Sodium in PDB 6wjz: Crystal Structure of Human Ribokinase in Complex with Ampcp

All present enzymatic activity of Crystal Structure of Human Ribokinase in Complex with Ampcp:
2.7.1.15;

The structure of Crystal Structure of Human Ribokinase in Complex with Ampcp, PDB code: 6wjz was solved by J.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.49 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.11, 71.86, 91.43, 90, 91.78, 90
R / Rfree (%)	15.2 / 18.6

The structure of Crystal Structure of Human Ribokinase in Complex with Ampcp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Ribokinase in Complex with Ampcp (pdb code 6wjz). 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 Human Ribokinase in Complex with Ampcp, PDB code: 6wjz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Ribokinase in Complex with Ampcp


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 Human Ribokinase in Complex with Ampcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:27.9 occ:1.00 O A:HOH571 2.2 36.0 1.0 O A:ALA304 2.5 33.0 1.0 O A:SER301 2.5 27.9 1.0 O A:HOH631 2.6 31.5 1.0 O A:ASP263 2.6 33.4 1.0 OG A:SER310 2.8 27.4 1.0 CB A:SER310 3.2 29.3 1.0 C A:SER301 3.5 26.6 1.0 O A:THR265 3.7 30.5 1.0 C A:ALA304 3.7 36.8 1.0 C A:ASP263 3.8 35.9 1.0 CA A:VAL302 4.0 27.7 1.0 CB A:ASP263 4.2 40.5 1.0 N A:VAL302 4.2 26.9 1.0 CG A:ASP263 4.3 44.1 1.0 OD2 A:ASP263 4.4 45.5 1.0 C A:ALA305 4.4 41.9 1.0 N A:ALA304 4.4 36.1 1.0 C A:VAL302 4.4 30.7 1.0 CA A:SER301 4.5 26.8 1.0 CA A:ASP263 4.5 39.2 1.0 N A:THR307 4.5 38.3 1.0 N A:ALA305 4.6 40.2 1.0 N A:GLY306 4.6 43.1 1.0 CA A:ALA305 4.6 42.0 1.0 OG A:SER301 4.6 25.0 1.0 CB A:SER301 4.6 24.9 1.0 CA A:ALA304 4.6 36.8 1.0 CA A:SER310 4.7 29.3 1.0 N A:THR265 4.7 33.3 1.0 O A:VAL302 4.7 32.8 1.0 N A:THR264 4.8 35.5 1.0 C A:THR265 4.8 31.4 1.0 O A:ALA305 4.8 40.9 1.0 C A:THR264 4.9 33.0 1.0 OD1 A:ASP263 4.9 44.2 1.0 O A:THR307 4.9 30.5 1.0 CA A:THR264 4.9 33.6 1.0 CA A:THR307 4.9 35.1 1.0 N A:ASP263 5.0 38.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Ribokinase in Complex with Ampcp


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 Human Ribokinase in Complex with Ampcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:27.6 occ:1.00 O B:HOH519 2.2 43.1 1.0 O B:ASP263 2.4 30.8 1.0 O B:HOH583 2.5 35.2 1.0 O B:ALA304 2.5 29.2 1.0 O B:SER301 2.6 28.6 1.0 OG B:SER310 2.9 33.0 1.0 CB B:SER310 3.3 32.8 1.0 C B:SER301 3.5 29.1 1.0 C B:ASP263 3.6 32.1 1.0 O B:THR265 3.7 32.8 1.0 C B:ALA304 3.8 30.3 1.0 CA B:VAL302 3.9 28.6 1.0 N B:VAL302 4.1 28.9 1.0 CB B:ASP263 4.1 35.1 1.0 CG B:ASP263 4.3 37.9 1.0 CA B:ASP263 4.3 33.5 1.0 C B:VAL302 4.3 28.6 1.0 OD2 B:ASP263 4.4 41.5 1.0 N B:ALA304 4.5 29.3 1.0 CA B:SER301 4.5 31.1 1.0 N B:THR265 4.5 32.3 1.0 N B:THR307 4.5 39.4 1.0 N B:THR264 4.5 31.2 1.0 O B:VAL302 4.6 28.5 1.0 OG B:SER301 4.6 31.3 1.0 C B:ALA305 4.6 36.0 1.0 CB B:SER301 4.6 29.4 1.0 N B:ALA305 4.7 31.8 1.0 CA B:ALA304 4.7 30.4 1.0 C B:THR264 4.7 31.4 1.0 N B:GLY306 4.7 40.0 1.0 C B:THR265 4.7 31.7 1.0 N B:ASP263 4.7 32.1 1.0 CA B:THR264 4.7 31.9 1.0 OD1 B:ASP263 4.8 41.2 1.0 CA B:ALA305 4.8 34.0 1.0 CA B:SER310 4.8 33.3 1.0 O B:ALA305 5.0 37.8 1.0 N B:GLN303 5.0 29.4 1.0

J.Park, J.Park. N/A N/A.