Sodium in PDB 3h1v: Human Glucokinase in Complex with A Synthetic Activator

All present enzymatic activity of Human Glucokinase in Complex with A Synthetic Activator:
2.7.1.2;

The structure of Human Glucokinase in Complex with A Synthetic Activator, PDB code: 3h1v was solved by K.Kamata, K.Takahashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.46 / 2.11
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	79.793, 79.793, 326.124, 90.00, 90.00, 120.00
R / Rfree (%)	23.2 / 28.4

The binding sites of Sodium atom in the Human Glucokinase in Complex with A Synthetic Activator (pdb code 3h1v). 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 Human Glucokinase in Complex with A Synthetic Activator, PDB code: 3h1v:

Sodium binding site 1 out of 1 in the 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 Human Glucokinase in Complex with A Synthetic Activator within 5.0Å range: probe atom residue distance (Å) B Occ X:Na600 b:38.0 occ:1.00 O X:GLY246 2.2 39.7 1.0 O X:MET238 2.3 29.6 1.0 O X:VAL244 2.4 34.9 1.0 O X:VAL241 2.7 31.9 1.0 C X:MET238 3.3 29.7 1.0 C X:GLY246 3.4 40.0 1.0 C X:VAL244 3.6 37.4 1.0 C X:VAL241 3.6 32.2 1.0 N X:GLY246 3.7 37.2 1.0 CE X:MET238 3.8 30.5 1.0 C X:GLU245 3.9 37.1 1.0 CA X:GLY246 4.0 38.3 1.0 N X:GLN239 4.2 30.1 1.0 CA X:MET238 4.2 28.4 1.0 CA X:GLN239 4.2 31.1 1.0 CA X:GLU245 4.3 38.5 1.0 OD2 X:ASP247 4.3 53.6 1.0 CB X:VAL241 4.4 29.2 1.0 CA X:VAL241 4.4 29.9 1.0 N X:GLU245 4.4 38.0 1.0 N X:VAL241 4.4 28.0 1.0 O X:GLU245 4.4 37.5 1.0 CB X:MET238 4.5 30.8 1.0 N X:ASP247 4.5 40.4 1.0 SD X:MET238 4.5 34.5 1.0 C X:GLN239 4.5 31.4 1.0 N X:GLU242 4.5 33.2 1.0 O X:GLN239 4.5 32.6 1.0 CA X:VAL244 4.6 36.6 1.0 N X:VAL244 4.6 36.0 1.0 CA X:GLU242 4.7 34.7 1.0 CA X:ASP247 4.8 43.4 1.0 CB X:VAL244 4.8 36.6 1.0 CG1 X:VAL241 4.9 28.1 1.0

K.Takahashi, N.Hashimoto, C.Nakama, K.Kamata, K.Sasaki, R.Yoshimoto, S.Ohyama, H.Hosaka, H.Maruki, Y.Nagata, J.Eiki, T.Nishimura. The Design and Optimization of A Series of 2-(Pyridin-2-Yl)-1H-Benzimidazole Compounds As Allosteric Glucokinase Activators. Bioorg.Med.Chem. V. 17 7042 2009.
ISSN: ISSN 0968-0896
PubMed: 19736020
DOI: 10.1016/J.BMC.2009.05.037