Fluorine in PDB 3t3i: Glycogen Phosphorylase B in Complex with GLCCF3U

All present enzymatic activity of Glycogen Phosphorylase B in Complex with GLCCF3U:
2.4.1.1;

The structure of Glycogen Phosphorylase B in Complex with GLCCF3U, PDB code: 3t3i was solved by A.L.Kantsadi, V.T.Skamnaki, D.D.Leonidas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	13.78 / 2.65
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.759, 128.759, 116.557, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 23.5

The binding sites of Fluorine atom in the Glycogen Phosphorylase B in Complex with GLCCF3U (pdb code 3t3i). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Glycogen Phosphorylase B in Complex with GLCCF3U, PDB code: 3t3i:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Glycogen Phosphorylase B in Complex with GLCCF3U


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 GLCCF3U within 5.0Å range: probe atom residue distance (Å) B Occ A:F843 b:25.9 occ:1.00 F1 A:GPW843 0.0 25.9 1.0 C7 A:GPW843 1.3 28.1 1.0 F3 A:GPW843 2.1 28.5 1.0 F2 A:GPW843 2.2 30.5 1.0 C5 A:GPW843 2.4 29.0 1.0 O4 A:GPW843 3.1 28.4 1.0 C4 A:GPW843 3.1 28.7 1.0 C6 A:GPW843 3.4 27.1 1.0 OD1 A:ASN284 3.4 24.8 1.0 CG2 A:THR378 3.6 16.3 1.0 CB A:ALA383 3.6 21.0 1.0 CB A:THR378 3.6 17.5 1.0 CA A:ASN284 3.8 25.9 1.0 CG A:ASN284 3.9 25.2 1.0 OG1 A:THR378 4.2 20.5 1.0 O A:ALA383 4.3 22.1 1.0 N A:ASN284 4.3 26.4 1.0 CB A:ASN284 4.4 25.6 1.0 N3 A:GPW843 4.5 26.9 1.0 ND2 A:ASN284 4.6 23.6 1.0 N1 A:GPW843 4.7 26.8 1.0 CA A:ALA383 4.7 21.8 1.0 C A:ASN284 4.8 26.0 1.0 C A:ALA383 4.8 22.1 1.0 OD2 A:ASP339 4.9 11.6 1.0 O A:HIS377 4.9 13.6 1.0 CA A:THR378 4.9 16.8 1.0 N A:THR378 5.0 14.9 1.0 C A:HIS377 5.0 14.2 1.0

Fluorine binding site 2 out of 3 in the Glycogen Phosphorylase B in Complex with GLCCF3U


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Glycogen Phosphorylase B in Complex with GLCCF3U within 5.0Å range: probe atom residue distance (Å) B Occ A:F843 b:30.5 occ:1.00 F2 A:GPW843 0.0 30.5 1.0 C7 A:GPW843 1.3 28.1 1.0 F3 A:GPW843 2.1 28.5 1.0 F1 A:GPW843 2.2 25.9 1.0 C5 A:GPW843 2.4 29.0 1.0 O4 A:GPW843 2.8 28.4 1.0 C4 A:GPW843 2.9 28.7 1.0 C6 A:GPW843 3.5 27.1 1.0 OD2 A:ASP339 3.6 11.6 1.0 CG A:ASP339 3.7 13.7 1.0 CD1 A:LEU136 3.8 17.0 1.0 NE2 A:HIS341 3.9 17.0 1.0 CE1 A:HIS341 4.0 18.1 1.0 OD1 A:ASP339 4.0 16.7 1.0 N3 A:GPW843 4.3 26.9 1.0 CB A:ASP339 4.3 13.0 1.0 N1 A:GPW843 4.6 26.8 1.0 CB A:HIS377 4.7 13.3 1.0 C2 A:GPW843 5.0 27.5 1.0 CG A:LEU136 5.0 16.9 1.0 CG2 A:THR378 5.0 16.3 1.0

Fluorine binding site 3 out of 3 in the Glycogen Phosphorylase B in Complex with GLCCF3U


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Glycogen Phosphorylase B in Complex with GLCCF3U within 5.0Å range: probe atom residue distance (Å) B Occ A:F843 b:28.5 occ:1.00 F3 A:GPW843 0.0 28.5 1.0 C7 A:GPW843 1.3 28.1 1.0 F2 A:GPW843 2.1 30.5 1.0 F1 A:GPW843 2.1 25.9 1.0 C5 A:GPW843 2.3 29.0 1.0 C6 A:GPW843 2.7 27.1 1.0 CB A:HIS377 3.1 13.3 1.0 C A:HIS377 3.3 14.2 1.0 OD1 A:ASP339 3.4 16.7 1.0 O A:HIS377 3.5 13.6 1.0 CB A:THR378 3.5 17.5 1.0 N A:THR378 3.6 14.9 1.0 C4 A:GPW843 3.6 28.7 1.0 CA A:HIS377 3.7 13.9 1.0 CG2 A:THR378 3.7 16.3 1.0 CG A:ASP339 3.8 13.7 1.0 OD2 A:ASP339 4.0 11.6 1.0 N1 A:GPW843 4.1 26.8 1.0 O4 A:GPW843 4.1 28.4 1.0 CA A:THR378 4.2 16.8 1.0 N A:HIS377 4.2 13.9 1.0 CG A:HIS377 4.3 12.4 1.0 CD1 A:LEU136 4.4 17.0 1.0 OD1 A:ASN284 4.5 24.8 1.0 OG1 A:THR378 4.6 20.5 1.0 CB A:ASP339 4.8 13.0 1.0 N3 A:GPW843 4.8 26.9 1.0 CD2 A:HIS377 4.8 14.9 1.0 C2 A:GPW843 4.9 27.5 1.0

A.L.Kantsadi, J.M.Hayes, S.Manta, V.T.Skamnaki, C.Kiritsis, A.M.Psarra, Z.Koutsogiannis, A.Dimopoulou, S.Theofanous, N.Nikoleousakos, P.Zoumpoulakis, M.Kontou, G.Papadopoulos, S.E.Zographos, D.Komiotis, D.D.Leonidas. The Sigma-Hole Phenomenon of Halogen Atoms Forms the Structural Basis of the Strong Inhibitory Potency of C5 Halogen Substituted Glucopyranosyl Nucleosides Towards Glycogen Phosphorylase  B Chemmedchem V. 7 722 2012.
ISSN: ISSN 1860-7179
PubMed: 22267166
DOI: 10.1002/CMDC.201100533