Sodium in PDB 3vf6: Glucokinase in Complex with Glucose and Activator

All present enzymatic activity of Glucokinase in Complex with Glucose and Activator:
2.7.1.2;

The structure of Glucokinase in Complex with Glucose and Activator, PDB code: 3vf6 was solved by S.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.81 / 1.86
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.850, 82.230, 86.140, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.5

The structure of Glucokinase in Complex with Glucose and Activator also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Sodium atom in the Glucokinase in Complex with Glucose and Activator (pdb code 3vf6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Glucokinase in Complex with Glucose and Activator, PDB code: 3vf6:

Sodium binding site 1 out of 1 in the Glucokinase in Complex with Glucose and Activator


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Glucokinase in Complex with Glucose and Activator within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:23.0 occ:1.00 O A:HOH835 2.2 29.3 1.0 O A:VAL244 2.2 22.2 1.0 O A:VAL241 2.3 19.7 1.0 O A:MET238 2.4 21.4 1.0 O A:GLY246 2.5 31.6 1.0 C A:VAL241 3.3 19.9 1.0 C A:VAL244 3.5 25.3 1.0 C A:MET238 3.5 21.2 1.0 C A:GLY246 3.6 32.9 1.0 N A:GLY246 3.9 29.6 1.0 CE A:MET238 4.1 23.0 1.0 CA A:VAL241 4.1 15.7 1.0 C A:GLU245 4.2 31.0 1.0 CB A:VAL241 4.2 17.7 1.0 N A:VAL241 4.2 16.7 1.0 N A:GLU242 4.2 17.8 1.0 CA A:GLY246 4.3 30.1 1.0 CA A:VAL244 4.4 21.4 1.0 N A:VAL244 4.4 22.3 1.0 CA A:GLU242 4.4 20.0 1.0 CA A:MET238 4.4 17.1 1.0 N A:GLU245 4.4 25.7 1.0 N A:GLN239 4.4 18.5 1.0 CA A:GLN239 4.5 19.0 1.0 CA A:GLU245 4.5 28.5 1.0 O A:HOH809 4.5 34.1 1.0 O A:HOH751 4.6 55.0 1.0 SD A:MET238 4.6 25.2 1.0 C A:GLN239 4.6 22.1 1.0 CB A:MET238 4.6 19.9 1.0 OD2 A:ASP247 4.6 64.0 1.0 N A:ASP247 4.7 30.3 1.0 C A:GLU242 4.7 24.6 1.0 O A:GLU245 4.7 30.7 1.0 O A:GLN239 4.8 22.5 1.0 CB A:VAL244 4.8 23.5 1.0 CG1 A:VAL241 4.9 16.5 1.0 O A:GLU242 4.9 23.4 1.0 CA A:ASP247 4.9 30.8 1.0

S.Liu, M.J.Ammirati, X.Song, J.D.Knafels, J.Zhang, S.E.Greasley, J.A.Pfefferkorn, X.Qiu. Insights Into Mechanism of Glucokinase Activation: Observation of Multiple Distinct Protein Conformations. J.Biol.Chem. V. 287 13598 2012.
ISSN: ISSN 0021-9258
PubMed: 22298776
DOI: 10.1074/JBC.M111.274126