Fluorine in PDB 8d0q: Human FUT9 Bound to Gdp-CF3-Fucose and H-Type 2

All present enzymatic activity of Human FUT9 Bound to Gdp-CF3-Fucose and H-Type 2:
2.4.1.152;

The structure of Human FUT9 Bound to Gdp-CF3-Fucose and H-Type 2, PDB code: 8d0q was solved by R.Kadirvelraj, Z.A.Wood, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.90 / 1.39
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	127.81, 127.81, 127.81, 90, 90, 90
R / Rfree (%)	15.2 / 17.2

The binding sites of Fluorine atom in the Human FUT9 Bound to Gdp-CF3-Fucose and H-Type 2 (pdb code 8d0q). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human FUT9 Bound to Gdp-CF3-Fucose and H-Type 2, PDB code: 8d0q:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Human FUT9 Bound to Gdp-CF3-Fucose and H-Type 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human FUT9 Bound to Gdp-CF3-Fucose and H-Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:26.1 occ:0.75 F35 A:6CK401 0.0 26.1 0.8 C34 A:6CK401 1.3 27.5 0.8 F37 A:6CK401 2.1 25.8 0.8 F36 A:6CK401 2.2 24.9 0.8 C27 A:6CK401 2.3 23.5 0.8 O26 A:6CK401 2.8 24.7 0.8 O5 C:FUC3 3.1 28.1 0.5 O5 D:FUC3 3.1 28.1 0.5 C6 C:FUC3 3.4 32.7 0.5 C6 D:FUC3 3.4 32.7 0.5 O A:HOH797 3.6 52.3 1.0 C5' A:GDP402 3.6 20.1 0.2 C28 A:6CK401 3.7 24.2 0.8 C15 A:6CK401 3.7 32.3 0.8 C5 C:FUC3 3.8 29.3 0.5 C5 D:FUC3 3.8 29.3 0.5 O4 C:NAG1 3.9 23.7 0.5 O4 D:NDG1 3.9 23.7 0.5 C14 A:6CK401 3.9 24.7 0.8 C2 C:GAL2 3.9 25.9 0.5 C2 D:GAL2 3.9 25.9 0.5 C25 A:6CK401 4.0 27.0 0.8 C4' A:GDP402 4.0 23.3 0.2 C1 C:FUC3 4.1 26.2 0.5 C1 D:FUC3 4.1 26.2 0.5 O29 A:6CK401 4.3 22.3 0.8 O13 A:6CK401 4.3 34.2 0.8 C1 C:GAL2 4.4 25.4 0.5 C1 D:GAL2 4.4 25.4 0.5 O3 C:NAG1 4.5 25.0 0.5 O3 D:NDG1 4.5 25.0 0.5 O2 C:GAL2 4.5 26.3 0.5 O2 D:GAL2 4.5 26.3 0.5 O4' A:GDP402 4.6 13.6 0.2 O4 C:GAL2 4.6 25.8 0.5 O4 D:GAL2 4.6 25.8 0.5 O5 C:GAL2 4.7 23.1 0.5 O5 D:GAL2 4.7 23.1 0.5 C3 C:NAG1 4.7 24.3 0.5 C3 D:NDG1 4.7 24.3 0.5 O1B A:GDP402 4.7 26.9 0.2 OE2 A:GLU255 4.7 27.6 1.0 C30 A:6CK401 4.8 24.5 0.8 O5' A:GDP402 4.8 30.2 0.2 OE1 A:GLU255 4.8 23.7 1.0 O A:HOH799 4.8 35.0 1.0 O24 A:6CK401 4.8 24.9 0.8 O16 A:6CK401 4.9 23.6 0.8 CD A:GLU255 4.9 27.0 1.0 C4 C:NAG1 4.9 24.1 0.5 C4 D:NDG1 4.9 24.1 0.5 O A:HOH535 5.0 52.1 1.0 C32 A:6CK401 5.0 25.1 0.8

