Sodium in PDB 3imx: Crystal Structure of Human Glucokinase in Complex with A Synthetic Activator

The structure of Crystal Structure of Human Glucokinase in Complex with A Synthetic Activator, PDB code: 3imx was solved by T.Stams, B.Vash, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.49 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.500, 90.300, 116.200, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Sodium atom in the Crystal Structure of Human Glucokinase in Complex with A Synthetic Activator (pdb code 3imx). 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 A Synthetic Activator, PDB code: 3imx:

Sodium binding site 1 out of 1 in the Crystal Structure of Human Glucokinase in Complex with A Synthetic 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 A Synthetic Activator within 5.0Å range: probe atom residue distance (Å) B Occ A:Na467 b:26.6 occ:1.00 O A:VAL244 2.4 26.8 1.0 O A:MET238 2.5 21.4 1.0 O A:VAL241 2.5 23.3 1.0 O A:GLY246 2.5 27.6 1.0 O A:HOH694 2.6 27.7 1.0 C A:MET238 3.4 23.8 1.0 C A:VAL241 3.5 25.5 1.0 C A:VAL244 3.5 28.4 1.0 C A:GLY246 3.7 30.8 1.0 CE A:MET238 3.8 22.7 1.0 N A:GLY246 3.9 31.9 1.0 C A:GLU245 4.0 31.4 1.0 CB A:VAL241 4.1 20.8 1.0 CA A:VAL241 4.2 22.6 1.0 CA A:MET238 4.2 21.6 1.0 N A:VAL241 4.2 21.8 1.0 CA A:GLY246 4.3 29.9 1.0 N A:GLN239 4.3 24.8 1.0 O A:HOH629 4.3 34.8 1.0 CB A:MET238 4.3 20.7 1.0 CA A:GLU245 4.4 32.9 1.0 CA A:GLN239 4.4 27.9 1.0 N A:GLU242 4.4 26.5 1.0 N A:GLU245 4.4 31.6 1.0 SD A:MET238 4.4 26.5 1.0 CA A:VAL244 4.5 27.6 1.0 N A:VAL244 4.5 28.3 1.0 O A:GLU245 4.5 31.9 1.0 CA A:GLU242 4.6 28.1 1.0 C A:GLN239 4.6 27.9 1.0 OD1 A:ASP247 4.6 40.1 1.0 CB A:VAL244 4.7 27.2 1.0 N A:ASP247 4.7 30.9 1.0 O A:GLN239 4.8 29.6 1.0 CG1 A:VAL241 4.8 17.4 1.0 C A:GLU242 4.9 28.8 1.0 CA A:ASP247 5.0 33.1 1.0

G.R.Bebernitz, V.Beaulieu, B.A.Dale, R.Deacon, A.Duttaroy, J.Gao, M.S.Grondine, R.C.Gupta, M.Kakmak, M.Kavana, L.C.Kirman, J.Liang, W.M.Maniara, S.Munshi, S.S.Nadkarni, H.F.Schuster, T.Stams, I.St Denny, P.M.Taslimi, B.Vash, S.L.Caplan. Investigation of Functionally Liver Selective Glucokinase Activators For the Treatment of Type 2 Diabetes. J.Med.Chem. V. 52 6142 2009.
ISSN: ISSN 0022-2623
PubMed: 19746978
DOI: 10.1021/JM900839K