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Sodium in PDB 3a0i: Human Glucokinase in Complex with A Synthetic Activator

Enzymatic activity of 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;

Protein crystallography data

The structure of Human Glucokinase in Complex with A Synthetic Activator, PDB code: 3a0i was solved by K.Kamata, M.Mitsuya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.37 / 2.20
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 79.732, 79.732, 321.975, 90.00, 90.00, 120.00
R / Rfree (%) 22.6 / 27.7

Other elements in 3a0i:

The structure of Human Glucokinase in Complex with A Synthetic Activator also contains other interesting chemical elements:

Fluorine (F) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Glucokinase in Complex with A Synthetic Activator (pdb code 3a0i). 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: 3a0i:

Sodium binding site 1 out of 1 in 3a0i

Go back to Sodium Binding Sites List in 3a0i
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:37.2
occ:1.00
O X:VAL244 2.2 31.7 1.0
O X:VAL241 2.3 29.7 1.0
O X:GLY246 2.4 35.1 1.0
O X:MET238 2.4 28.1 1.0
C X:VAL241 3.3 28.3 1.0
C X:VAL244 3.4 33.6 1.0
C X:MET238 3.5 27.6 1.0
C X:GLY246 3.5 36.9 1.0
N X:GLY246 3.7 33.3 1.0
CE X:MET238 4.0 32.9 1.0
C X:GLU245 4.0 33.9 1.0
CA X:GLY246 4.1 34.3 1.0
CA X:VAL241 4.1 24.6 1.0
OD2 X:ASP247 4.2 51.3 1.0
N X:GLU242 4.2 28.2 1.0
N X:VAL241 4.3 24.9 1.0
N X:GLU245 4.3 35.1 1.0
CA X:GLU242 4.3 29.7 1.0
CB X:VAL241 4.3 22.7 1.0
CA X:GLU245 4.4 35.3 1.0
CA X:MET238 4.4 28.2 1.0
N X:GLN239 4.4 26.9 1.0
CA X:VAL244 4.4 31.4 1.0
CA X:GLN239 4.4 27.8 1.0
N X:VAL244 4.4 31.2 1.0
CB X:MET238 4.6 30.6 1.0
C X:GLN239 4.6 27.3 1.0
O X:GLU245 4.6 35.2 1.0
SD X:MET238 4.7 33.0 1.0
CB X:VAL244 4.7 30.7 1.0
N X:ASP247 4.7 37.4 1.0
C X:GLU242 4.7 30.8 1.0
O X:GLN239 4.8 27.6 1.0

Reference:

M.Mitsuya, K.Kamata, M.Bamba, H.Watanabe, Y.Sasaki, K.Sasaki, S.Ohyama, H.Hosaka, Y.Nagata, J.Eiki, T.Nishimura. Discovery of Novel 3,6-Disubstituted 2-Pyridinecarboxamide Derivatives As Gk Activators Bioorg.Med.Chem.Lett. V. 19 2718 2009.
ISSN: ISSN 0960-894X
PubMed: 19362831
DOI: 10.1016/J.BMCL.2009.03.137
Page generated: Mon Oct 7 05:44:25 2024

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