Sodium in PDB 5syk: Crystal Structure of B. Pseudomallei Katg Treated with Hydrogen Peroxide

All present enzymatic activity of Crystal Structure of B. Pseudomallei Katg Treated with Hydrogen Peroxide:
1.11.1.21;

The structure of Crystal Structure of B. Pseudomallei Katg Treated with Hydrogen Peroxide, PDB code: 5syk 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 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.720, 116.200, 174.660, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 17.9

The structure of Crystal Structure of B. Pseudomallei Katg Treated with Hydrogen Peroxide 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 Treated with Hydrogen Peroxide (pdb code 5syk). 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 Treated with Hydrogen Peroxide, PDB code: 5syk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of B. Pseudomallei Katg Treated with Hydrogen Peroxide


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 Treated with Hydrogen Peroxide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:16.5 occ:1.00 O A:GLY124 2.3 14.6 1.0 O A:HOH1473 2.3 19.5 1.0 O A:GLY122 2.4 14.8 1.0 O A:HOH1131 2.4 19.5 1.0 O A:SER494 2.5 15.6 1.0 C A:SER494 3.3 15.5 1.0 C A:GLY124 3.4 14.7 1.0 C A:GLY122 3.5 15.1 1.0 C A:ARG123 3.6 14.6 1.0 N A:GLY124 3.6 14.3 1.0 CA A:ARG123 3.6 15.8 1.0 O A:HOH1528 4.0 16.8 1.0 CA A:SER494 4.0 14.2 1.0 O A:HOH1053 4.0 26.8 1.0 N A:ARG123 4.0 14.7 1.0 OD2 A:ASP427 4.1 17.8 1.0 CA A:GLY124 4.1 14.7 1.0 CB A:ASP427 4.1 19.4 1.0 O A:ARG123 4.1 13.3 1.0 N A:ASP495 4.2 15.2 1.0 CB A:SER494 4.2 15.4 1.0 CA A:ASP495 4.4 15.5 1.0 N A:GLY125 4.6 14.5 1.0 CB A:ASP495 4.6 15.6 1.0 CD1 A:TYR117 4.6 17.0 1.0 CG A:ASP427 4.6 20.1 1.0 CL A:CL803 4.6 33.2 1.0 CA A:GLY122 4.8 15.1 1.0 CA A:GLY125 4.9 13.6 1.0 CE1 A:TYR117 4.9 16.6 1.0 CB A:ARG123 4.9 16.7 1.0 OG A:SER494 5.0 14.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of B. Pseudomallei Katg Treated with Hydrogen Peroxide


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 Treated with Hydrogen Peroxide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:16.0 occ:1.00 O B:HOH1499 2.3 19.1 1.0 O B:GLY122 2.4 13.8 1.0 O B:GLY124 2.4 15.9 1.0 O B:HOH1117 2.4 21.2 1.0 O B:SER494 2.5 14.9 1.0 C B:SER494 3.3 13.8 1.0 C B:GLY122 3.5 13.6 1.0 C B:GLY124 3.5 13.9 1.0 C B:ARG123 3.6 14.7 1.0 CA B:ARG123 3.6 14.1 1.0 N B:GLY124 3.6 14.3 1.0 CA B:SER494 3.9 14.5 1.0 O B:HOH1540 4.0 17.7 1.0 N B:ARG123 4.0 13.4 1.0 O B:HOH928 4.1 28.9 1.0 OD2 B:ASP427 4.1 19.3 1.0 CB B:SER494 4.1 14.1 1.0 N B:ASP495 4.1 13.7 1.0 CA B:GLY124 4.1 14.7 1.0 O B:ARG123 4.2 14.0 1.0 CB B:ASP427 4.2 19.2 1.0 CA B:ASP495 4.4 15.1 1.0 CB B:ASP495 4.5 15.0 1.0 CD1 B:TYR117 4.6 15.2 1.0 CL B:CL803 4.6 32.0 1.0 N B:GLY125 4.7 13.6 1.0 CG B:ASP427 4.7 18.9 1.0 CA B:GLY122 4.7 14.1 1.0 CE1 B:TYR117 4.8 16.6 1.0 CB B:ARG123 4.9 14.5 1.0 OG B:SER494 4.9 14.2 1.0 OE2 B:GLU128 5.0 31.0 1.0 CA B:GLY125 5.0 13.0 1.0

P.C.Loewen, X.Carpena, P.Vidossich, I.Fita, C.Rovira. An Ionizable Active-Site Tryptophan Imparts Catalase Activity to A Peroxidase Core. J. Am. Chem. Soc. V. 136 7249 2014.
ISSN: ESSN 1520-5126
PubMed: 24785434
DOI: 10.1021/JA502794E