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Fluorine in PDB 3zcq: Rabbit Muscle Glycogen Phosphorylase B in Complex with N-(4- Trifluoromethyl-Benzoyl)-N-Beta-D-Glucopyranosyl Urea Determined at 2.15 A Resolution

Enzymatic activity of Rabbit Muscle Glycogen Phosphorylase B in Complex with N-(4- Trifluoromethyl-Benzoyl)-N-Beta-D-Glucopyranosyl Urea Determined at 2.15 A Resolution

All present enzymatic activity of Rabbit Muscle Glycogen Phosphorylase B in Complex with N-(4- Trifluoromethyl-Benzoyl)-N-Beta-D-Glucopyranosyl Urea Determined at 2.15 A Resolution:
2.4.1.1;

Protein crystallography data

The structure of Rabbit Muscle Glycogen Phosphorylase B in Complex with N-(4- Trifluoromethyl-Benzoyl)-N-Beta-D-Glucopyranosyl Urea Determined at 2.15 A Resolution, PDB code: 3zcq was solved by E.D.Chrysina, V.Nagy, N.Felfoldi, B.Konya, K.Telepo, J.P.Praly, T.Docsa, P.Gergely, K.M.Alexacou, J.M.Hayes, M.Konstantakaki, R.Kardakaris, D.D.Leonidas, S.E.Zographos, N.G.Oikonomakos, L.Somsak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.59 / 2.15
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 128.650, 128.650, 116.903, 90.00, 90.00, 90.00
R / Rfree (%) 18.18 / 21.743

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Rabbit Muscle Glycogen Phosphorylase B in Complex with N-(4- Trifluoromethyl-Benzoyl)-N-Beta-D-Glucopyranosyl Urea Determined at 2.15 A Resolution (pdb code 3zcq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Rabbit Muscle Glycogen Phosphorylase B in Complex with N-(4- Trifluoromethyl-Benzoyl)-N-Beta-D-Glucopyranosyl Urea Determined at 2.15 A Resolution, PDB code: 3zcq:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3zcq

Go back to Fluorine Binding Sites List in 3zcq
Fluorine binding site 1 out of 3 in the Rabbit Muscle Glycogen Phosphorylase B in Complex with N-(4- Trifluoromethyl-Benzoyl)-N-Beta-D-Glucopyranosyl Urea Determined at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Rabbit Muscle Glycogen Phosphorylase B in Complex with N-(4- Trifluoromethyl-Benzoyl)-N-Beta-D-Glucopyranosyl Urea Determined at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:29.6
occ:1.00
 F1 A:62N998 0.0 29.6 1.0
C15 A:62N998 1.3 27.5 1.0
F3 A:62N998 2.1 28.7 1.0
F2 A:62N998 2.1 28.2 1.0
C12 A:62N998 2.4 26.1 1.0
O A:HOH2131 2.7 29.3 1.0
C11 A:62N998 3.1 25.3 1.0
C13 A:62N998 3.4 24.4 1.0
O A:ALA383 3.4 26.8 1.0
O A:HOH2122 3.8 26.1 1.0
NE2 A:HIS341 3.8 17.1 1.0
CB A:PHE286 4.2 27.9 1.0
CA A:PHE286 4.3 28.2 1.0
CG A:GLU385 4.3 24.6 1.0
CD1 A:PHE286 4.3 25.9 1.0
C A:ALA383 4.3 26.2 1.0
C10 A:62N998 4.4 23.9 1.0
CD2 A:HIS341 4.5 17.3 1.0
O A:HOH2115 4.6 29.3 1.0
C14 A:62N998 4.6 22.9 1.0
N A:PHE286 4.7 28.4 1.0
CG A:PHE286 4.7 26.9 1.0
CE1 A:HIS341 4.8 17.9 1.0
CA A:ALA383 4.8 26.0 1.0
CD A:GLU385 5.0 25.1 1.0
C9 A:62N998 5.0 22.2 1.0

