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Sodium in PDB 4iwv: Crystals Structure of Human Glucokinase in Complex with Small Molecule Activator

Enzymatic activity of Crystals Structure of Human Glucokinase in Complex with Small Molecule Activator

All present enzymatic activity of Crystals Structure of Human Glucokinase in Complex with Small Molecule Activator:
2.7.1.2;

Protein crystallography data

The structure of Crystals Structure of Human Glucokinase in Complex with Small Molecule Activator, PDB code: 4iwv was solved by D.J.Ogg, D.Hargreaves, S.Gerhardt, L.Flavell, M.Mcalister, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.46 / 2.10
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 77.938, 77.938, 85.350, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 25

Other elements in 4iwv:

The structure of Crystals Structure of Human Glucokinase in Complex with Small Molecule Activator also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystals Structure of Human Glucokinase in Complex with Small Molecule Activator (pdb code 4iwv). 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 Crystals Structure of Human Glucokinase in Complex with Small Molecule Activator, PDB code: 4iwv:

Sodium binding site 1 out of 1 in 4iwv

Go back to Sodium Binding Sites List in 4iwv
Sodium binding site 1 out of 1 in the Crystals Structure of Human Glucokinase in Complex with Small Molecule Activator


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystals Structure of Human Glucokinase in Complex with Small Molecule Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:34.8
occ:1.00
 O A:VAL244 2.2 39.7 1.0
O A:VAL241 2.3 32.6 1.0
O A:MET238 2.3 39.1 1.0
O A:HOH696 2.5 36.1 1.0
O A:GLY246 2.6 48.1 1.0
C A:VAL241 3.2 34.5 1.0
C A:MET238 3.4 40.7 1.0
C A:VAL244 3.4 41.3 1.0
C A:GLY246 3.8 46.1 1.0
N A:GLY246 3.9 42.0 1.0
C A:GLU245 4.0 41.7 1.0
CA A:VAL241 4.1 32.5 1.0
CE A:MET238 4.1 35.5 1.0
CB A:VAL241 4.1 31.2 1.0
O A:HOH694 4.1 49.9 1.0
N A:GLU242 4.1 33.1 1.0
N A:VAL241 4.2 33.8 1.0
CA A:MET238 4.2 35.0 1.0
N A:GLN239 4.3 38.5 1.0
CA A:GLU242 4.3 33.9 1.0
CA A:GLN239 4.3 37.2 1.0
N A:GLU245 4.3 45.0 1.0
N A:VAL244 4.3 39.4 1.0
CA A:GLU245 4.4 47.6 1.0
CA A:VAL244 4.4 39.7 1.0
CA A:GLY246 4.4 42.4 1.0
CB A:MET238 4.4 33.0 1.0
O A:GLU245 4.4 39.6 1.0
O A:HOH689 4.4 45.9 1.0
C A:GLN239 4.5 34.4 1.0
O A:GLN239 4.5 34.8 1.0
SD A:MET238 4.6 34.6 1.0
C A:GLU242 4.6 36.3 1.0
CB A:VAL244 4.7 38.9 1.0
CG1 A:VAL241 4.7 31.2 1.0
OD1 A:ASP247 4.8 53.3 1.0
N A:ASP247 4.9 47.2 1.0
O A:GLU242 4.9 36.6 1.0

Reference:

M.J.Waring, S.N.Bennett, S.Boyd, L.Campbell, R.D.M.Davies, D.J.Ogg, D.Hargreaves, N.G.Martin, G.Robb, S.Wilkinson, P.Macpaul, J.M.Wood. Optimising Pharmacokinetics of Glucokinase Activators with Matched Triplicate Design Sets the Discovery of AZD3651 and AZD9485 To Be Published.
Page generated: Sun Aug 17 19:55:15 2025

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