Sodium in PDB 6b9b: Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei with Maltose Bound

All present enzymatic activity of Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei with Maltose Bound:
1.11.1.21;

The structure of Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei with Maltose Bound, PDB code: 6b9b 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)	50.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.419, 115.088, 174.975, 90.00, 90.00, 90.00
R / Rfree (%)	13.5 / 16.2

The structure of Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei with Maltose 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 the Catalase-Peroxidase From B. Pseudomallei with Maltose Bound (pdb code 6b9b). 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 Catalase-Peroxidase From B. Pseudomallei with Maltose Bound, PDB code: 6b9b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei with Maltose 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 the Catalase-Peroxidase From B. Pseudomallei with Maltose Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:19.3 occ:1.00 O A:GLY124 2.3 17.2 1.0 O A:HOH1066 2.4 21.6 1.0 O A:SER494 2.4 18.5 1.0 O A:HOH1450 2.4 20.3 1.0 O A:GLY122 2.4 18.8 1.0 C A:SER494 3.2 19.1 1.0 C A:GLY124 3.5 18.3 1.0 C A:GLY122 3.6 18.4 1.0 N A:GLY124 3.6 17.0 1.0 CA A:ARG123 3.6 18.5 1.0 C A:ARG123 3.6 17.5 1.0 O A:HOH1488 3.9 21.1 1.0 CA A:SER494 3.9 17.3 1.0 O A:HOH1024 4.0 29.4 1.0 OD2 A:ASP427 4.0 18.7 1.0 N A:ARG123 4.1 17.3 1.0 N A:ASP495 4.1 16.3 1.0 CB A:ASP427 4.1 20.7 1.0 O A:ARG123 4.1 16.4 1.0 CA A:GLY124 4.1 18.4 1.0 CB A:SER494 4.1 19.4 1.0 CA A:ASP495 4.4 18.9 1.0 N A:GLY125 4.6 17.5 1.0 CG A:ASP427 4.6 21.9 1.0 CB A:ASP495 4.6 16.9 1.0 CL A:CL803 4.6 36.2 1.0 CD1 A:TYR117 4.6 20.0 1.0 O A:HOH1145 4.8 43.5 1.0 CA A:GLY122 4.8 17.8 1.0 CA A:GLY125 4.9 17.4 1.0 CE1 A:TYR117 4.9 19.6 1.0 CB A:ARG123 4.9 18.9 1.0 OE2 A:GLU128 5.0 31.2 1.0 OG A:SER494 5.0 18.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei with Maltose 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 the Catalase-Peroxidase From B. Pseudomallei with Maltose Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:19.6 occ:1.00 O B:HOH1474 2.3 24.2 1.0 O B:GLY124 2.4 17.2 1.0 O B:GLY122 2.4 16.8 1.0 O B:HOH1068 2.4 21.8 1.0 O B:SER494 2.4 18.3 1.0 C B:SER494 3.2 18.7 1.0 C B:GLY122 3.5 17.3 1.0 C B:GLY124 3.5 18.0 1.0 C B:ARG123 3.6 16.4 1.0 N B:GLY124 3.6 18.9 1.0 CA B:ARG123 3.6 17.2 1.0 CA B:SER494 4.0 17.6 1.0 O B:HOH1518 4.0 20.1 1.0 N B:ARG123 4.0 15.7 1.0 O B:HOH1016 4.0 30.1 1.0 N B:ASP495 4.1 18.0 1.0 CB B:SER494 4.1 18.0 1.0 O B:ARG123 4.1 16.5 1.0 OD2 B:ASP427 4.1 20.3 1.0 CB B:ASP427 4.2 20.1 1.0 CA B:GLY124 4.2 17.0 1.0 CA B:ASP495 4.5 16.8 1.0 CB B:ASP495 4.6 17.2 1.0 CD1 B:TYR117 4.6 17.0 1.0 N B:GLY125 4.6 15.9 1.0 CG B:ASP427 4.7 19.1 1.0 CL B:CL803 4.7 38.2 1.0 CA B:GLY122 4.8 17.5 1.0 CE1 B:TYR117 4.9 18.4 1.0 CA B:GLY125 4.9 16.3 1.0 CB B:ARG123 4.9 16.2 1.0 OE2 B:GLU128 4.9 31.4 1.0 OG B:SER494 5.0 17.4 1.0

P.C.Loewen, P.M.De Silva, L.J.Donald, J.Switala, J.Villanueva, I.Fita, A.Kumar. Katg-Mediated Oxidation Leading to Reduced Susceptibility of Bacteria to Kanamycin. Acs Omega V. 3 4213 2018.
ISSN: ESSN 2470-1343
PubMed: 29732452
DOI: 10.1021/ACSOMEGA.8B00356