Magnesium in PDB 8ke6: Pylrs C-Terminus Domain Mutant Bound with L-3-Chlorophenylalanine and Ampnp

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

The structure of Pylrs C-Terminus Domain Mutant Bound with L-3-Chlorophenylalanine and Ampnp, PDB code: 8ke6 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)	26.29 / 1.90
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	105.162, 105.162, 72.446, 90, 90, 120
R / Rfree (%)	17.3 / 18.8

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

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Pylrs C-Terminus Domain Mutant Bound with L-3-Chlorophenylalanine and Ampnp (pdb code 8ke6). 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-Chlorophenylalanine and Ampnp, PDB code: 8ke6:
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-Chlorophenylalanine 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-Chlorophenylalanine and Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:29.5 occ:1.00 O A:HOH619 2.2 41.4 1.0 OG A:SER399 2.2 30.2 1.0 O1B A:ANP501 2.2 31.5 1.0 O2A A:ANP501 2.3 29.3 1.0 O A:HOH744 2.3 39.7 1.0 OE1 A:GLU396 2.4 31.5 1.0 CD A:GLU396 3.0 35.5 1.0 OE2 A:GLU396 3.0 37.8 1.0 PB A:ANP501 3.3 30.2 1.0 CB A:SER399 3.3 28.3 1.0 PA A:ANP501 3.3 30.4 1.0 O3A A:ANP501 3.4 27.1 1.0 N3B A:ANP501 3.8 27.2 1.0 O A:HOH607 4.0 42.2 1.0 O1A A:ANP501 4.2 27.4 1.0 O A:HOH646 4.3 39.3 1.0 O3' A:ANP501 4.4 23.9 1.0 O A:HOH632 4.4 45.8 1.0 CG A:GLU396 4.4 30.6 1.0 CA A:SER399 4.4 30.9 1.0 OD1 A:ASP389 4.5 36.4 1.0 N A:SER399 4.5 26.7 1.0 O5' A:ANP501 4.6 25.4 1.0 O2B A:ANP501 4.6 29.0 1.0 C5' A:ANP501 4.8 26.2 1.0 C3' A:ANP501 4.8 24.8 1.0

Magnesium binding site 2 out of 2 in the Pylrs C-Terminus Domain Mutant Bound with L-3-Chlorophenylalanine 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-Chlorophenylalanine and Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:28.1 occ:1.00 O2G A:ANP501 2.0 27.7 1.0 O2B A:ANP501 2.0 29.0 1.0 O A:HOH689 2.1 31.4 1.0 O A:HOH616 2.1 26.2 1.0 O A:HOH696 2.1 31.2 1.0 O A:HOH666 2.1 28.8 1.0 PB A:ANP501 3.3 30.2 1.0 PG A:ANP501 3.3 29.2 1.0 N3B A:ANP501 3.8 27.2 1.0 NH2 A:ARG330 3.9 25.3 1.0 O3G A:ANP501 3.9 33.5 1.0 NE2 A:HIS338 4.1 30.5 1.0 OE2 A:GLU332 4.2 29.4 1.0 O A:HOH776 4.2 39.3 1.0 O A:HOH632 4.2 45.8 1.0 O1B A:ANP501 4.3 31.5 1.0 O3A A:ANP501 4.3 27.1 1.0 OE2 A:GLU283 4.3 57.1 1.0 O A:HOH727 4.4 46.6 1.0 OE1 A:GLU283 4.4 52.7 1.0 OE1 A:GLU332 4.4 27.5 1.0 CD2 A:HIS338 4.5 27.1 1.0 O1G A:ANP501 4.5 29.3 1.0 OE1 A:GLN287 4.6 44.5 1.0 NE2 A:GLN287 4.6 40.0 1.0 N7 A:ANP501 4.6 25.6 1.0 CD A:GLU283 4.7 57.8 1.0 CD A:GLU332 4.7 34.9 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