Fluorine in PDB 8ke2: Pylrs C-Terminus Domain Mutant Bound with L-3- Trifluoromethylphenylalanine and Ampnp

All present enzymatic activity of Pylrs C-Terminus Domain Mutant Bound with L-3- Trifluoromethylphenylalanine and Ampnp:
6.1.1.26;

The structure of Pylrs C-Terminus Domain Mutant Bound with L-3- Trifluoromethylphenylalanine and Ampnp, PDB code: 8ke2 was solved by J.H.Weng, M.D.Tsai, Y.S.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.38 / 2.20
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	105.508, 105.508, 71.13, 90, 90, 120
R / Rfree (%)	19.4 / 22.1

The structure of Pylrs C-Terminus Domain Mutant Bound with L-3- Trifluoromethylphenylalanine and Ampnp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Pylrs C-Terminus Domain Mutant Bound with L-3- Trifluoromethylphenylalanine and Ampnp (pdb code 8ke2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Pylrs C-Terminus Domain Mutant Bound with L-3- Trifluoromethylphenylalanine and Ampnp, PDB code: 8ke2:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Pylrs C-Terminus Domain Mutant Bound with L-3- Trifluoromethylphenylalanine and Ampnp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pylrs C-Terminus Domain Mutant Bound with L-3- Trifluoromethylphenylalanine and Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:41.2 occ:1.00 F10 A:FX9504 0.0 41.2 1.0 C09 A:FX9504 1.3 40.6 1.0 F12 A:FX9504 2.1 39.8 1.0 F11 A:FX9504 2.1 43.5 1.0 CE2 A:FX9504 2.3 35.1 1.0 CD2 A:FX9504 2.8 35.3 1.0 CZ A:FX9504 3.4 36.3 1.0 CD1 A:LEU305 3.5 25.9 1.0 CA A:ALA302 3.5 24.2 1.0 O A:HOH638 3.7 30.5 1.0 N A:ALA302 3.7 24.7 1.0 CB A:ALA302 3.8 25.6 1.0 O A:HOH723 3.9 35.5 1.0 OXT A:FX9504 4.0 37.1 1.0 OE1 A:GLN348 4.1 27.7 1.0 CG A:FX9504 4.1 38.5 1.0 C A:LEU301 4.2 23.9 1.0 CG A:LEU305 4.3 29.1 1.0 CB A:LEU305 4.3 23.2 1.0 C A:FX9504 4.4 38.5 1.0 CE1 A:FX9504 4.6 37.0 1.0 O A:LEU301 4.6 20.0 1.0 O A:FX9504 4.6 34.4 1.0 CB A:LEU301 4.6 22.4 1.0 CD A:GLN348 4.7 33.8 1.0 C A:ALA302 4.8 25.1 1.0 O A:HOH710 4.8 45.4 1.0 CD1 A:FX9504 4.8 36.8 1.0 CA A:LEU301 4.9 23.1 1.0

Fluorine binding site 2 out of 3 in the Pylrs C-Terminus Domain Mutant Bound with L-3- Trifluoromethylphenylalanine and Ampnp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pylrs C-Terminus Domain Mutant Bound with L-3- Trifluoromethylphenylalanine and Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:43.5 occ:1.00 F11 A:FX9504 0.0 43.5 1.0 C09 A:FX9504 1.3 40.6 1.0 F12 A:FX9504 2.1 39.8 1.0 F10 A:FX9504 2.1 41.2 1.0 CE2 A:FX9504 2.3 35.1 1.0 CZ A:FX9504 2.7 36.3 1.0 OE1 A:GLN348 3.4 27.7 1.0 CD A:GLN348 3.4 33.8 1.0 CG A:GLN348 3.5 28.0 1.0 CD2 A:FX9504 3.6 35.3 1.0 O A:PHE347 3.6 24.1 1.0 O A:HOH723 3.8 35.5 1.0 CB A:GLN348 3.8 27.5 1.0 O A:HOH638 4.0 30.5 1.0 CE1 A:FX9504 4.1 37.0 1.0 NE2 A:GLN348 4.1 27.4 1.0 CA A:GLY419 4.1 26.3 1.0 N A:ALA420 4.2 25.5 1.0 CD1 A:LEU305 4.2 25.9 1.0 C A:PHE347 4.3 26.2 1.0 C A:GLY419 4.4 27.6 1.0 O A:ALA420 4.5 28.5 1.0 CA A:GLN348 4.5 24.2 1.0 CG A:FX9504 4.7 38.5 1.0 N A:GLN348 4.7 26.2 1.0 CZ3 A:TRP417 4.8 27.9 1.0 N A:PHE347 4.9 26.4 1.0 CD1 A:FX9504 4.9 36.8 1.0 C A:ALA420 4.9 27.5 1.0

Fluorine binding site 3 out of 3 in the Pylrs C-Terminus Domain Mutant Bound with L-3- Trifluoromethylphenylalanine and Ampnp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pylrs C-Terminus Domain Mutant Bound with L-3- Trifluoromethylphenylalanine and Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:39.8 occ:1.00 F12 A:FX9504 0.0 39.8 1.0 C09 A:FX9504 1.3 40.6 1.0 F10 A:FX9504 2.1 41.2 1.0 F11 A:FX9504 2.1 43.5 1.0 CE2 A:FX9504 2.4 35.1 1.0 CD2 A:FX9504 3.0 35.3 1.0 O A:ALA420 3.2 28.5 1.0 CD1 A:LEU305 3.3 25.9 1.0 CZ A:FX9504 3.4 36.3 1.0 N A:PHE347 3.4 26.4 1.0 CA A:GLY346 3.5 23.7 1.0 O A:PHE347 3.5 24.1 1.0 C A:GLY346 3.6 25.1 1.0 C A:ALA420 3.9 27.5 1.0 C A:PHE347 3.9 26.2 1.0 N A:ALA420 4.2 25.5 1.0 CA A:PHE347 4.2 25.8 1.0 CG A:FX9504 4.2 38.5 1.0 CE1 A:FX9504 4.5 37.0 1.0 O A:GLY346 4.6 23.8 1.0 N A:GLY421 4.6 28.5 1.0 CG A:LEU305 4.6 29.1 1.0 CA A:ALA420 4.7 24.7 1.0 N A:GLN348 4.8 26.2 1.0 OE1 A:GLN348 4.8 27.7 1.0 CA A:GLY421 4.8 24.9 1.0 CB A:GLN348 4.8 27.5 1.0 N A:GLY346 4.9 23.2 1.0 CD1 A:FX9504 4.9 36.8 1.0

H.K.Jiang, J.H.Weng, Y.H.Wang, J.C.Tsou, P.J.Chen, A.L.A.Ko, D.Soll, M.D.Tsai, Y.S.Wang. Rational Design of the Genetic Code Expansion Toolkit For in Vivo Encoding of D-Amino Acids Front Genet 2023.
DOI: 10.3389/FGENE.2023.1277489