Fluorine in PDB 8zwr: Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5

The structure of Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5, PDB code: 8zwr was solved by J.M.Lo, C.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.71 / 1.94
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.739, 85.737, 87.73, 90, 95.52, 90
R / Rfree (%)	19.3 / 21.6

The structure of Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5 also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Fluorine atom in the Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5 (pdb code 8zwr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5, PDB code: 8zwr:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:13.5 occ:1.00 F2' A:UPF403 0.0 13.5 1.0 C2' A:UPF403 1.3 11.8 1.0 C1' A:UPF403 2.3 13.4 1.0 C3' A:UPF403 2.3 12.6 1.0 O3B A:UPF403 2.7 11.5 1.0 O3' A:UPF403 2.8 12.1 1.0 OD2 A:ASP156 3.0 10.7 1.0 O1B A:UPF403 3.0 11.7 1.0 O A:HOH626 3.2 17.2 1.0 O A:HOH508 3.3 15.7 1.0 PB A:UPF403 3.4 13.5 1.0 CG2 A:THR217 3.5 10.1 1.0 N A:THR217 3.6 9.2 1.0 O5' A:UPF403 3.6 13.0 1.0 C4' A:UPF403 3.6 11.7 1.0 CA A:THR217 3.9 9.7 1.0 C A:GLY216 4.0 10.1 1.0 C5' A:UPF403 4.1 11.4 1.0 O4' A:UPF403 4.2 10.6 1.0 O A:HOH524 4.2 18.7 1.0 MN A:MN401 4.2 11.7 1.0 O2B A:UPF403 4.3 12.6 1.0 CG A:ASP156 4.3 12.7 1.0 CB A:THR217 4.3 10.9 1.0 C5D A:UPF403 4.4 14.7 1.0 CA A:GLY216 4.4 9.2 1.0 O A:GLY216 4.5 10.7 1.0 N A:GLY216 4.7 8.8 1.0 O3A A:UPF403 4.7 13.7 1.0 NE2 A:HIS285 4.8 10.0 1.0 OG A:SER215 4.8 10.2 1.0

Fluorine binding site 2 out of 2 in the Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5 within 5.0Å range: probe atom residue distance (Å) B Occ B:F403 b:29.7 occ:1.00 F2' B:UPF403 0.0 29.7 1.0 C2' B:UPF403 1.3 28.9 1.0 C3' B:UPF403 2.3 29.1 1.0 C1' B:UPF403 2.3 33.1 1.0 O3' B:UPF403 2.7 31.5 1.0 O3B B:UPF403 2.7 32.7 1.0 OD2 B:ASP156 2.8 28.4 1.0 O2B B:UPF403 3.1 33.8 1.0 O B:HOH534 3.2 33.9 1.0 O B:HOH507 3.3 29.7 1.0 CG2 B:THR217 3.5 26.3 1.0 PB B:UPF403 3.5 32.8 1.0 N B:THR217 3.5 25.4 1.0 C4' B:UPF403 3.6 30.1 1.0 O5' B:UPF403 3.6 28.2 1.0 CA B:THR217 3.8 26.4 1.0 C B:GLY216 3.9 25.9 1.0 C5' B:UPF403 4.1 31.0 1.0 CG B:ASP156 4.1 31.0 1.0 C5D B:UPF403 4.1 32.5 1.0 O4' B:UPF403 4.1 29.8 1.0 MN B:MN401 4.3 31.7 1.0 CB B:THR217 4.3 27.9 1.0 O1B B:UPF403 4.4 29.4 1.0 O B:GLY216 4.4 27.2 1.0 CA B:GLY216 4.4 26.7 1.0 O B:HOH503 4.5 28.6 1.0 N B:GLY216 4.7 26.2 1.0 O3A B:UPF403 4.7 32.0 1.0 OD1 B:ASP156 4.8 33.2 1.0 O2A B:UPF403 5.0 30.5 1.0 NE2 B:HIS285 5.0 33.4 1.0

J.M.Lo, C.C.Kung, T.R.Cheng, C.H.Wong, C.Ma. Structure-Based Mechanism and Specificity of Human Galactosyltransferase Beta 3GALT5. J.Am.Chem.Soc. 2025.
ISSN: ESSN 1520-5126
PubMed: 40130308
DOI: 10.1021/JACS.4C11724