Fluorine in PDB 2vfz: Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose

All present enzymatic activity of Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose:
2.4.1.151; 2.4.1.87;

The structure of Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose, PDB code: 2vfz was solved by H.Jamaluddin, P.Tumbale, S.G.Withers, K.R.Acharya, K.Brew, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.06 / 2.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.735, 64.759, 66.468, 83.34, 83.95, 70.14
R / Rfree (%)	17.8 / 23.3

The structure of Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose (pdb code 2vfz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose, PDB code: 2vfz:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:F1360 b:50.3 occ:1.00 F2' A:UPF1360 0.0 50.3 1.0 C2' A:UPF1360 1.4 48.9 1.0 C1' A:UPF1360 2.4 49.1 1.0 C3' A:UPF1360 2.4 48.0 1.0 O3B A:UPF1360 2.7 47.4 1.0 OD2 A:ASP225 2.7 20.6 1.0 O3' A:UPF1360 2.9 46.2 1.0 CE1 A:HIS280 2.9 14.7 1.0 CB A:ALA282 3.2 16.2 1.0 N A:ALA282 3.3 16.9 1.0 ND1 A:HIS280 3.4 16.4 1.0 CA A:ALA282 3.5 16.1 1.0 O5' A:UPF1360 3.7 50.1 1.0 NE2 A:HIS280 3.7 17.1 1.0 CG A:ASP225 3.7 21.3 1.0 O A:HOH2202 3.8 27.8 1.0 C4' A:UPF1360 3.8 48.3 1.0 C A:ALA281 3.8 18.9 1.0 OD1 A:ASP225 4.1 22.0 1.0 MN A:MN1361 4.2 41.3 1.0 PB A:UPF1360 4.2 44.3 1.0 C5' A:UPF1360 4.2 49.7 1.0 OE2 A:GLU317 4.2 22.2 1.0 O4' A:UPF1360 4.3 47.6 1.0 N A:ALA281 4.3 17.6 1.0 O1B A:UPF1360 4.4 45.9 1.0 CG A:HIS280 4.4 16.0 1.0 O A:ALA281 4.4 20.8 1.0 CA A:ALA281 4.4 18.8 1.0 O A:HOH2173 4.5 40.4 1.0 CB A:ALA281 4.5 18.4 1.0 CD2 A:HIS280 4.5 18.2 1.0 CB A:ASP225 4.9 18.5 1.0 C A:ALA282 5.0 16.6 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:F2364 b:32.9 occ:1.00 F2' B:UPF2364 0.0 32.9 1.0 C2' B:UPF2364 1.4 32.5 1.0 C1' B:UPF2364 2.4 32.1 1.0 C3' B:UPF2364 2.4 32.3 1.0 O3B B:UPF2364 2.7 30.8 1.0 O3' B:UPF2364 2.9 32.5 1.0 NE2 B:HIS1280 3.0 12.4 1.0 CD2 B:HIS1280 3.1 16.2 1.0 N B:ALA1282 3.2 18.0 1.0 CB B:ALA1282 3.3 16.2 1.0 OD2 B:ASP1225 3.4 22.7 1.0 CA B:ALA1282 3.5 17.7 1.0 O5' B:UPF2364 3.7 33.2 1.0 O B:HOH2199 3.7 30.9 1.0 OE2 B:GLU1317 3.7 24.0 1.0 C4' B:UPF2364 3.8 32.1 1.0 C B:ALA1281 3.8 18.2 1.0 CG B:ASP1225 4.0 23.3 1.0 N B:ALA1281 4.0 18.6 1.0 CE1 B:HIS1280 4.1 17.1 1.0 OD1 B:ASP1225 4.2 24.7 1.0 PB B:UPF2364 4.2 26.5 1.0 CA B:ALA1281 4.2 18.0 1.0 O4' B:UPF2364 4.2 29.6 1.0 C5' B:UPF2364 4.2 33.1 1.0 CB B:ALA1281 4.2 17.5 1.0 CG B:HIS1280 4.2 15.8 1.0 O B:HOH2247 4.3 14.4 1.0 MN B:MN2365 4.3 26.0 1.0 O1B B:UPF2364 4.4 29.6 1.0 O B:ALA1281 4.5 18.7 1.0 ND1 B:HIS1280 4.7 16.2 1.0 CD B:GLU1317 4.7 23.8 1.0 C B:HIS1280 4.8 19.2 1.0

H.Jamaluddin, P.Tumbale, S.G.Withers, K.R.Acharya, K.Brew. Conformational Changes Induced By Binding Udp-2F- Galactose to Alpha-1,3 Galactosyltransferase- Implications For Catalysis J.Mol.Biol. V. 369 1270 2007.
ISSN: ISSN 0022-2836
PubMed: 17493636
DOI: 10.1016/J.JMB.2007.04.012