Fluorine binding site 2 out of 3 in the Human FUT9 Bound to Gdp-CF3-Fucose and H-Type 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human FUT9 Bound to Gdp-CF3-Fucose and H-Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:24.9 occ:0.75 F36 A:6CK401 0.0 24.9 0.8 C34 A:6CK401 1.3 27.5 0.8 F37 A:6CK401 2.1 25.8 0.8 F35 A:6CK401 2.2 26.1 0.8 C27 A:6CK401 2.3 23.5 0.8 O4 C:GAL2 2.7 25.8 0.5 O4 D:GAL2 2.7 25.8 0.5 C28 A:6CK401 2.9 24.2 0.8 O A:HOH619 3.1 28.1 1.0 O A:HOH799 3.3 35.0 1.0 O A:HOH797 3.4 52.3 1.0 C2 C:GAL2 3.4 25.9 0.5 C2 D:GAL2 3.4 25.9 0.5 O26 A:6CK401 3.5 24.7 0.8 O29 A:6CK401 3.5 22.3 0.8 OE1 A:GLU255 3.6 23.7 1.0 C4 C:GAL2 3.8 24.9 0.5 C4 D:GAL2 3.8 24.9 0.5 O3 C:GAL2 3.9 26.7 0.5 O3 D:GAL2 3.9 26.7 0.5 C3 C:GAL2 3.9 26.1 0.5 C3 D:GAL2 3.9 26.1 0.5 O5 C:GAL2 4.0 23.1 0.5 O5 D:GAL2 4.0 23.1 0.5 O5 C:FUC3 4.0 28.1 0.5 O5 D:FUC3 4.0 28.1 0.5 CD A:GLU255 4.1 27.0 1.0 C1 C:GAL2 4.1 25.4 0.5 C1 D:GAL2 4.1 25.4 0.5 O4 C:NAG1 4.3 23.7 0.5 O4 D:NDG1 4.3 23.7 0.5 C30 A:6CK401 4.3 24.5 0.8 C1 C:FUC3 4.3 26.2 0.5 C1 D:FUC3 4.3 26.2 0.5 O2 C:GAL2 4.5 26.3 0.5 O2 D:GAL2 4.5 26.3 0.5 OE2 A:GLU255 4.5 27.6 1.0 C5 C:GAL2 4.5 23.8 0.5 C5 D:GAL2 4.5 23.8 0.5 C25 A:6CK401 4.7 27.0 0.8 CE2 A:TYR168 4.7 20.5 1.0 O3 C:NAG1 4.9 25.0 0.5 O3 D:NDG1 4.9 25.0 0.5 CG A:GLU255 4.9 22.4 1.0

Fluorine binding site 3 out of 3 in the Human FUT9 Bound to Gdp-CF3-Fucose and H-Type 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human FUT9 Bound to Gdp-CF3-Fucose and H-Type 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:25.8 occ:0.75 F37 A:6CK401 0.0 25.8 0.8 C34 A:6CK401 1.3 27.5 0.8 F36 A:6CK401 2.1 24.9 0.8 F35 A:6CK401 2.1 26.1 0.8 C27 A:6CK401 2.4 23.5 0.8 OE2 A:GLU255 2.7 27.6 1.0 O26 A:6CK401 2.7 24.7 0.8 CD A:GLU255 2.8 27.0 1.0 OE1 A:GLU255 2.8 23.7 1.0 O29 A:6CK401 2.9 22.3 0.8 C28 A:6CK401 3.1 24.2 0.8 C14 A:6CK401 3.2 24.7 0.8 C4' A:GDP402 3.3 23.3 0.2 C15 A:6CK401 3.4 32.3 0.8 C5' A:GDP402 3.4 20.1 0.2 O A:HOH797 3.6 52.3 1.0 CG A:GLU255 3.8 22.4 1.0 NZ A:LYS256 3.9 30.1 1.0 O A:HOH619 4.0 28.1 1.0 C25 A:6CK401 4.1 27.0 0.8 O13 A:6CK401 4.2 34.2 0.8 C38 A:6CK401 4.2 25.9 0.8 C3' A:GDP402 4.2 22.9 0.2 O39 A:6CK401 4.3 24.1 0.8 O4' A:GDP402 4.3 13.6 0.2 O3' A:GDP402 4.3 27.4 0.2 O1B A:GDP402 4.3 26.9 0.2 O A:HOH717 4.4 44.8 1.0 C30 A:6CK401 4.4 24.5 0.8 O A:HOH799 4.7 35.0 1.0 C32 A:6CK401 4.7 25.1 0.8 O4 C:GAL2 4.7 25.8 0.5 O4 D:GAL2 4.7 25.8 0.5 O24 A:6CK401 4.8 24.9 0.8 O16 A:6CK401 4.8 23.6 0.8 O5' A:GDP402 4.8 30.2 0.2 O5 C:FUC3 5.0 28.1 0.5 O5 D:FUC3 5.0 28.1 0.5

R.Kadirvelraj, B.M.Boruah, S.Wang, D.Chapla, C.Huang, A.Ramiah, K.L.Hudson, A.R.Prudden, G.J.Boons, S.G.Withers, Z.A.Wood, K.W.Moremen. Structural Basis For Lewis Antigen Synthesis By the Alpha 1,3-Fucosyltransferase FUT9. Nat.Chem.Biol. 2023.
ISSN: ESSN 1552-4469
PubMed: 37202521
DOI: 10.1038/S41589-023-01345-Y