Fluorine binding site 2 out of 3 in 3zcq

Go back to Fluorine Binding Sites List in 3zcq
Fluorine binding site 2 out of 3 in the Rabbit Muscle Glycogen Phosphorylase B in Complex with N-(4- Trifluoromethyl-Benzoyl)-N-Beta-D-Glucopyranosyl Urea Determined at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Rabbit Muscle Glycogen Phosphorylase B in Complex with N-(4- Trifluoromethyl-Benzoyl)-N-Beta-D-Glucopyranosyl Urea Determined at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:28.2
occ:1.00
 F2 A:62N998 0.0 28.2 1.0
C15 A:62N998 1.3 27.5 1.0
F1 A:62N998 2.1 29.6 1.0
F3 A:62N998 2.2 28.7 1.0
C12 A:62N998 2.4 26.1 1.0
C13 A:62N998 2.8 24.4 1.0
O A:HOH2114 3.3 39.9 1.0
O A:HOH2122 3.3 26.1 1.0
O A:HOH2111 3.4 25.0 1.0
O A:HOH2115 3.4 29.3 1.0
O A:ASN282 3.5 24.1 1.0
C11 A:62N998 3.6 25.3 1.0
ND2 A:ASN282 3.7 25.1 1.0
C14 A:62N998 4.1 22.9 1.0
NH2 A:ARG292 4.5 21.1 1.0
CA A:PHE286 4.5 28.2 1.0
CG A:ASN282 4.5 25.2 1.0
NE2 A:HIS341 4.6 17.1 1.0
O A:HOH2131 4.6 29.3 1.0
O A:PHE285 4.7 28.5 1.0
C A:ASN282 4.7 24.2 1.0
CD1 A:PHE286 4.8 25.9 1.0
C10 A:62N998 4.8 23.9 1.0
CZ A:ARG292 4.9 20.5 1.0
OD1 A:ASN282 4.9 27.2 1.0
CB A:PHE286 5.0 27.9 1.0
N A:PHE286 5.0 28.4 1.0
C9 A:62N998 5.0 22.2 1.0

Fluorine binding site 3 out of 3 in 3zcq

Go back to Fluorine Binding Sites List in 3zcq
Fluorine binding site 3 out of 3 in the Rabbit Muscle Glycogen Phosphorylase B in Complex with N-(4- Trifluoromethyl-Benzoyl)-N-Beta-D-Glucopyranosyl Urea Determined at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Rabbit Muscle Glycogen Phosphorylase B in Complex with N-(4- Trifluoromethyl-Benzoyl)-N-Beta-D-Glucopyranosyl Urea Determined at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F998

b:28.7
occ:1.00
 F3 A:62N998 0.0 28.7 1.0
C15 A:62N998 1.3 27.5 1.0
F1 A:62N998 2.1 29.6 1.0
F2 A:62N998 2.2 28.2 1.0
C12 A:62N998 2.3 26.1 1.0
C11 A:62N998 2.8 25.3 1.0
N A:PHE286 3.4 28.4 1.0
CA A:PHE286 3.4 28.2 1.0
C A:PHE285 3.5 28.9 1.0
O A:PHE285 3.5 28.5 1.0
C13 A:62N998 3.5 24.4 1.0
O A:ASN282 3.8 24.1 1.0
CB A:PHE286 4.0 27.9 1.0
ND2 A:ASN282 4.0 25.1 1.0
N A:PHE285 4.1 28.6 1.0
C10 A:62N998 4.2 23.9 1.0
O A:ALA383 4.2 26.8 1.0
CA A:PHE285 4.3 29.2 1.0
CA A:ALA383 4.5 26.0 1.0
O A:HOH2131 4.5 29.3 1.0
O A:HOH2115 4.5 29.3 1.0
C A:ASP283 4.6 26.1 1.0
C A:ASN282 4.6 24.2 1.0
N A:ASN284 4.7 27.1 1.0
C14 A:62N998 4.7 22.9 1.0
C A:ALA383 4.7 26.2 1.0
CA A:ASP283 4.7 25.4 1.0
C A:ASN284 4.7 28.7 1.0
C A:PHE286 4.7 28.6 1.0
CB A:ALA383 4.8 25.7 1.0
C9 A:62N998 4.9 22.2 1.0
CD1 A:PHE286 5.0 25.9 1.0
CG A:ASN282 5.0 25.2 1.0
O A:ASP283 5.0 25.9 1.0
O A:HOH2111 5.0 25.0 1.0

Reference:

E.D.Chrysina, V.Nagy, N.Felfoldi, B.Konya, K.Telepo, J.P.Praly, T.Docsa, P.Gergely, K.M.Alexacou, J.M.Hayes, M.Konstantakaki, R.Kardakaris, D.D.Leonidas, S.E.Zographos, N.G.Oikonomakos, L.Somsak. Synthesis, Kinetic, Computational and Crystallographic Evaluation of N-Acyl-N-Beta-D- Glucopyranosyl)Ureas, Nanomolar Glucose Analogue Inhibitors of Glycogen Phosphorylase, Potential Antidiabetic Agents To Be Published.
Page generated: Mon Jul 14 20:10:26 2025

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