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Fluorine in PDB 3ms4: Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone

Enzymatic activity of Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone

All present enzymatic activity of Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone:
2.4.1.1;

Protein crystallography data

The structure of Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone, PDB code: 3ms4 was solved by K.-M.Alexacou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.43 / 2.07
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 128.915, 128.915, 116.965, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone (pdb code 3ms4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone, PDB code: 3ms4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3ms4

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Fluorine binding site 1 out of 6 in the Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F920

b:51.9
occ:1.00
 F1 A:21N920 0.0 51.9 1.0
C15 A:21N920 1.3 51.9 1.0
F3 A:21N920 2.1 54.1 1.0
F2 A:21N920 2.2 53.8 1.0
C12 A:21N920 2.3 50.6 1.0
C11 A:21N920 3.0 47.7 1.0
C13 A:21N920 3.4 48.5 1.0
CB A:ARG60 3.5 35.1 1.0
CG A:PRO229 3.7 31.5 1.0
CD1 A:LEU63 3.8 38.1 1.0
CE3 A:TRP189 3.8 33.6 1.0
CD A:PRO229 4.0 31.2 1.0
CG A:ARG60 4.1 36.3 1.0
CD A:ARG60 4.1 37.6 1.0
O A:PRO188 4.1 35.6 1.0
CA A:TRP189 4.2 35.0 1.0
C10 A:21N920 4.3 47.5 1.0
CZ3 A:TRP189 4.3 33.9 1.0
CA A:ARG60 4.3 35.0 1.0
O A:TRP189 4.4 37.6 1.0
O A:ARG60 4.5 34.8 1.0
C A:TRP189 4.5 35.6 1.0
C14 A:21N920 4.5 48.1 1.0
CB A:LEU63 4.8 39.3 1.0
CB A:PRO229 4.8 31.5 1.0
C A:ARG60 4.8 34.4 1.0
CD2 A:TRP189 4.9 31.9 1.0
CB A:TRP189 4.9 34.5 1.0
CG A:LEU63 4.9 39.7 1.0
C9 A:21N920 4.9 47.8 1.0

Fluorine binding site 2 out of 6 in 3ms4

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Fluorine binding site 2 out of 6 in the Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F920

b:53.8
occ:1.00
 F2 A:21N920 0.0 53.8 1.0
C15 A:21N920 1.3 51.9 1.0
F3 A:21N920 2.1 54.1 1.0
F1 A:21N920 2.2 51.9 1.0
C12 A:21N920 2.3 50.6 1.0
C13 A:21N920 2.7 48.5 1.0
O A:ARG60 3.2 34.8 1.0
CB A:LEU63 3.3 39.3 1.0
CD1 A:LEU63 3.6 38.1 1.0
C11 A:21N920 3.6 47.7 1.0
CG1 A:VAL64 3.8 41.4 1.0
CB A:ARG60 3.9 35.1 1.0
C A:ARG60 4.0 34.4 1.0
C14 A:21N920 4.1 48.1 1.0
CG A:LEU63 4.1 39.7 1.0
CA A:ARG60 4.2 35.0 1.0
CG A:ARG60 4.3 36.3 1.0
N A:VAL64 4.3 40.1 1.0
CE3 A:TRP67 4.3 40.0 1.0
CG A:PRO229 4.3 31.5 1.0
CA A:LEU63 4.4 39.3 1.0
C A:LEU63 4.5 39.7 1.0
CZ3 A:TRP67 4.5 40.4 1.0
CA A:VAL64 4.7 40.3 1.0
C10 A:21N920 4.8 47.5 1.0
CD A:ARG60 4.8 37.6 1.0
CB A:PRO229 4.8 31.5 1.0
N A:LEU63 4.8 39.0 1.0
CB A:VAL64 4.9 40.7 1.0
C9 A:21N920 4.9 47.8 1.0
CD A:PRO229 4.9 31.2 1.0

Fluorine binding site 3 out of 6 in 3ms4

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Fluorine binding site 3 out of 6 in the Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F920

b:54.1
occ:1.00
 F3 A:21N920 0.0 54.1 1.0
C15 A:21N920 1.3 51.9 1.0
F2 A:21N920 2.1 53.8 1.0
F1 A:21N920 2.1 51.9 1.0
C12 A:21N920 2.3 50.6 1.0
C11 A:21N920 2.9 47.7 1.0
CZ3 A:TRP67 2.9 40.4 1.0
CG A:PRO229 3.1 31.5 1.0
CD A:PRO229 3.2 31.2 1.0
CE3 A:TRP67 3.2 40.0 1.0
C13 A:21N920 3.4 48.5 1.0
CB A:PRO229 3.7 31.5 1.0
CH2 A:TRP67 3.8 38.9 1.0
C10 A:21N920 4.2 47.5 1.0
CD2 A:TRP67 4.3 39.8 1.0
N A:PRO229 4.3 31.1 1.0
CD1 A:LEU63 4.4 38.1 1.0
O A:TRP189 4.5 37.6 1.0
C14 A:21N920 4.6 48.1 1.0
CA A:PRO229 4.7 31.5 1.0
CB A:LEU63 4.7 39.3 1.0
CZ2 A:TRP67 4.7 38.3 1.0
C9 A:21N920 4.9 47.8 1.0
CE2 A:TRP67 4.9 39.3 1.0

