Sodium in PDB 3wnu: The Crystal Structure of Catalase-Peroxidase, Katg, From Synechococcus PCC7942

All present enzymatic activity of The Crystal Structure of Catalase-Peroxidase, Katg, From Synechococcus PCC7942:
1.11.1.21;

The structure of The Crystal Structure of Catalase-Peroxidase, Katg, From Synechococcus PCC7942, PDB code: 3wnu was solved by T.Tada, K.Wada, S.Kamachi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.39 / 2.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	108.744, 108.744, 202.888, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.6

The structure of The Crystal Structure of Catalase-Peroxidase, Katg, From Synechococcus PCC7942 also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Sodium atom in the The Crystal Structure of Catalase-Peroxidase, Katg, From Synechococcus PCC7942 (pdb code 3wnu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Crystal Structure of Catalase-Peroxidase, Katg, From Synechococcus PCC7942, PDB code: 3wnu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Crystal Structure of Catalase-Peroxidase, Katg, From Synechococcus PCC7942


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Catalase-Peroxidase, Katg, From Synechococcus PCC7942 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:27.8 occ:1.00 O A:GLY105 2.3 25.9 1.0 O A:GLY107 2.3 24.4 1.0 O A:HOH1325 2.3 21.2 1.0 O A:SER476 2.4 26.5 1.0 O A:HOH1078 2.4 29.4 1.0 C A:SER476 3.2 25.8 1.0 C A:GLY107 3.4 26.4 1.0 C A:GLY105 3.4 27.9 1.0 N A:GLY107 3.5 24.9 1.0 CA A:ARG106 3.5 23.4 1.0 C A:ARG106 3.6 22.9 1.0 O A:HOH936 3.6 25.4 1.0 O A:HOH1134 3.8 28.9 1.0 CA A:SER476 3.9 25.9 1.0 N A:ARG106 4.0 26.5 1.0 OD2 A:ASP413 4.0 27.4 1.0 CB A:SER476 4.0 25.6 1.0 CB A:ASP413 4.0 29.0 1.0 CA A:GLY107 4.0 25.0 1.0 N A:ASP477 4.1 31.8 1.0 O A:ARG106 4.3 23.2 1.0 CD1 A:TYR100 4.4 28.1 1.0 CA A:ASP477 4.5 30.4 1.0 N A:GLY108 4.5 27.6 1.0 CG A:ASP413 4.5 25.4 1.0 CB A:ASP477 4.6 29.2 1.0 CA A:GLY105 4.7 27.3 1.0 CE1 A:TYR100 4.7 29.9 1.0 CA A:GLY108 4.8 25.5 1.0 CB A:ARG106 4.9 26.8 1.0 OG A:SER476 4.9 27.1 1.0

Sodium binding site 2 out of 2 in the The Crystal Structure of Catalase-Peroxidase, Katg, From Synechococcus PCC7942


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Catalase-Peroxidase, Katg, From Synechococcus PCC7942 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na803 b:27.1 occ:1.00 O A:HIS317 2.3 30.6 1.0 O A:THR264 2.4 25.4 1.0 O A:GLN320 2.4 29.1 1.0 OD2 A:ASP322 2.5 29.3 1.0 OD1 A:ASP322 2.8 31.6 1.0 OG1 A:THR315 2.8 25.1 1.0 CG A:ASP322 2.9 31.7 1.0 C A:HIS317 3.4 31.4 1.0 C A:GLN320 3.6 30.6 1.0 C A:THR264 3.6 25.0 1.0 CB A:THR315 3.7 28.7 1.0 O A:HOH1253 3.8 27.1 1.0 CG2 A:THR264 3.9 26.1 1.0 CG2 A:THR315 4.0 31.0 1.0 CA A:PRO318 4.0 30.5 1.0 N A:PRO318 4.1 30.8 1.0 N A:GLN320 4.2 28.8 1.0 CB A:ASP322 4.2 29.2 1.0 CA A:GLN320 4.3 30.8 1.0 CA A:HIS317 4.3 31.0 1.0 CB A:HIS317 4.4 34.1 1.0 CA A:THR264 4.5 24.4 1.0 N A:ASP322 4.5 31.3 1.0 C A:PRO318 4.5 28.3 1.0 N A:HIS317 4.6 31.9 1.0 N A:VAL265 4.6 26.0 1.0 CG1 A:VAL265 4.6 33.0 1.0 CA A:VAL265 4.6 25.1 1.0 N A:TRP321 4.6 26.8 1.0 C A:TRP321 4.7 28.5 1.0 CG A:GLN320 4.7 45.7 1.0 O A:HOH944 4.7 28.8 1.0 CA A:TRP321 4.8 27.2 1.0 CB A:THR264 4.8 26.5 1.0 CA A:ASP322 4.9 27.6 1.0 O A:PRO318 4.9 32.9 1.0 N A:THR319 4.9 32.2 1.0 O A:HOH1073 5.0 35.5 1.0

S.Kamachi, K.Wada, M.Tamoi, S.Shigeoka, T.Tada. The 2.2 Aa Resolution Structure of the Catalase-Peroxidase Katg From Synechococcus Elongatus PCC7942. Acta Crystallogr.,Sect.F V. 70 288 2014.
ISSN: ESSN 1744-3091
DOI: 10.1107/S2053230X14002052