Magnesium in PDB 8ke1: Pylrs C-Terminus Domain Mutant Bound with L-3-Bromophenylalanine and Ampnp

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

The structure of Pylrs C-Terminus Domain Mutant Bound with L-3-Bromophenylalanine and Ampnp, PDB code: 8ke1 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)	28.00 / 2.50
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	104.959, 104.959, 71.114, 90, 90, 120
R / Rfree (%)	16.7 / 20.7

The structure of Pylrs C-Terminus Domain Mutant Bound with L-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 L-3-Bromophenylalanine and Ampnp (pdb code 8ke1). 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-Bromophenylalanine and Ampnp, PDB code: 8ke1:
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-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 L-3-Bromophenylalanine and Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:29.4 occ:1.00 O A:HOH669 2.2 50.1 1.0 OG A:SER399 2.3 37.0 1.0 O1B A:ANP501 2.3 31.3 1.0 O2A A:ANP501 2.4 29.0 1.0 OE1 A:GLU396 2.5 36.0 1.0 OE2 A:GLU396 3.1 46.0 1.0 CD A:GLU396 3.1 38.5 1.0 PB A:ANP501 3.3 27.8 1.0 CB A:SER399 3.3 24.8 1.0 PA A:ANP501 3.5 28.2 1.0 O3A A:ANP501 3.5 33.4 1.0 N3B A:ANP501 3.7 32.3 1.0 O1A A:ANP501 4.2 33.4 1.0 O A:HOH641 4.3 42.9 1.0 CG A:GLU396 4.5 31.6 1.0 CA A:SER399 4.5 36.5 1.0 OD1 A:ASP389 4.5 43.3 1.0 O3' A:ANP501 4.6 30.2 1.0 O2B A:ANP501 4.6 28.5 1.0 N A:SER399 4.7 33.2 1.0 O5' A:ANP501 4.8 29.4 1.0

Magnesium binding site 2 out of 2 in the Pylrs C-Terminus Domain Mutant Bound with L-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 L-3-Bromophenylalanine and Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:29.7 occ:1.00 O A:HOH625 2.1 30.4 1.0 O2G A:ANP501 2.1 30.0 1.0 O2B A:ANP501 2.1 28.5 1.0 O A:HOH623 2.1 26.1 1.0 O A:HOH636 2.2 35.4 1.0 O A:HOH654 2.2 33.4 1.0 PG A:ANP501 3.5 36.6 1.0 PB A:ANP501 3.5 27.8 1.0 N3B A:ANP501 4.0 32.3 1.0 NH2 A:ARG330 4.0 32.3 1.0 O3G A:ANP501 4.1 41.5 1.0 OE2 A:GLU332 4.1 32.6 1.0 NE2 A:HIS338 4.2 34.5 1.0 OE2 A:GLU283 4.3 62.7 1.0 OE1 A:GLU283 4.3 61.1 1.0 O1B A:ANP501 4.3 31.3 1.0 OE1 A:GLN287 4.3 48.5 1.0 NE2 A:GLN287 4.4 42.1 1.0 OE1 A:GLU332 4.4 36.5 1.0 O3A A:ANP501 4.5 33.4 1.0 CD A:GLU283 4.5 70.4 1.0 CD2 A:HIS338 4.6 34.8 1.0 O1G A:ANP501 4.6 30.1 1.0 CD A:GLU332 4.7 34.3 1.0 N7 A:ANP501 4.8 29.9 1.0 CD A:GLN287 4.8 50.0 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