Magnesium 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:

Fluorine

(F)

3 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pylrs C-Terminus Domain Mutant Bound with D-3- Trifluoromethylphenylalanine and Ampnp, PDB code: 8ke3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pylrs C-Terminus Domain Mutant Bound with D-3- Trifluoromethylphenylalanine and Ampnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg502 b:23.4 occ:1.00 O2A A:ANP501 2.2 18.6 1.0 O A:HOH642 2.2 28.8 1.0 OG A:SER399 2.3 21.6 1.0 O1B A:ANP501 2.3 25.0 1.0 OE2 A:GLU396 2.5 26.2 1.0 OE1 A:GLU396 2.9 28.2 1.0 CD A:GLU396 3.0 26.2 1.0 CB A:SER399 3.3 21.8 1.0 PB A:ANP501 3.3 21.7 1.0 PA A:ANP501 3.3 19.8 1.0 O3A A:ANP501 3.5 22.3 1.0 N3B A:ANP501 3.8 28.6 1.0 O1A A:ANP501 4.0 19.4 1.0 OD1 A:ASP389 4.4 30.6 1.0 CA A:SER399 4.5 21.2 1.0 CG A:GLU396 4.5 20.8 1.0 O3' A:ANP501 4.5 16.9 1.0 N A:SER399 4.6 18.4 1.0 O5' A:ANP501 4.6 19.3 1.0 O2B A:ANP501 4.7 22.9 1.0 C3' A:ANP501 4.8 16.1 1.0 O A:HOH627 4.8 33.5 1.0 C5' A:ANP501 4.9 24.1 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg503 b:22.6 occ:1.00 O2G A:ANP501 1.9 19.1 1.0 O A:HOH640 2.0 18.9 1.0 O A:HOH663 2.0 20.7 1.0 O2B A:ANP501 2.1 22.9 1.0 O A:HOH607 2.1 19.2 1.0 O A:HOH661 2.3 25.0 1.0 PG A:ANP501 3.3 22.6 1.0 PB A:ANP501 3.5 21.7 1.0 NH2 A:ARG330 3.9 17.4 1.0 O3G A:ANP501 3.9 23.1 1.0 N3B A:ANP501 4.0 28.6 1.0 OE2 A:GLU332 4.1 19.7 1.0 NE2 A:HIS338 4.1 23.2 1.0 OE1 A:GLU283 4.2 36.7 1.0 O A:HOH707 4.2 29.5 1.0 OE1 A:GLU332 4.3 19.3 1.0 OE2 A:GLU283 4.3 45.0 1.0 O1B A:ANP501 4.3 25.0 1.0 O1G A:ANP501 4.4 22.1 1.0 NE2 A:GLN287 4.4 24.1 1.0 OE1 A:GLN287 4.5 28.9 1.0 CD2 A:HIS338 4.5 19.3 1.0 O3A A:ANP501 4.5 22.3 1.0 CD A:GLU283 4.6 41.8 1.0 CD A:GLU332 4.6 22.1 1.0 N7 A:ANP501 4.6 17.2 1.0 CD A:GLN287 4.9 26.6 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