Sodium in PDB 3s41: Glucokinase in Complex with Activator and Glucose

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

The structure of Glucokinase in Complex with Activator and Glucose, PDB code: 3s41 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 / 2.18
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 (%)	19 / 24.6

The binding sites of Sodium atom in the Glucokinase in Complex with Activator and Glucose (pdb code 3s41). 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 Activator and Glucose, PDB code: 3s41:

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


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 Activator and Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na600 b:17.7 occ:1.00 O A:VAL241 2.3 20.5 1.0 O A:VAL244 2.3 23.9 1.0 O A:GLY246 2.3 31.6 1.0 O A:MET238 2.4 23.3 1.0 C A:VAL241 3.3 20.8 1.0 C A:GLY246 3.5 31.4 1.0 C A:MET238 3.5 23.6 1.0 C A:VAL244 3.5 25.6 1.0 N A:GLY246 3.8 26.3 1.0 CE A:MET238 4.0 18.6 1.0 CA A:VAL241 4.1 18.8 1.0 CA A:GLY246 4.2 26.3 1.0 CB A:VAL241 4.2 22.5 1.0 C A:GLU245 4.3 30.0 1.0 N A:GLU242 4.3 15.1 1.0 N A:VAL241 4.3 17.7 1.0 N A:GLN239 4.4 20.0 1.0 CA A:MET238 4.4 17.3 1.0 N A:GLU245 4.4 26.3 1.0 CA A:GLN239 4.4 19.4 1.0 CA A:VAL244 4.5 20.4 1.0 CA A:GLU242 4.5 15.4 1.0 O A:HOH540 4.5 29.5 1.0 N A:ASP247 4.5 28.9 1.0 CA A:GLU245 4.5 28.2 1.0 N A:VAL244 4.5 21.8 1.0 C A:GLN239 4.6 23.0 1.0 CB A:MET238 4.7 18.4 1.0 SD A:MET238 4.7 22.3 1.0 CA A:ASP247 4.7 29.0 1.0 O A:GLN239 4.7 23.4 1.0 C A:GLU242 4.8 25.1 1.0 CB A:VAL244 4.9 22.3 1.0 O A:GLU245 4.9 30.1 1.0 CG1 A:VAL241 5.0 21.4 1.0 O A:GLU242 5.0 27.4 1.0

J.A.Pfefferkorn, A.Guzman-Perez, P.J.Oates, J.Litchfield, G.Aspnes, A.Basak, J.Benbow, M.A.Berliner, J.Bian, C.Choi, K.Freeman-Cook, J.W.Corbett, M.Didiuk, J.R.Dunetz, K.J.Filipski, W.M.Hungerford, C.S.Jones, K.Karki, A.Ling, J.-C.Li, L.Patel, C.Perreault, H.Risley, J.Saenz, W.Song, M.Tu, R.Aiello, K.Atkinson, N.Barucci, D.Beebe, P.Bourassa, F.Bourbounais, A.M.Brodeur, R.Burbey, J.Chen, T.D'aquila, D.R.Derksen, N.Haddish-Berhane, C.Huang, J.Landro, A.L.Lapworth, M.Macdougall, D.Perregaux, J.Pettersen, A.Robertson, B.Tan, J.L.Treadway, S.Liu, X.Qiu, J.Knafels, M.Ammirati, X.Song, P.Dasilva-Jardine, S.Liras, L.Sweet, T.P.Rolph. Designing Glucokinase Activators with Reduced Hypoglycemia Risk: Discovery of N,N-Dimethyl-5-(2-Methyl-6-((5-Methylpyrazin-2-Yl)- Carbamoyl)Benzofuran-4-Yloxy)Pyrimidine-2-Carboxamide As A Clinical Candidate For the Treatment of Type 2 Diabetes Mellitus Medchemcomm V. 2 828 2011.
ISSN: ISSN 2040-2503
DOI: 10.1039/C1MD00116G