Sodium in PDB 5syh: Structure of D141A Variant of B. Pseudomallei Katg

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

The structure of Structure of D141A Variant of B. Pseudomallei Katg, PDB code: 5syh 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 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.770, 113.450, 174.650, 90.00, 90.00, 90.00
R / Rfree (%)	14 / 17.1

The structure of Structure of D141A Variant of B. Pseudomallei Katg 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 (pdb code 5syh). 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, PDB code: 5syh:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:15.5 occ:1.00 O A:GLY124 2.3 14.4 1.0 O A:HOH1490 2.4 17.9 1.0 O A:GLY122 2.4 13.4 1.0 O A:SER494 2.4 15.2 1.0 O A:HOH1026 2.4 18.9 1.0 C A:SER494 3.3 17.1 1.0 C A:GLY124 3.5 14.8 1.0 C A:GLY122 3.5 13.0 1.0 CA A:ARG123 3.5 12.4 1.0 N A:GLY124 3.5 14.4 1.0 C A:ARG123 3.6 13.6 1.0 N A:ARG123 3.9 12.6 1.0 CA A:SER494 4.0 15.2 1.0 OD2 A:ASP427 4.0 18.9 1.0 O A:HOH1541 4.0 21.1 1.0 O A:HOH972 4.1 29.4 1.0 CA A:GLY124 4.1 14.8 1.0 CB A:SER494 4.1 16.7 1.0 O A:ARG123 4.1 13.5 1.0 N A:ASP495 4.1 14.1 1.0 CB A:ASP427 4.1 16.8 1.0 CA A:ASP495 4.5 14.8 1.0 CB A:ASP495 4.6 14.3 1.0 N A:GLY125 4.6 13.3 1.0 CL A:CL803 4.6 33.5 1.0 CG A:ASP427 4.6 21.3 1.0 CD1 A:TYR117 4.7 14.1 1.0 CA A:GLY122 4.7 14.0 1.0 CB A:ARG123 4.8 15.2 1.0 CE1 A:TYR117 4.8 13.9 1.0 OE2 A:GLU128 4.9 35.7 1.0 CA A:GLY125 4.9 12.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:15.8 occ:1.00 O B:HOH1515 2.3 19.1 1.0 O B:GLY124 2.3 14.2 1.0 O B:GLY122 2.4 13.8 1.0 O B:HOH992 2.4 18.6 1.0 O B:SER494 2.4 15.8 1.0 C B:SER494 3.3 15.9 1.0 C B:GLY124 3.5 14.8 1.0 C B:GLY122 3.5 13.6 1.0 CA B:ARG123 3.5 12.2 1.0 C B:ARG123 3.6 12.9 1.0 N B:GLY124 3.6 13.8 1.0 O B:HOH1558 4.0 21.6 1.0 CA B:SER494 4.0 14.3 1.0 N B:ARG123 4.0 12.4 1.0 OD2 B:ASP427 4.0 19.9 1.0 O B:HOH1124 4.0 33.7 1.0 CB B:SER494 4.1 15.1 1.0 O B:ARG123 4.1 12.8 1.0 N B:ASP495 4.2 13.0 1.0 CA B:GLY124 4.2 14.1 1.0 CB B:ASP427 4.2 17.4 1.0 CA B:ASP495 4.6 14.1 1.0 N B:GLY125 4.6 13.5 1.0 CD1 B:TYR117 4.6 15.5 1.0 CB B:ASP495 4.6 13.5 1.0 CL B:CL803 4.6 33.2 1.0 CG B:ASP427 4.7 19.4 1.0 CA B:GLY122 4.8 13.5 1.0 CE1 B:TYR117 4.9 13.4 1.0 CA B:GLY125 4.9 13.4 1.0 CB B:ARG123 4.9 13.3 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