Sodium in PDB 5sx1: Crystal Structure of D141E Variant of B. Pseudomallei Katg

All present enzymatic activity of Crystal Structure of D141E Variant of B. Pseudomallei Katg:
1.11.1.21;

The structure of Crystal Structure of D141E Variant of B. Pseudomallei Katg, PDB code: 5sx1 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 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.739, 116.198, 175.018, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 19.1

The structure of Crystal Structure of D141E Variant of B. Pseudomallei Katg also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of D141E Variant of B. Pseudomallei Katg (pdb code 5sx1). 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 D141E Variant of B. Pseudomallei Katg, PDB code: 5sx1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of D141E Variant of B. Pseudomallei Katg


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 D141E Variant of B. Pseudomallei Katg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:17.3 occ:1.00 O A:GLY124 2.4 15.4 1.0 O A:HOH980 2.4 20.4 1.0 O A:HOH962 2.4 23.4 1.0 O A:GLY122 2.4 16.1 1.0 O A:SER494 2.4 15.8 1.0 C A:SER494 3.3 14.0 1.0 C A:GLY124 3.5 14.4 1.0 C A:GLY122 3.5 13.1 1.0 C A:ARG123 3.6 13.9 1.0 N A:GLY124 3.6 15.4 1.0 CA A:ARG123 3.6 14.0 1.0 O A:HOH1299 3.9 21.2 1.0 OD2 A:ASP427 4.0 17.8 1.0 CA A:SER494 4.1 13.1 1.0 N A:ARG123 4.1 13.8 1.0 O A:HOH984 4.1 37.5 1.0 CB A:ASP427 4.1 19.2 1.0 N A:ASP495 4.1 12.7 1.0 CA A:GLY124 4.2 15.8 1.0 O A:ARG123 4.2 13.5 1.0 CB A:SER494 4.2 13.1 1.0 CA A:ASP495 4.4 13.9 1.0 CB A:ASP495 4.5 14.1 1.0 CG A:ASP427 4.6 21.9 1.0 N A:GLY125 4.6 14.7 1.0 OE2 A:GLU128 4.7 42.2 1.0 CD1 A:TYR117 4.7 15.2 1.0 OE2 A:GLU198 4.7 37.7 1.0 CA A:GLY122 4.8 14.9 1.0 CA A:GLY125 4.9 13.6 1.0 OE1 A:GLU198 4.9 29.6 1.0 CE1 A:TYR117 4.9 14.3 1.0 CB A:ARG123 4.9 15.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of D141E Variant of B. Pseudomallei Katg


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 D141E Variant of B. Pseudomallei Katg within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:15.8 occ:1.00 O B:HOH941 2.3 24.5 1.0 O B:GLY122 2.4 13.6 1.0 O B:GLY124 2.4 14.7 1.0 O B:HOH963 2.4 25.6 1.0 O B:SER494 2.4 15.5 1.0 C B:SER494 3.3 14.2 1.0 C B:GLY122 3.5 13.1 1.0 C B:GLY124 3.6 13.2 1.0 C B:ARG123 3.6 14.4 1.0 CA B:ARG123 3.7 14.1 1.0 N B:GLY124 3.7 14.0 1.0 CA B:SER494 4.0 13.8 1.0 N B:ARG123 4.0 12.3 1.0 O B:HOH1124 4.1 21.1 1.0 OD2 B:ASP427 4.1 17.9 1.0 CB B:SER494 4.1 14.0 1.0 N B:ASP495 4.2 13.5 1.0 O B:ARG123 4.2 14.1 1.0 O B:HOH964 4.2 37.3 1.0 CA B:GLY124 4.2 13.2 1.0 CB B:ASP427 4.2 17.4 1.0 CA B:ASP495 4.5 13.4 1.0 CB B:ASP495 4.5 13.9 1.0 OE2 B:GLU128 4.6 37.6 1.0 OE2 B:GLU198 4.6 31.6 1.0 N B:GLY125 4.7 13.2 1.0 CD1 B:TYR117 4.7 14.5 1.0 CG B:ASP427 4.7 17.9 1.0 CA B:GLY122 4.8 13.2 1.0 OE1 B:GLU198 4.9 31.1 1.0 CE1 B:TYR117 4.9 14.4 1.0 CA B:GLY125 4.9 13.2 1.0 CB B:ARG123 4.9 14.5 1.0 OG B:SER494 5.0 14.6 1.0

T.Deemagarn, B.Wiseman, X.Carpena, A.Ivancich, I.Fita, P.C.Loewen. Two Alternative Substrate Paths For Compound I Formation and Reduction in Catalase-Peroxidase Katg From Burkholderia Pseudomallei. Proteins V. 66 219 2007.
ISSN: ESSN 1097-0134
PubMed: 17063492