Fluorine in PDB 8ke3: Pylrs C-Terminus Domain Mutant Bound with D-3- Trifluoromethylphenylalanine and Ampnp

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

The structure of Pylrs C-Terminus Domain Mutant Bound with D-3- Trifluoromethylphenylalanine and Ampnp, PDB code: 8ke3 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)	34.26 / 1.90
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	104.67, 104.67, 71.813, 90, 90, 120
R / Rfree (%)	18.4 / 20.7

The structure of Pylrs C-Terminus Domain Mutant Bound with D-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 D-3- Trifluoromethylphenylalanine and Ampnp (pdb code 8ke3). 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 D-3- Trifluoromethylphenylalanine and Ampnp, PDB code: 8ke3:
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 D-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 D-3- Trifluoromethylphenylalanine and Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:36.3 occ:0.54 F10 A:FXC504 0.0 36.3 0.5 C09 A:FXC504 1.3 30.6 0.5 F12 A:FXC504 2.1 32.3 0.5 F11 A:FXC504 2.3 27.4 0.5 CE2 A:FXC504 2.4 29.7 0.5 CD2 A:FXC504 2.7 30.2 0.5 CZ A:FXC504 3.6 28.0 0.5 CZ3 A:TRP417 3.7 18.6 1.0 CH2 A:TRP417 3.7 23.6 1.0 CG A:FXC504 4.0 27.3 0.5 O A:HOH648 4.2 30.6 1.0 CA A:FXC504 4.4 29.0 0.5 C A:GLY419 4.6 20.2 1.0 O A:GLY419 4.6 14.2 1.0 CE1 A:FXC504 4.7 25.5 0.5 N A:FXC504 4.8 29.9 0.5 N A:ALA420 4.8 15.4 1.0 CE3 A:TRP417 4.8 16.9 1.0 N A:GLY401 4.8 21.9 1.0 CZ2 A:TRP417 4.8 22.9 1.0 CD1 A:FXC504 4.8 26.0 0.5 CB A:FXC504 4.9 28.2 0.5 CA A:GLY419 5.0 17.0 1.0 O A:HOH636 5.0 24.2 1.0 OXT A:FXC504 5.0 33.4 0.5

Fluorine binding site 2 out of 3 in the Pylrs C-Terminus Domain Mutant Bound with D-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 D-3- Trifluoromethylphenylalanine and Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:27.4 occ:0.54 F11 A:FXC504 0.0 27.4 0.5 C09 A:FXC504 1.4 30.6 0.5 F10 A:FXC504 2.3 36.3 0.5 F12 A:FXC504 2.4 32.3 0.5 CE2 A:FXC504 2.5 29.7 0.5 O A:HOH636 2.8 24.2 1.0 CZ A:FXC504 3.2 28.0 0.5 O A:HOH648 3.3 30.6 1.0 CD2 A:FXC504 3.4 30.2 0.5 NE2 A:GLN348 3.8 19.8 1.0 CB A:ALA302 3.9 16.7 1.0 CH2 A:TRP417 3.9 23.6 1.0 CD A:GLN348 4.1 27.6 1.0 CZ3 A:TRP417 4.1 18.6 1.0 OE1 A:GLN348 4.2 20.5 1.0 CE1 A:FXC504 4.5 25.5 0.5 CA A:ALA302 4.6 18.7 1.0 CZ2 A:TRP417 4.6 22.9 1.0 CG A:FXC504 4.6 27.3 0.5 CZ A:TYR306 4.8 26.7 1.0 OH A:TYR306 4.8 24.4 1.0 CE2 A:TYR306 4.9 22.6 1.0 CE3 A:TRP417 4.9 16.9 1.0

Fluorine binding site 3 out of 3 in the Pylrs C-Terminus Domain Mutant Bound with D-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 D-3- Trifluoromethylphenylalanine and Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:32.3 occ:0.54 F12 A:FXC504 0.0 32.3 0.5 C09 A:FXC504 1.3 30.6 0.5 F10 A:FXC504 2.1 36.3 0.5 CE2 A:FXC504 2.2 29.7 0.5 F11 A:FXC504 2.4 27.4 0.5 CZ A:FXC504 2.7 28.0 0.5 CZ3 A:TRP417 3.2 18.6 1.0 CD2 A:FXC504 3.3 30.2 0.5 CD A:GLN348 3.6 27.6 1.0 CA A:GLY419 3.6 17.0 1.0 NE2 A:GLN348 3.7 19.8 1.0 CG A:GLN348 3.7 20.3 1.0 C A:GLY419 3.8 20.2 1.0 CE3 A:TRP417 3.9 16.9 1.0 CH2 A:TRP417 3.9 23.6 1.0 CE1 A:FXC504 4.0 25.5 0.5 OE1 A:GLN348 4.0 20.5 1.0 N A:ALA420 4.0 15.4 1.0 N A:GLY419 4.2 16.8 1.0 O A:HOH636 4.2 24.2 1.0 O A:GLY419 4.3 14.2 1.0 O A:PHE347 4.3 15.0 1.0 CG A:FXC504 4.4 27.3 0.5 CB A:GLN348 4.6 17.7 1.0 CD1 A:FXC504 4.7 26.0 0.5 C A:ILE418 4.8 14.1 1.0 O A:ILE418 4.9 14.9 1.0 CA A:ALA420 4.9 14.0 1.0 CZ2 A:TRP417 4.9 22.9 1.0 CD2 A:TRP417 4.9 18.4 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