Sodium in PDB 5syj: Crystal Structure of the D141A Variant of B. Pseudomallei Katgin Complex with Isoniazid

All present enzymatic activity of Crystal Structure of the D141A Variant of B. Pseudomallei Katgin Complex with Isoniazid:
1.11.1.21;

The structure of Crystal Structure of the D141A Variant of B. Pseudomallei Katgin Complex with Isoniazid, PDB code: 5syj 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 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.640, 114.640, 174.990, 90.00, 90.00, 90.00
R / Rfree (%)	14 / 17

The structure of Crystal Structure of the D141A Variant of B. Pseudomallei Katgin Complex with Isoniazid 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 the D141A Variant of B. Pseudomallei Katgin Complex with Isoniazid (pdb code 5syj). 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 D141A Variant of B. Pseudomallei Katgin Complex with Isoniazid, PDB code: 5syj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the D141A Variant of B. Pseudomallei Katgin Complex with Isoniazid


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 D141A Variant of B. Pseudomallei Katgin Complex with Isoniazid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:21.6 occ:1.00 O A:GLY124 2.3 21.9 1.0 O A:HOH1368 2.4 20.7 1.0 O A:GLY122 2.4 21.9 1.0 O A:SER494 2.4 20.1 1.0 O A:HOH1148 2.4 21.9 1.0 C A:SER494 3.2 19.7 1.0 C A:GLY124 3.5 21.2 1.0 C A:GLY122 3.5 19.9 1.0 N A:GLY124 3.6 20.4 1.0 C A:ARG123 3.6 22.2 1.0 CA A:ARG123 3.6 19.9 1.0 O A:HOH1406 3.9 24.3 1.0 CA A:SER494 3.9 21.0 1.0 N A:ARG123 4.0 19.4 1.0 OD2 A:ASP427 4.1 22.8 1.0 N A:ASP495 4.1 19.8 1.0 CB A:SER494 4.1 20.8 1.0 CA A:GLY124 4.2 21.1 1.0 O A:ARG123 4.2 20.7 1.0 CB A:ASP427 4.2 22.4 1.0 O A:HOH996 4.3 35.5 1.0 CA A:ASP495 4.5 21.0 1.0 CL A:CL803 4.5 35.3 1.0 N A:GLY125 4.6 22.0 1.0 CB A:ASP495 4.6 20.9 1.0 CG A:ASP427 4.6 24.6 1.0 OE2 A:GLU128 4.7 33.2 1.0 CD1 A:TYR117 4.8 21.0 1.0 CA A:GLY122 4.8 20.1 1.0 CB A:ARG123 4.9 21.4 1.0 CA A:GLY125 4.9 19.6 1.0 OG A:SER494 5.0 21.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the D141A Variant of B. Pseudomallei Katgin Complex with Isoniazid


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 D141A Variant of B. Pseudomallei Katgin Complex with Isoniazid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:20.2 occ:1.00 O B:GLY124 2.3 18.2 1.0 O B:HOH1345 2.3 20.9 1.0 O B:GLY122 2.4 17.8 1.0 O B:SER494 2.4 19.1 1.0 O B:HOH971 2.4 22.4 1.0 C B:SER494 3.2 20.6 1.0 C B:GLY122 3.5 17.0 1.0 C B:GLY124 3.5 17.6 1.0 N B:GLY124 3.6 19.9 1.0 C B:ARG123 3.6 19.3 1.0 CA B:ARG123 3.6 18.9 1.0 O B:HOH1418 3.9 24.3 1.0 CA B:SER494 3.9 19.4 1.0 N B:ARG123 4.1 17.6 1.0 OD2 B:ASP427 4.1 21.2 1.0 N B:ASP495 4.1 17.4 1.0 CB B:SER494 4.1 19.2 1.0 CA B:GLY124 4.2 17.6 1.0 O B:ARG123 4.2 19.8 1.0 CB B:ASP427 4.2 22.0 1.0 O B:HOH986 4.3 31.9 1.0 CA B:ASP495 4.5 18.1 1.0 OE2 B:GLU128 4.6 30.2 1.0 CB B:ASP495 4.6 17.9 1.0 N B:GLY125 4.6 16.4 1.0 CL B:CL803 4.6 30.4 1.0 CD1 B:TYR117 4.7 21.6 1.0 CG B:ASP427 4.7 24.5 1.0 CA B:GLY122 4.8 17.0 1.0 CA B:GLY125 4.9 18.6 1.0 O B:HOH972 4.9 29.6 1.0 OG B:SER494 4.9 18.8 1.0 CB B:ARG123 4.9 18.2 1.0 CE1 B:TYR117 5.0 21.9 1.0

P.Vidossich, P.C.Loewen, X.Carpena, G.Fiorin, I.Fita, C.Rovira. Binding of the Antitubercular Pro-Drug Isoniazid in the Heme Access Channel of Catalase-Peroxidase (Katg). A Combined Structural and Metadynamics Investigation. J Phys Chem B V. 118 2924 2014.
ISSN: ISSN 1520-5207
PubMed: 24568093
DOI: 10.1021/JP4123425