Sodium in PDB 2fv7: Crystal Structure of Human Ribokinase

All present enzymatic activity of Crystal Structure of Human Ribokinase:
2.7.1.15;

The structure of Crystal Structure of Human Ribokinase, PDB code: 2fv7 was solved by W.M.Rabeh, W.Tempel, L.Nedyalkova, C.Arrowsmith, A.Edwards, M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.530, 72.978, 90.958, 90.00, 91.08, 90.00
R / Rfree (%)	19.8 / 24.8

The structure of Crystal Structure of Human Ribokinase also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Ribokinase (pdb code 2fv7). 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, PDB code: 2fv7:
Jump to Sodium binding site number: 1; 2;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:34.1 occ:1.00 O A:HOH879 2.2 27.3 1.0 O A:ALA304 2.4 32.6 1.0 O A:SER301 2.5 30.9 1.0 O A:HOH878 2.5 29.5 1.0 O A:ASP263 2.6 36.5 1.0 OG A:SER310 2.7 28.4 1.0 CB A:SER310 3.2 30.4 1.0 C A:SER301 3.5 29.7 1.0 C A:ALA304 3.6 32.6 1.0 C A:ASP263 3.7 36.9 1.0 O A:THR265 4.0 33.9 1.0 CA A:VAL302 4.1 29.4 1.0 CB A:ASP263 4.1 37.8 1.0 N A:VAL302 4.2 29.5 1.0 OD2 A:ASP263 4.2 39.0 1.0 CG A:ASP263 4.3 38.8 1.0 CA A:ALA305 4.3 33.4 1.0 N A:THR307 4.4 34.9 1.0 N A:ALA305 4.4 33.0 1.0 N A:ALA304 4.4 32.0 1.0 C A:VAL302 4.4 30.0 1.0 CA A:ASP263 4.5 37.5 1.0 CA A:SER301 4.5 29.3 1.0 C A:ALA305 4.5 34.1 1.0 O A:VAL302 4.5 29.6 1.0 CA A:ALA304 4.6 32.3 1.0 CB A:SER301 4.6 29.4 1.0 N A:GLY306 4.6 34.4 1.0 OG A:SER301 4.7 30.7 1.0 CA A:SER310 4.7 30.5 1.0 N A:THR264 4.7 36.3 1.0 O A:THR307 4.8 34.1 1.0 CA A:THR307 4.8 34.5 1.0 N A:THR265 4.8 34.9 1.0 CA A:THR264 4.9 35.9 1.0 N A:ASP263 4.9 38.0 1.0 C A:THR264 4.9 35.1 1.0 O A:ALA305 5.0 34.5 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:29.5 occ:1.00 O B:HOH845 2.3 23.7 1.0 O B:ASP263 2.3 29.3 1.0 O B:HOH853 2.4 29.1 1.0 O B:SER301 2.4 24.9 1.0 O B:ALA304 2.4 28.0 1.0 OG B:SER310 3.1 27.2 1.0 CB B:SER310 3.3 29.1 1.0 C B:SER301 3.4 25.7 1.0 C B:ASP263 3.5 29.8 1.0 C B:ALA304 3.6 27.9 1.0 CA B:VAL302 3.9 26.1 1.0 O B:THR265 3.9 30.4 1.0 CB B:ASP263 4.0 29.6 1.0 N B:VAL302 4.1 25.6 1.0 CA B:ASP263 4.2 30.0 1.0 C B:VAL302 4.2 26.5 1.0 CG B:ASP263 4.3 31.9 1.0 N B:ALA304 4.3 27.2 1.0 OD2 B:ASP263 4.4 33.1 1.0 O B:VAL302 4.4 26.8 1.0 N B:THR264 4.5 30.3 1.0 N B:ALA305 4.5 28.4 1.0 CA B:ALA304 4.5 27.4 1.0 CA B:ALA305 4.5 29.4 1.0 CA B:SER301 4.5 25.9 1.0 N B:ASP263 4.5 29.7 1.0 OG B:SER301 4.6 27.6 1.0 N B:THR307 4.7 35.1 1.0 C B:ALA305 4.7 29.9 1.0 CB B:SER301 4.7 26.1 1.0 CA B:THR264 4.7 30.8 1.0 N B:THR265 4.7 31.6 1.0 C B:THR264 4.8 31.3 1.0 CA B:SER310 4.8 29.4 1.0 N B:GLY306 4.8 31.5 1.0 N B:GLN303 4.9 26.9 1.0 OD1 B:ASP263 4.9 35.2 1.0 C B:THR265 5.0 31.3 1.0

W.M.Rabeh, W.Tempel, L.Nedyalkova, C.Arrowsmith, A.Edwards, M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park, Structural Genomics Consortium (Sgc). Crystal Structure of Human Ribokinase To Be Published.