Sodium in PDB 5sxs: Crystal Structure of Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp Bound

All present enzymatic activity of Crystal Structure of Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp Bound:
1.11.1.21;

The structure of Crystal Structure of Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp Bound, PDB code: 5sxs 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 / 1.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.436, 114.172, 174.232, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 19.3

The structure of Crystal Structure of Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp 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 Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp Bound (pdb code 5sxs). 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 Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp Bound, PDB code: 5sxs:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp 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 Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:16.7 occ:1.00 O A:GLY124 2.3 17.8 1.0 O A:SER494 2.3 16.3 1.0 O A:GLY122 2.4 18.0 1.0 O A:HOH1405 2.5 21.9 1.0 O A:HOH1155 2.5 22.5 1.0 C A:SER494 3.2 16.7 1.0 C A:GLY124 3.5 17.5 1.0 C A:GLY122 3.5 17.5 1.0 N A:GLY124 3.5 17.6 1.0 C A:ARG123 3.6 17.8 1.0 CA A:ARG123 3.6 18.7 1.0 CA A:SER494 4.0 17.1 1.0 O A:HOH1459 4.0 18.2 1.0 N A:ARG123 4.0 17.4 1.0 OD2 A:ASP427 4.0 18.4 1.0 O A:HOH1092 4.0 30.8 1.0 N A:ASP495 4.1 16.6 1.0 CA A:GLY124 4.1 18.3 1.0 CB A:ASP427 4.1 17.6 1.0 O A:ARG123 4.1 18.2 1.0 CB A:SER494 4.2 18.4 1.0 CA A:ASP495 4.4 16.8 1.0 N A:GLY125 4.6 17.8 1.0 CG A:ASP427 4.6 18.0 1.0 CB A:ASP495 4.6 16.9 1.0 CL A:CL803 4.6 25.7 0.8 CD1 A:TYR117 4.7 18.0 1.0 CA A:GLY122 4.8 17.4 1.0 CB A:ARG123 4.9 19.9 1.0 OE2 A:GLU128 4.9 25.0 1.0 CA A:GLY125 4.9 16.7 1.0 OG A:SER494 4.9 18.3 1.0 CE1 A:TYR117 5.0 18.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp 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 Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:18.2 occ:1.00 O B:GLY124 2.3 18.1 1.0 O B:GLY122 2.3 15.6 1.0 O B:SER494 2.3 18.1 1.0 O B:HOH1406 2.3 16.4 1.0 O B:HOH1153 2.5 17.0 1.0 C B:SER494 3.1 17.1 1.0 C B:GLY122 3.5 16.0 1.0 C B:GLY124 3.5 18.7 1.0 N B:GLY124 3.6 18.7 1.0 C B:ARG123 3.6 18.1 1.0 CA B:ARG123 3.6 17.0 1.0 CA B:SER494 3.9 17.1 1.0 N B:ASP495 4.0 17.5 1.0 OD2 B:ASP427 4.0 17.8 1.0 N B:ARG123 4.0 16.0 1.0 O B:HOH1523 4.0 20.4 1.0 CB B:ASP427 4.1 20.6 1.0 CB B:SER494 4.1 16.6 1.0 O B:HOH1092 4.2 27.1 1.0 O B:ARG123 4.2 17.0 1.0 CA B:GLY124 4.2 18.9 1.0 CA B:ASP495 4.4 17.5 1.0 CB B:ASP495 4.5 16.6 1.0 CG B:ASP427 4.6 19.9 1.0 N B:GLY125 4.6 17.6 1.0 CD1 B:TYR117 4.7 16.4 1.0 CL B:CL803 4.7 20.8 0.8 CA B:GLY122 4.8 16.1 1.0 OE2 B:GLU128 4.9 26.5 1.0 OG B:SER494 4.9 17.6 1.0 CA B:GLY125 4.9 17.0 1.0 CB B:ARG123 4.9 17.1 1.0 CE1 B:TYR117 4.9 15.9 1.0

B.Wiseman, X.Carpena, M.Feliz, L.J.Donald, M.Pons, I.Fita, P.C.Loewen. Isonicotinic Acid Hydrazide Conversion to Isonicotinyl-Nad By Catalase-Peroxidases. J. Biol. Chem. V. 285 26662 2010.
ISSN: ESSN 1083-351X
PubMed: 20554537
DOI: 10.1074/JBC.M110.139428