Fluorine binding site 4 out of 6 in 3ms4

Go back to Fluorine Binding Sites List in 3ms4
Fluorine binding site 4 out of 6 in the Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:54.3
occ:1.00
 F1 A:21N998 0.0 54.3 1.0
C15 A:21N998 1.3 54.0 1.0
F3 A:21N998 2.1 55.2 1.0
F2 A:21N998 2.2 55.3 1.0
C12 A:21N998 2.3 52.7 1.0
O A:ASN282 2.9 46.5 1.0
C11 A:21N998 3.0 51.0 1.0
N A:ASN282 3.1 42.5 1.0
C A:ASN282 3.1 45.9 1.0
O A:TYR280 3.2 34.1 1.0
OD1 A:ASN282 3.3 52.1 1.0
C13 A:21N998 3.3 51.2 1.0
CG A:ASN282 3.4 48.3 1.0
C A:TYR280 3.5 35.2 1.0
CA A:ASN282 3.6 45.1 1.0
CB A:TYR280 3.7 35.2 1.0
ND2 A:ASN282 3.7 50.6 1.0
N A:ASP283 3.7 47.0 1.0
C A:PRO281 3.8 40.1 1.0
N A:PRO281 4.0 36.4 1.0
CB A:ASN282 4.1 45.4 1.0
ND2 A:ASN133 4.2 29.5 1.0
CA A:ASP283 4.2 48.2 1.0
CA A:PRO281 4.2 38.4 1.0
CA A:TYR280 4.3 34.4 1.0
C10 A:21N998 4.3 50.4 1.0
C14 A:21N998 4.5 50.0 1.0
O A:PRO281 4.6 39.8 1.0
CG A:TYR280 4.9 36.3 1.0
CG A:ASN133 4.9 33.0 1.0
C9 A:21N998 4.9 49.2 1.0
CB A:ASP283 5.0 47.7 1.0

Fluorine binding site 5 out of 6 in 3ms4

Go back to Fluorine Binding Sites List in 3ms4
Fluorine binding site 5 out of 6 in the Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:55.3
occ:1.00
 F2 A:21N998 0.0 55.3 1.0
C15 A:21N998 1.3 54.0 1.0
F1 A:21N998 2.2 54.3 1.0
F3 A:21N998 2.2 55.2 1.0
C12 A:21N998 2.3 52.7 1.0
C13 A:21N998 2.7 51.2 1.0
O A:HOH947 3.5 45.7 1.0
CZ A:ARG292 3.6 36.6 1.0
NH2 A:ARG292 3.6 37.8 1.0
C11 A:21N998 3.6 51.0 1.0
ND2 A:ASN282 3.6 50.6 1.0
NE A:ARG292 3.8 36.1 1.0
O A:ASN282 3.8 46.5 1.0
OD1 A:ASN282 3.9 52.1 1.0
CB A:TYR280 4.0 35.2 1.0
NH1 A:ARG292 4.0 35.4 1.0
CG A:ASN282 4.0 48.3 1.0
C14 A:21N998 4.1 50.0 1.0
O A:HOH946 4.4 45.9 1.0
CD A:ARG292 4.5 35.5 1.0
C A:ASN282 4.6 45.9 1.0
O A:HOH859 4.6 46.6 1.0
O A:TYR280 4.7 34.1 1.0
CG A:TYR280 4.7 36.3 1.0
C10 A:21N998 4.7 50.4 1.0
C9 A:21N998 4.9 49.2 1.0
C A:TYR280 5.0 35.2 1.0
N A:ASN282 5.0 42.5 1.0

Fluorine binding site 6 out of 6 in 3ms4

Go back to Fluorine Binding Sites List in 3ms4
Fluorine binding site 6 out of 6 in the Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Glycogen Phosphorylase Complexed with 4-Trifluoromethylbenzaldehyde-4- (Beta-D-Glucopyranosyl)-Thiosemicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:55.2
occ:1.00
 F3 A:21N998 0.0 55.2 1.0
C15 A:21N998 1.3 54.0 1.0
F1 A:21N998 2.1 54.3 1.0
F2 A:21N998 2.2 55.3 1.0
C12 A:21N998 2.3 52.7 1.0
C11 A:21N998 2.8 51.0 1.0
NH1 A:ARG292 3.1 35.4 1.0
O A:TYR280 3.1 34.1 1.0
O A:HOH859 3.2 46.6 1.0
CZ A:ARG292 3.4 36.6 1.0
CB A:TYR280 3.4 35.2 1.0
NH2 A:ARG292 3.5 37.8 1.0
C13 A:21N998 3.5 51.2 1.0
C A:TYR280 3.9 35.2 1.0
ND2 A:ASN133 4.0 29.5 1.0
OE1 A:GLU88 4.1 34.7 1.0
C10 A:21N998 4.2 50.4 1.0
NE A:ARG292 4.2 36.1 1.0
CA A:TYR280 4.2 34.4 1.0
O A:HOH862 4.4 29.3 1.0
C14 A:21N998 4.6 50.0 1.0
CG A:TYR280 4.7 36.3 1.0
N A:TYR280 4.7 33.0 1.0
OD1 A:ASN282 4.8 52.1 1.0
CD A:ARG292 4.8 35.5 1.0
N A:PRO281 4.9 36.4 1.0
O A:ASN282 4.9 46.5 1.0
C9 A:21N998 4.9 49.2 1.0
CD1 A:LEU279 5.0 28.8 1.0

Reference:

K.M.Alexacou, A.C.Tenchiu Deleanu, E.D.Chrysina, M.D.Charavgi, I.D.Kostas, S.E.Zographos, N.G.Oikonomakos, D.D.Leonidas. The Binding of Beta-D-Glucopyranosyl-Thiosemicarbazone Derivatives to Glycogen Phosphorylase: A New Class of Inhibitors Bioorg.Med.Chem. V. 18 7911 2010.
ISSN: ISSN 0968-0896
PubMed: 20947361
DOI: 10.1016/J.BMC.2010.09.039
Page generated: Wed Jul 31 20:43:53 2024

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