase Katg of B. Pseudomallei at pH 6.5


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. Pseudomallei at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:23.7 occ:1.00 O B:HOH1066 2.3 24.0 1.0 O B:GLY124 2.3 17.2 1.0 O B:GLY122 2.4 14.0 1.0 O B:SER494 2.4 18.3 1.0 O B:HOH1064 2.5 34.2 1.0 C B:SER494 3.2 18.2 1.0 C B:GLY122 3.5 13.8 1.0 C B:GLY124 3.5 17.1 1.0 C B:ARG123 3.6 15.7 1.0 CA B:ARG123 3.6 14.8 1.0 N B:GLY124 3.6 16.5 1.0 CA B:SER494 4.0 15.6 1.0 O B:HOH1053 4.0 41.7 1.0 O B:HOH1185 4.0 21.8 1.0 N B:ARG123 4.0 13.7 1.0 OD2 B:ASP427 4.0 22.5 1.0 N B:ASP495 4.1 14.8 1.0 CB B:SER494 4.1 15.3 1.0 O B:ARG123 4.1 15.1 1.0 CB B:ASP427 4.2 20.6 1.0 CA B:GLY124 4.2 15.7 1.0 CA B:ASP495 4.4 15.5 1.0 CB B:ASP495 4.5 17.0 1.0 CD1 B:TYR117 4.6 17.5 1.0 CG B:ASP427 4.6 23.6 1.0 N B:GLY125 4.6 15.6 1.0 OE2 B:GLU198 4.7 42.0 1.0 CA B:GLY122 4.8 14.8 1.0 CB B:ARG123 4.9 15.2 1.0 CE1 B:TYR117 4.9 16.3 1.0 CA B:GLY125 4.9 14.8 1.0 OG B:SER494 5.0 15.5 1.0 OE1 B:GLU198 5.0 36.9 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