Sodium in PDB 5l02: S324T Variant of B. Pseudomallei Katg

All present enzymatic activity of S324T Variant of B. Pseudomallei Katg:
1.11.1.21;

The structure of S324T Variant of B. Pseudomallei Katg, PDB code: 5l02 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)	30.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.502, 114.630, 174.925, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 21.1

The structure of S324T Variant of B. Pseudomallei Katg also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the S324T Variant of B. Pseudomallei Katg (pdb code 5l02). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the S324T Variant of B. Pseudomallei Katg, PDB code: 5l02:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the S324T 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 S324T Variant of B. Pseudomallei Katg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:21.5 occ:1.00 O A:SER494 2.3 21.8 1.0 O A:GLY122 2.3 20.1 1.0 O A:GLY124 2.3 20.8 1.0 O A:HOH957 2.4 23.7 1.0 O A:HOH1203 2.5 25.3 1.0 C A:SER494 3.2 21.4 1.0 C A:GLY124 3.5 20.0 1.0 C A:GLY122 3.5 20.1 1.0 C A:ARG123 3.6 19.0 1.0 CA A:ARG123 3.6 20.9 1.0 N A:GLY124 3.6 18.8 1.0 O A:HOH945 3.8 37.9 1.0 N A:ARG123 4.0 20.2 1.0 CA A:SER494 4.0 20.3 1.0 OD2 A:ASP427 4.0 25.4 1.0 CB A:ASP427 4.0 24.8 1.0 O A:HOH1250 4.1 23.9 1.0 N A:ASP495 4.1 22.0 1.0 O A:ARG123 4.1 18.4 1.0 CA A:GLY124 4.2 20.7 1.0 CB A:SER494 4.2 20.3 1.0 CA A:ASP495 4.4 22.9 1.0 CB A:ASP495 4.5 21.4 1.0 CG A:ASP427 4.6 26.3 1.0 N A:GLY125 4.6 20.1 1.0 CD1 A:TYR117 4.6 20.2 1.0 OE2 A:GLU198 4.7 38.5 0.8 OE2 A:GLU128 4.8 47.5 1.0 CA A:GLY122 4.8 20.4 1.0 OE1 A:GLU198 4.8 27.1 0.8 CE1 A:TYR117 4.8 20.6 1.0 CA A:GLY125 4.9 19.4 1.0 CB A:ARG123 4.9 21.0 1.0 OG A:SER494 5.0 20.6 1.0

Sodium binding site 2 out of 2 in the S324T 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 S324T Variant of B. Pseudomallei Katg within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:22.9 occ:1.00 O B:HOH974 2.3 26.1 1.0 O B:GLY122 2.3 19.5 1.0 O B:GLY124 2.3 20.5 1.0 O B:HOH1157 2.3 31.4 1.0 O B:SER494 2.3 22.6 1.0 C B:SER494 3.2 21.1 1.0 C B:GLY122 3.5 19.3 1.0 C B:GLY124 3.5 19.9 1.0 N B:GLY124 3.6 21.7 1.0 C B:ARG123 3.6 20.1 1.0 CA B:ARG123 3.6 18.9 1.0 O B:HOH1353 3.9 25.1 1.0 CA B:SER494 4.0 20.2 1.0 N B:ASP495 4.0 19.8 1.0 N B:ARG123 4.0 18.1 1.0 O B:HOH958 4.1 41.7 1.0 CB B:ASP427 4.1 24.8 1.0 OD2 B:ASP427 4.1 25.1 1.0 CA B:GLY124 4.1 20.3 1.0 O B:ARG123 4.1 19.4 1.0 CB B:SER494 4.2 19.6 1.0 CA B:ASP495 4.4 20.9 1.0 CB B:ASP495 4.5 21.7 1.0 CD1 B:TYR117 4.6 19.5 1.0 OE2 B:GLU198 4.6 38.7 1.0 N B:GLY125 4.7 20.2 1.0 CG B:ASP427 4.7 27.6 1.0 CA B:GLY122 4.7 20.3 1.0 OE2 B:GLU128 4.8 45.1 1.0 CE1 B:TYR117 4.8 19.5 1.0 CB B:ARG123 4.9 19.0 1.0 CA B:GLY125 4.9 19.7 1.0 OG B:SER494 5.0 20.1 1.0 OE1 B:GLU198 5.0 35.2 1.0

T.Deemagarn, X.Carpena, R.Singh, B.Wiseman, I.Fita, P.C.Loewen. Structural Characterization of the SER324THR Variant of the Catalase-Peroxidase (Katg) From Burkholderia Pseudomallei J. Mol. Biol. V. 345 21 2005.
ISSN: ISSN 0022-2836
PubMed: 15567407