Sodium in PDB 5syi: Structure of D141A Variant of B. Pseudomallei Katg Complexed with Inh

All present enzymatic activity of Structure of D141A Variant of B. Pseudomallei Katg Complexed with Inh:
1.11.1.21;

The structure of Structure of D141A Variant of B. Pseudomallei Katg Complexed with Inh, PDB code: 5syi 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 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.770, 115.590, 174.570, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 17

The structure of Structure of D141A Variant of B. Pseudomallei Katg Complexed with Inh also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Structure of D141A Variant of B. Pseudomallei Katg Complexed with Inh (pdb code 5syi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of D141A Variant of B. Pseudomallei Katg Complexed with Inh, PDB code: 5syi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of D141A Variant of B. Pseudomallei Katg Complexed with Inh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of D141A Variant of B. Pseudomallei Katg Complexed with Inh within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:16.4 occ:1.00 O A:GLY124 2.3 15.2 1.0 O A:HOH1480 2.3 20.4 1.0 O A:HOH991 2.3 19.8 1.0 O A:GLY122 2.4 14.6 1.0 O A:SER494 2.4 16.8 1.0 C A:SER494 3.2 16.1 1.0 C A:GLY124 3.5 15.8 1.0 C A:GLY122 3.6 14.8 1.0 C A:ARG123 3.6 14.2 1.0 N A:GLY124 3.6 15.6 1.0 CA A:ARG123 3.7 14.4 1.0 O A:HOH1543 3.9 21.6 1.0 OD2 A:ASP427 3.9 16.9 1.0 CA A:SER494 4.0 14.8 1.0 O A:HOH1015 4.1 36.1 1.0 N A:ARG123 4.1 14.5 1.0 N A:ASP495 4.1 15.6 1.0 CA A:GLY124 4.1 15.8 1.0 CB A:ASP427 4.2 16.4 1.0 O A:ARG123 4.2 14.4 1.0 CB A:SER494 4.2 15.2 1.0 CA A:ASP495 4.4 15.2 1.0 CL A:CL803 4.6 33.9 1.0 N A:GLY125 4.6 14.1 1.0 CG A:ASP427 4.6 18.9 1.0 CB A:ASP495 4.6 14.9 1.0 CD1 A:TYR117 4.7 15.3 1.0 OE2 A:GLU128 4.8 32.5 1.0 CA A:GLY122 4.8 14.8 1.0 CA A:GLY125 4.8 14.0 1.0 CB A:ARG123 4.9 16.1 1.0 CE1 A:TYR117 5.0 14.9 1.0

Sodium binding site 2 out of 2 in the Structure of D141A Variant of B. Pseudomallei Katg Complexed with Inh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of D141A Variant of B. Pseudomallei Katg Complexed with Inh within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:17.1 occ:1.00 O B:GLY124 2.4 14.9 1.0 O B:HOH1475 2.4 21.1 1.0 O B:HOH989 2.4 21.1 1.0 O B:GLY122 2.4 13.5 1.0 O B:SER494 2.4 15.6 1.0 C B:SER494 3.2 15.6 1.0 C B:GLY122 3.5 14.3 1.0 C B:GLY124 3.5 15.7 1.0 N B:GLY124 3.6 14.5 1.0 C B:ARG123 3.6 15.0 1.0 CA B:ARG123 3.7 14.2 1.0 O B:HOH1529 3.9 20.1 1.0 CA B:SER494 3.9 15.6 1.0 OD2 B:ASP427 4.0 18.4 1.0 N B:ARG123 4.1 13.2 1.0 CB B:SER494 4.1 15.1 1.0 O B:ARG123 4.1 14.5 1.0 N B:ASP495 4.1 14.3 1.0 CA B:GLY124 4.2 14.6 1.0 CB B:ASP427 4.2 18.2 1.0 O B:HOH1149 4.2 29.2 1.0 CA B:ASP495 4.4 14.6 1.0 CB B:ASP495 4.6 15.1 1.0 CL B:CL803 4.6 31.6 1.0 N B:GLY125 4.7 14.3 1.0 CD1 B:TYR117 4.7 14.6 1.0 CG B:ASP427 4.7 18.1 1.0 OE2 B:GLU128 4.8 31.5 1.0 CA B:GLY122 4.8 14.9 1.0 CE1 B:TYR117 4.9 14.2 1.0 CA B:GLY125 4.9 15.6 1.0 CB B:ARG123 4.9 14.5 1.0 OG B:SER494 4.9 15.8 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