Sodium in PDB 5sw5: Crystal Structure of Native Catalase-Peroxidase Katg at PH7.5

All present enzymatic activity of Crystal Structure of Native Catalase-Peroxidase Katg at PH7.5:
1.11.1.21;

The structure of Crystal Structure of Native Catalase-Peroxidase Katg at PH7.5, PDB code: 5sw5 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 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.343, 114.851, 174.860, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 18.4

The structure of Crystal Structure of Native Catalase-Peroxidase Katg at PH7.5 also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Native Catalase-Peroxidase Katg at PH7.5 (pdb code 5sw5). 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 Native Catalase-Peroxidase Katg at PH7.5, PDB code: 5sw5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Native Catalase-Peroxidase Katg at PH7.5


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 Native Catalase-Peroxidase Katg at PH7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:23.6 occ:1.00 O A:SER494 2.3 22.7 1.0 O A:GLY124 2.3 22.5 1.0 O A:HOH982 2.3 18.6 1.0 O A:HOH1237 2.4 26.7 1.0 O A:GLY122 2.4 24.2 1.0 C A:SER494 3.2 20.8 1.0 C A:GLY124 3.5 20.8 1.0 C A:GLY122 3.6 20.5 1.0 C A:ARG123 3.6 19.3 1.0 N A:GLY124 3.6 20.1 1.0 CA A:ARG123 3.7 19.7 1.0 O A:HOH1169 3.9 24.2 1.0 O A:HOH934 3.9 32.0 1.0 OD2 A:ASP427 4.0 22.8 1.0 CA A:SER494 4.0 20.2 1.0 N A:ASP495 4.0 19.6 1.0 CB A:ASP427 4.1 23.7 1.0 N A:ARG123 4.1 18.9 1.0 CA A:GLY124 4.1 21.8 1.0 O A:ARG123 4.2 19.1 1.0 CB A:SER494 4.3 21.5 1.0 CA A:ASP495 4.4 21.5 1.0 CG A:ASP427 4.5 22.4 1.0 CB A:ASP495 4.5 19.4 1.0 N A:GLY125 4.6 20.9 1.0 OE2 A:GLU128 4.6 51.2 1.0 CD1 A:TYR117 4.7 21.2 1.0 OE2 A:GLU198 4.8 45.3 1.0 CA A:GLY122 4.8 20.6 1.0 CA A:GLY125 4.9 19.6 1.0 CB A:ARG123 4.9 19.8 1.0 CE1 A:TYR117 4.9 21.2 1.0 OE1 A:GLU198 5.0 38.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Native Catalase-Peroxidase Katg at PH7.5


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 Native Catalase-Peroxidase Katg at PH7.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:22.2 occ:1.00 O B:HOH1065 2.3 22.8 1.0 O B:GLY122 2.3 18.0 1.0 O B:GLY124 2.3 20.8 1.0 O B:SER494 2.3 19.7 1.0 O B:HOH1111 2.4 27.1 1.0 C B:SER494 3.2 20.5 1.0 C B:GLY122 3.5 18.0 1.0 C B:GLY124 3.5 18.2 1.0 C B:ARG123 3.6 19.0 1.0 CA B:ARG123 3.6 19.1 1.0 N B:GLY124 3.6 19.3 1.0 CA B:SER494 4.0 19.4 1.0 O B:HOH1255 4.0 22.2 1.0 O B:HOH960 4.0 33.4 1.0 N B:ASP495 4.0 20.1 1.0 N B:ARG123 4.0 18.3 1.0 OD2 B:ASP427 4.1 22.6 1.0 O B:ARG123 4.1 17.8 1.0 CB B:ASP427 4.1 22.5 1.0 CA B:GLY124 4.2 18.7 1.0 CB B:SER494 4.2 19.0 1.0 CA B:ASP495 4.4 19.0 1.0 CB B:ASP495 4.5 19.4 1.0 CD1 B:TYR117 4.6 23.2 1.0 N B:GLY125 4.6 19.3 1.0 CG B:ASP427 4.6 24.1 1.0 OE2 B:GLU128 4.7 48.5 1.0 CA B:GLY122 4.7 18.9 1.0 OE2 B:GLU198 4.8 32.3 1.0 CE1 B:TYR117 4.8 23.3 1.0 CB B:ARG123 4.9 19.8 1.0 CA B:GLY125 4.9 18.5 1.0 OG B:SER494 5.0 18.1 1.0

X.Carpena, B.Wiseman, T.Deemagarn, R.Singh, J.Switala, A.Ivancich, I.Fita, P.C.Loewen. A Molecular Switch and Electronic Circuit Modulate Catalase Activity in Catalase-Peroxidases. Embo Rep. V. 6 1156 2005.
ISSN: ISSN 1469-221X
PubMed: 16211084