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Fluorine in PDB 3vev: Glucokinase in Complex with An Activator and Glucose

Enzymatic activity of Glucokinase in Complex with An Activator and Glucose

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

Protein crystallography data

The structure of Glucokinase in Complex with An Activator and Glucose, PDB code: 3vev was solved by S.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.14 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.170, 82.110, 86.220, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20

Other elements in 3vev:

The structure of Glucokinase in Complex with An Activator and Glucose also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Glucokinase in Complex with An Activator and Glucose (pdb code 3vev). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Glucokinase in Complex with An Activator and Glucose, PDB code: 3vev:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3vev

Go back to Fluorine Binding Sites List in 3vev
Fluorine binding site 1 out of 3 in the Glucokinase in Complex with An Activator and Glucose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Glucokinase in Complex with An Activator and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:45.6
occ:1.00
F1 A:0H4502 0.0 45.6 1.0
C8 A:0H4502 1.3 43.0 1.0
F2 A:0H4502 2.1 42.9 1.0
F3 A:0H4502 2.1 45.3 1.0
C6 A:0H4502 2.4 38.0 1.0
H4 A:0H4502 2.9 36.3 0.0
C5 A:0H4502 3.0 36.3 1.0
C7 A:0H4502 3.4 34.0 1.0
CD2 A:LEU451 3.5 35.1 1.0
H5 A:0H4502 3.7 34.0 0.0
CD1 A:LEU451 4.1 31.0 1.0
CD1 A:TYR215 4.3 35.6 1.0
CG A:LEU451 4.3 30.9 1.0
C4 A:0H4502 4.3 34.0 1.0
C9 A:0H4502 4.6 33.7 1.0
O A:HOH833 4.7 34.5 1.0
CB A:LEU451 4.7 25.3 1.0
O A:HOH904 4.8 45.6 1.0
CE1 A:TYR215 4.9 38.3 1.0
N1 A:0H4502 5.0 30.9 1.0

Fluorine binding site 2 out of 3 in 3vev

Go back to Fluorine Binding Sites List in 3vev
Fluorine binding site 2 out of 3 in the Glucokinase in Complex with An Activator and Glucose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Glucokinase in Complex with An Activator and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:42.9
occ:1.00
F2 A:0H4502 0.0 42.9 1.0
C8 A:0H4502 1.3 43.0 1.0
F3 A:0H4502 2.1 45.3 1.0
F1 A:0H4502 2.1 45.6 1.0
C6 A:0H4502 2.4 38.0 1.0
H4 A:0H4502 2.7 36.3 0.0
C5 A:0H4502 2.9 36.3 1.0
CA A:TYR215 3.5 25.7 1.0
C7 A:0H4502 3.5 34.0 1.0
CD2 A:TYR214 3.6 24.3 1.0
CD1 A:TYR215 3.7 35.6 1.0
CE2 A:TYR214 3.8 25.9 1.0
CB A:TYR215 3.8 27.7 1.0
H5 A:0H4502 3.9 34.0 0.0
N A:TYR215 4.0 23.8 1.0
CD1 A:LEU451 4.2 31.0 1.0
C4 A:0H4502 4.2 34.0 1.0
CG A:TYR215 4.3 32.4 1.0
C A:TYR214 4.6 24.3 1.0
CE1 A:HIS218 4.6 34.4 1.0
C A:TYR215 4.7 31.6 1.0
C9 A:0H4502 4.7 33.7 1.0
O A:TYR214 4.7 22.5 1.0
O A:TYR215 4.8 32.9 1.0
O A:ILE211 4.8 21.5 1.0
CD2 A:LEU451 4.8 35.1 1.0
CE1 A:TYR215 4.8 38.3 1.0
CG A:TYR214 4.8 22.5 1.0
H3 A:0H4502 4.9 34.0 0.0
N1 A:0H4502 4.9 30.9 1.0

Fluorine binding site 3 out of 3 in 3vev

Go back to Fluorine Binding Sites List in 3vev
Fluorine binding site 3 out of 3 in the Glucokinase in Complex with An Activator and Glucose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Glucokinase in Complex with An Activator and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:45.3
occ:1.00
F3 A:0H4502 0.0 45.3 1.0
C8 A:0H4502 1.3 43.0 1.0
F2 A:0H4502 2.1 42.9 1.0
F1 A:0H4502 2.1 45.6 1.0
C6 A:0H4502 2.4 38.0 1.0
H5 A:0H4502 2.6 34.0 0.0
C7 A:0H4502 2.8 34.0 1.0
C5 A:0H4502 3.7 36.3 1.0
CE2 A:TYR214 4.0 25.9 1.0
H4 A:0H4502 4.0 36.3 0.0
CE1 A:HIS218 4.1 34.4 1.0
O A:HOH784 4.1 49.7 1.0
C9 A:0H4502 4.3 33.7 1.0
CD2 A:TYR214 4.5 24.3 1.0
NE2 A:HIS218 4.5 35.5 1.0
C4 A:0H4502 4.8 34.0 1.0

Reference:

S.Liu, M.J.Ammirati, X.Song, J.D.Knafels, J.Zhang, S.E.Greasley, J.A.Pfefferkorn, X.Qiu. Insights Into Mechanism of Glucokinase Activation: Observation of Multiple Distinct Protein Conformations. J.Biol.Chem. V. 287 13598 2012.
ISSN: ISSN 0021-9258
PubMed: 22298776
DOI: 10.1074/JBC.M111.274126
Page generated: Sun Dec 13 11:56:59 2020

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