Magnesium in PDB 8ke4: Pylrs C-Terminus Domain Mutant Bound with D-3-Bromophenylalanine and Ampnp

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

The structure of Pylrs C-Terminus Domain Mutant Bound with D-3-Bromophenylalanine and Ampnp, PDB code: 8ke4 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)	28.17 / 1.75
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	105.198, 105.198, 71.694, 90, 90, 120
R / Rfree (%)	17.2 / 18.4

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

Bromine

(Br)

1 atom

The binding sites of Magnesium atom in the Pylrs C-Terminus Domain Mutant Bound with D-3-Bromophenylalanine and Ampnp (pdb code 8ke4). 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-Bromophenylalanine and Ampnp, PDB code: 8ke4:
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-Bromophenylalanine 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-Bromophenylalanine and Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:21.5 occ:1.00 O1B A:ANP501 2.2 25.4 1.0 OG A:SER399 2.3 23.6 1.0 O2A A:ANP501 2.3 24.6 1.0 OE1 A:GLU396 2.5 25.6 1.0 OE2 A:GLU396 2.9 31.8 1.0 CD A:GLU396 3.0 28.4 1.0 CB A:SER399 3.3 24.6 1.0 PB A:ANP501 3.4 23.9 1.0 PA A:ANP501 3.4 22.3 1.0 O3A A:ANP501 3.6 22.4 1.0 N3B A:ANP501 3.9 23.8 1.0 O A:HOH630 3.9 38.1 1.0 O1A A:ANP501 4.3 21.9 1.0 OD1 A:ASP389 4.3 31.6 1.0 O A:HOH797 4.4 42.9 1.0 CG A:GLU396 4.4 25.2 1.0 O A:HOH723 4.5 37.9 1.0 CA A:SER399 4.5 22.2 1.0 O5' A:ANP501 4.7 21.7 1.0 N A:SER399 4.7 20.5 1.0 O2B A:ANP501 4.7 23.4 1.0 O A:HOH631 4.7 35.3 1.0 O3' A:ANP501 4.7 21.9 1.0 O A:HOH632 4.9 43.6 1.0 C5' A:ANP501 4.9 22.4 1.0

Magnesium binding site 2 out of 2 in the Pylrs C-Terminus Domain Mutant Bound with D-3-Bromophenylalanine 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-Bromophenylalanine and Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:23.9 occ:1.00 O2B A:ANP501 1.9 23.4 1.0 O2G A:ANP501 2.0 23.5 1.0 O A:HOH609 2.1 25.1 1.0 O A:HOH697 2.2 25.1 1.0 O A:HOH719 2.3 25.1 1.0 O A:HOH621 2.3 25.1 1.0 PB A:ANP501 3.3 23.9 1.0 PG A:ANP501 3.3 23.7 1.0 N3B A:ANP501 3.7 23.8 1.0 NH2 A:ARG330 3.8 23.2 1.0 O3G A:ANP501 3.9 25.1 1.0 NE2 A:HIS338 4.1 25.7 1.0 OE2 A:GLU332 4.2 23.0 1.0 O A:HOH723 4.2 37.9 1.0 O A:HOH825 4.2 33.5 1.0 O3A A:ANP501 4.2 22.4 1.0 O A:HOH669 4.3 41.5 1.0 OE2 A:GLU283 4.3 43.1 1.0 O1B A:ANP501 4.3 25.4 1.0 OE1 A:GLU283 4.4 39.8 1.0 OE1 A:GLU332 4.5 24.1 1.0 CD2 A:HIS338 4.5 23.4 1.0 OE1 A:GLN287 4.5 29.8 1.0 O1G A:ANP501 4.5 24.0 1.0 N7 A:ANP501 4.6 21.8 1.0 CD A:GLU283 4.6 44.6 1.0 NE2 A:GLN287 4.6 28.2 1.0 CD A:GLU332 4.8 26.8 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