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Fluorine in PDB 3sym: Glycogen Phosphorylase B in Complex with 3 -C-(Hydroxymethyl)-Beta-D- Glucopyranonucleoside of 5-Fluorouracil

Enzymatic activity of Glycogen Phosphorylase B in Complex with 3 -C-(Hydroxymethyl)-Beta-D- Glucopyranonucleoside of 5-Fluorouracil

All present enzymatic activity of Glycogen Phosphorylase B in Complex with 3 -C-(Hydroxymethyl)-Beta-D- Glucopyranonucleoside of 5-Fluorouracil:
2.4.1.1;

Protein crystallography data

The structure of Glycogen Phosphorylase B in Complex with 3 -C-(Hydroxymethyl)-Beta-D- Glucopyranonucleoside of 5-Fluorouracil, PDB code: 3sym was solved by V.T.Skamnaki, A.L.Katsandi, M.Kontou, D.D.Leonidas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 13.86 / 2.40
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 128.324, 128.324, 116.461, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 20.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Glycogen Phosphorylase B in Complex with 3 -C-(Hydroxymethyl)-Beta-D- Glucopyranonucleoside of 5-Fluorouracil (pdb code 3sym). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Glycogen Phosphorylase B in Complex with 3 -C-(Hydroxymethyl)-Beta-D- Glucopyranonucleoside of 5-Fluorouracil, PDB code: 3sym:

Fluorine binding site 1 out of 1 in 3sym

Go back to Fluorine Binding Sites List in 3sym
Fluorine binding site 1 out of 1 in the Glycogen Phosphorylase B in Complex with 3 -C-(Hydroxymethyl)-Beta-D- Glucopyranonucleoside of 5-Fluorouracil


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Glycogen Phosphorylase B in Complex with 3 -C-(Hydroxymethyl)-Beta-D- Glucopyranonucleoside of 5-Fluorouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F843

b:23.9
occ:1.00
 F1 A:GP0843 0.0 23.9 1.0
C2 A:GP0843 1.3 21.8 1.0
C1 A:GP0843 2.3 20.9 1.0
C3 A:GP0843 2.4 22.3 1.0
O3 A:GP0843 2.8 23.5 1.0
CG2 A:THR378 3.2 19.6 1.0
OD1 A:ASN284 3.4 34.6 1.0
CB A:THR378 3.4 19.7 1.0
N1 A:GP0843 3.6 19.9 1.0
N4 A:GP0843 3.7 21.4 1.0
O A:HIS377 3.8 16.6 1.0
CG A:ASN284 3.8 33.4 1.0
CB A:HIS377 4.0 14.8 1.0
C A:HIS377 4.0 16.4 1.0
C5 A:GP0843 4.1 20.6 1.0
OD1 A:ASP339 4.2 23.8 1.0
ND2 A:ASN284 4.2 33.2 1.0
CA A:ASN284 4.3 30.8 1.0
N A:THR378 4.3 17.6 1.0
OG1 A:THR378 4.4 21.1 1.0
CA A:THR378 4.5 19.3 1.0
CB A:ALA383 4.6 22.6 1.0
CA A:HIS377 4.6 15.3 1.0
CB A:ASN284 4.7 31.5 1.0
N A:ASN284 4.7 31.1 1.0
C1' A:GP0843 4.8 18.6 1.0
O2' A:GP0843 4.9 16.9 1.0
O A:HOH1087 5.0 21.8 1.0
CD1 A:LEU136 5.0 21.7 1.0

Reference:

S.Manta, A.Xipnitou, C.Kiritsis, A.L.Kantsadi, J.M.Hayes, V.T.Skamnaki, C.Lamprakis, M.Kontou, P.Zoumpoulakis, S.E.Zographos, D.D.Leonidas, D.Komiotis. 3'-Axial Ch(2) Oh Substitution on Glucopyranose Does Not Increase Glycogen Phosphorylase Inhibitory Potency. Qm/Mm-Pbsa Calculations Suggest Why. Chem.Biol.Drug Des. V. 79 663 2012.
ISSN: ISSN 1747-0277
PubMed: 22296957
DOI: 10.1111/J.1747-0285.2012.01349.X
Page generated: Mon Jul 14 19:24:15 2025

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