Sodium in PDB 5sx7: Crystal Structure of Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5

All present enzymatic activity of Crystal Structure of Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5:
1.11.1.21;

The structure of Crystal Structure of Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5, PDB code: 5sx7 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 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.413, 114.948, 173.998, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 18.9

The structure of Crystal Structure of Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5 also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5 (pdb code 5sx7). 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 Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5, PDB code: 5sx7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5


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 Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:20.2 occ:1.00 O A:GLY124 2.3 17.2 1.0 O A:SER494 2.4 14.9 1.0 O A:HOH1386 2.4 33.0 1.0 O A:HOH1023 2.4 21.0 1.0 O A:GLY122 2.4 17.5 1.0 C A:SER494 3.3 14.9 1.0 C A:GLY124 3.5 15.4 1.0 C A:GLY122 3.6 16.2 1.0 N A:GLY124 3.6 14.5 1.0 C A:ARG123 3.6 14.9 1.0 CA A:ARG123 3.7 15.0 1.0 O A:HOH1032 3.8 35.7 1.0 O A:HOH1182 3.8 15.4 1.0 OD2 A:ASP427 3.9 18.3 1.0 CB A:ASP427 4.0 17.9 1.0 CA A:SER494 4.0 13.6 1.0 N A:ARG123 4.1 14.8 1.0 N A:ASP495 4.1 14.5 1.0 CA A:GLY124 4.2 16.1 1.0 O A:ARG123 4.2 13.4 1.0 CB A:SER494 4.3 14.0 1.0 CA A:ASP495 4.4 14.6 1.0 CG A:ASP427 4.5 18.8 1.0 N A:GLY125 4.6 15.3 1.0 CB A:ASP495 4.6 14.4 1.0 CD1 A:TYR117 4.7 16.3 1.0 CA A:GLY122 4.9 15.7 1.0 CA A:GLY125 4.9 14.6 1.0 CE1 A:TYR117 4.9 16.5 1.0 OE2 A:GLU198 4.9 23.5 1.0 CB A:ARG123 5.0 14.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5


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 Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na803 b:16.8 occ:1.00 O B:GLY124 2.3 12.9 1.0 O B:SER494 2.3 15.7 1.0 O B:GLY122 2.3 12.9 1.0 O B:HOH1051 2.4 17.6 1.0 O B:HOH1005 2.4 29.4 1.0 C B:SER494 3.2 14.4 1.0 C B:GLY122 3.5 13.0 1.0 C B:GLY124 3.5 12.7 1.0 C B:ARG123 3.6 12.9 1.0 N B:GLY124 3.7 13.7 1.0 CA B:ARG123 3.7 12.4 1.0 CA B:SER494 3.9 12.3 1.0 O B:HOH1234 4.0 17.8 1.0 N B:ARG123 4.0 12.7 1.0 N B:ASP495 4.0 13.4 1.0 O B:HOH1010 4.1 28.8 1.0 CB B:ASP427 4.1 15.2 1.0 OD2 B:ASP427 4.1 18.2 1.0 CB B:SER494 4.1 12.1 1.0 CA B:GLY124 4.2 12.8 1.0 O B:ARG123 4.2 12.1 1.0 OE2 B:GLU128 4.4 40.1 1.0 CA B:ASP495 4.4 13.5 1.0 CB B:ASP495 4.6 13.8 1.0 CG B:ASP427 4.6 16.6 1.0 N B:GLY125 4.6 11.9 1.0 CD1 B:TYR117 4.7 13.7 1.0 CA B:GLY122 4.8 12.9 1.0 OE2 B:GLU198 4.8 25.1 1.0 CE1 B:TYR117 4.9 13.0 1.0 OG B:SER494 4.9 11.9 1.0 CA B:GLY125 5.0 12.3 1.0 CB B:ARG123 5.0 12.2 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