Magnesium 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:

Fluorine

(F)

3 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pylrs C-Terminus Domain Mutant Bound with L-3- Trifluoromethylphenylalanine and Ampnp, PDB code: 8ke2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pylrs C-Terminus Domain Mutant Bound with L-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 L-3- Trifluoromethylphenylalanine and Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:29.4 occ:1.00 OG A:SER399 2.2 36.2 1.0 O A:HOH712 2.3 41.0 1.0 O2B A:ANP503 2.4 33.3 1.0 O2A A:ANP503 2.4 29.7 1.0 OE1 A:GLU396 2.6 32.3 1.0 OE2 A:GLU396 2.8 44.4 1.0 CD A:GLU396 3.0 34.5 1.0 CB A:SER399 3.3 24.4 1.0 PB A:ANP503 3.3 27.7 1.0 PA A:ANP503 3.4 30.2 1.0 O3A A:ANP503 3.5 34.9 1.0 O A:HOH642 3.7 42.4 1.0 N3B A:ANP503 3.7 30.6 1.0 O1A A:ANP503 4.0 34.9 1.0 O A:HOH602 4.1 39.3 1.0 O A:HOH687 4.3 34.5 1.0 OD1 A:ASP389 4.4 39.9 1.0 O3' A:ANP503 4.5 27.3 1.0 CA A:SER399 4.5 32.9 1.0 CG A:GLU396 4.5 27.9 1.0 N A:SER399 4.7 30.1 1.0 O1B A:ANP503 4.7 35.2 1.0 O5' A:ANP503 4.8 33.3 1.0 C3' A:ANP503 4.9 29.4 1.0

Magnesium binding site 2 out of 2 in the Pylrs C-Terminus Domain Mutant Bound with L-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 L-3- Trifluoromethylphenylalanine and Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:37.7 occ:1.00 O A:HOH601 1.8 26.5 1.0 O A:HOH606 2.1 31.8 1.0 O2G A:ANP503 2.1 28.7 1.0 O A:HOH615 2.3 32.3 1.0 O1B A:ANP503 2.3 35.2 1.0 O A:HOH617 2.8 33.7 1.0 OE2 A:GLU332 3.5 28.1 1.0 NH2 A:ARG330 3.6 27.6 1.0 PG A:ANP503 3.6 30.8 1.0 PB A:ANP503 3.8 27.7 1.0 OE1 A:GLU332 3.8 30.6 1.0 NE2 A:GLN287 4.0 36.1 1.0 NE2 A:HIS338 4.0 34.4 1.0 OE1 A:GLN287 4.0 43.4 1.0 CD A:GLU332 4.1 29.8 1.0 OE1 A:GLU283 4.2 59.6 1.0 O3G A:ANP503 4.2 35.4 1.0 CD2 A:HIS338 4.3 29.1 1.0 N7 A:ANP503 4.3 28.0 1.0 N3B A:ANP503 4.4 30.6 1.0 OE2 A:GLU283 4.4 58.0 1.0 CD A:GLN287 4.5 42.0 1.0 CD A:ARG330 4.6 21.5 1.0 CD A:GLU283 4.6 57.7 1.0 O1G A:ANP503 4.6 27.2 1.0 O2B A:ANP503 4.6 33.3 1.0 O A:HOH602 4.7 39.3 1.0 O3A A:ANP503 4.7 34.9 1.0 CZ A:ARG330 4.8 30.2 1.0 C8 A:ANP503 4.9 25.1 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