Sodium in PDB 5sxr: Crystal Structure of B. Pseudomallei Katg with Nad Bound

All present enzymatic activity of Crystal Structure of B. Pseudomallei Katg with Nad Bound:
1.11.1.21;

The structure of Crystal Structure of B. Pseudomallei Katg with Nad Bound, PDB code: 5sxr 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 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.580, 114.920, 174.480, 90.00, 90.00, 90.00
R / Rfree (%)	13.9 / 16.5

The structure of Crystal Structure of B. Pseudomallei Katg with Nad Bound 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 B. Pseudomallei Katg with Nad Bound (pdb code 5sxr). 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 B. Pseudomallei Katg with Nad Bound, PDB code: 5sxr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of B. Pseudomallei Katg with Nad Bound


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 B. Pseudomallei Katg with Nad Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:16.3 occ:1.00 O A:GLY124 2.3 15.8 1.0 O A:HOH1492 2.3 20.6 1.0 O A:GLY122 2.4 15.2 1.0 O A:HOH1097 2.4 19.6 1.0 O A:SER494 2.5 17.2 1.0 C A:SER494 3.3 17.9 1.0 C A:GLY124 3.5 16.5 1.0 C A:GLY122 3.5 17.2 1.0 C A:ARG123 3.5 16.9 1.0 CA A:ARG123 3.6 15.6 1.0 N A:GLY124 3.6 15.3 1.0 O A:HOH1528 3.9 20.6 1.0 CA A:SER494 4.0 15.7 1.0 O A:HOH1015 4.0 30.5 1.0 N A:ARG123 4.0 15.6 1.0 OD2 A:ASP427 4.0 19.1 1.0 O A:ARG123 4.1 16.6 1.0 N A:ASP495 4.1 16.0 1.0 CA A:GLY124 4.1 17.3 1.0 CB A:SER494 4.1 16.0 1.0 CB A:ASP427 4.1 18.2 1.0 CA A:ASP495 4.5 17.1 1.0 N A:GLY125 4.6 15.4 1.0 CL A:CL803 4.6 31.0 1.0 CB A:ASP495 4.6 16.7 1.0 CD1 A:TYR117 4.6 16.3 1.0 CG A:ASP427 4.6 19.7 1.0 CA A:GLY122 4.7 16.1 1.0 CA A:GLY125 4.9 16.7 1.0 O A:HOH944 4.9 41.5 1.0 CB A:ARG123 4.9 17.1 1.0 CE1 A:TYR117 4.9 15.4 1.0 OG A:SER494 5.0 15.8 1.0 OE2 A:GLU128 5.0 30.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of B. Pseudomallei Katg with Nad Bound


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 B. Pseudomallei Katg with Nad Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:17.3 occ:1.00 O B:HOH1544 2.3 19.8 1.0 O B:GLY124 2.3 15.0 1.0 O B:GLY122 2.4 14.5 1.0 O B:HOH1132 2.4 18.8 1.0 O B:SER494 2.5 16.8 1.0 C B:SER494 3.3 16.6 1.0 C B:GLY122 3.5 15.2 1.0 C B:GLY124 3.5 15.4 1.0 N B:GLY124 3.6 15.4 1.0 C B:ARG123 3.6 14.9 1.0 CA B:ARG123 3.6 15.1 1.0 O B:HOH1581 3.9 20.5 1.0 CA B:SER494 4.0 15.6 1.0 N B:ARG123 4.0 14.9 1.0 O B:HOH1113 4.0 29.5 1.0 OD2 B:ASP427 4.1 19.9 1.0 CB B:SER494 4.1 15.9 1.0 O B:ARG123 4.1 14.5 1.0 CA B:GLY124 4.2 15.8 1.0 N B:ASP495 4.2 14.8 1.0 CB B:ASP427 4.2 19.6 1.0 CA B:ASP495 4.5 14.8 1.0 CB B:ASP495 4.6 15.2 1.0 N B:GLY125 4.6 14.7 1.0 CD1 B:TYR117 4.6 15.5 1.0 CL B:CL803 4.7 32.2 1.0 CG B:ASP427 4.7 20.5 1.0 CA B:GLY122 4.8 14.1 1.0 OE2 B:GLU128 4.9 29.9 1.0 CA B:GLY125 4.9 15.8 1.0 CB B:ARG123 4.9 15.2 1.0 CE1 B:TYR117 4.9 15.3 1.0 OG B:SER494 5.0 16.1 1.0

B.Wiseman, X.Carpena, M.Feliz, L.J.Donald, M.Pons, I.Fita, P.C.Loewen. Isonicotinic Acid Hydrazide Conversion to Isonicotinyl-Nad By Catalase-Peroxidases. J. Biol. Chem. V. 285 26662 2010.
ISSN: ESSN 1083-351X
PubMed: 20554537
DOI: 10.1074/JBC.M110.139428