Sodium in PDB 4dhy: Crystal Structure of Human Glucokinase in Complex with Glucose and Activator

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

The structure of Crystal Structure of Human Glucokinase in Complex with Glucose and Activator, PDB code: 4dhy was solved by S.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.90 / 2.38
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.010, 82.200, 86.160, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 24.4

The binding sites of Sodium atom in the Crystal Structure of Human Glucokinase in Complex with Glucose and Activator (pdb code 4dhy). 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 Crystal Structure of Human Glucokinase in Complex with Glucose and Activator, PDB code: 4dhy:

Sodium binding site 1 out of 1 in the Crystal Structure of Human 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 Crystal Structure of Human Glucokinase in Complex with Glucose and Activator within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:18.1 occ:1.00 O A:VAL241 2.3 21.9 1.0 O A:MET238 2.3 24.7 1.0 O A:VAL244 2.3 23.0 1.0 O A:GLY246 2.4 30.1 1.0 C A:VAL241 3.3 22.3 1.0 C A:MET238 3.5 24.2 1.0 C A:GLY246 3.5 30.5 1.0 C A:VAL244 3.6 24.6 1.0 N A:GLY246 3.8 25.5 1.0 CE A:MET238 4.1 20.1 1.0 CA A:VAL241 4.1 20.2 1.0 N A:GLU242 4.2 16.7 1.0 CA A:GLY246 4.2 25.6 1.0 N A:VAL241 4.2 19.6 1.0 CB A:VAL241 4.3 24.0 1.0 C A:GLU245 4.3 29.3 1.0 N A:GLN239 4.3 20.1 1.0 CA A:GLN239 4.4 19.4 1.0 CA A:MET238 4.4 18.1 1.0 CA A:GLU242 4.4 17.7 1.0 N A:GLU245 4.4 24.9 1.0 O A:HOH674 4.5 27.7 1.0 C A:GLN239 4.5 22.7 1.0 CA A:VAL244 4.5 20.2 1.0 N A:ASP247 4.5 29.2 1.0 CA A:GLU245 4.5 27.2 1.0 N A:VAL244 4.6 21.9 1.0 CB A:MET238 4.7 19.8 1.0 O A:GLN239 4.7 23.8 1.0 CA A:ASP247 4.7 29.1 1.0 C A:GLU242 4.8 25.8 1.0 SD A:MET238 4.8 23.4 1.0 CB A:VAL244 4.9 21.9 1.0 O A:GLU242 4.9 27.6 1.0 O A:GLU245 4.9 28.8 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