Magnesium in PDB 8zvc: Shost with Prpp-Mg

The structure of Shost with Prpp-Mg, PDB code: 8zvc was solved by Y.Yu, Q.Chen, H.Pu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.52 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.779, 79.153, 89.988, 90, 90, 90
R / Rfree (%)	16.4 / 19.7

The binding sites of Magnesium atom in the Shost with Prpp-Mg (pdb code 8zvc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Shost with Prpp-Mg, PDB code: 8zvc:

Magnesium binding site 1 out of 1 in the Shost with Prpp-Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Shost with Prpp-Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg606 b:15.4 occ:1.00 HO3 A:PRP601 2.0 17.4 1.0 O2 A:PRP601 2.2 15.5 1.0 O1B A:PRP601 2.3 20.9 1.0 O A:HOH862 2.3 18.9 1.0 HO3 A:GOL603 2.4 24.6 1.0 O3 A:GOL603 2.4 20.4 1.0 O3 A:PRP601 2.4 14.5 1.0 O1 A:PRP601 2.4 16.9 1.0 HO2 A:PRP601 2.5 18.6 1.0 C2 A:PRP601 3.0 13.8 1.0 H11 A:GOL603 3.2 29.4 1.0 C3 A:PRP601 3.2 13.9 1.0 C1 A:PRP601 3.3 15.2 1.0 PB A:PRP601 3.4 19.4 1.0 O3A A:PRP601 3.4 19.3 1.0 PA A:PRP601 3.6 18.3 1.0 HA2 A:GLY239 3.6 21.3 1.0 O A:HOH740 3.6 16.3 1.0 C3 A:GOL603 3.7 30.4 1.0 C1 A:GOL603 3.8 24.5 1.0 H2 A:GOL603 3.9 38.5 1.0 H3 A:PRP601 3.9 16.8 1.0 O1 A:GOL603 4.0 27.2 1.0 H2 A:PRP601 4.0 16.6 1.0 C2 A:GOL603 4.0 32.0 1.0 H1 A:PRP601 4.1 18.3 1.0 HD2 A:TYR237 4.1 17.6 1.0 O1A A:PRP601 4.2 19.8 1.0 O4 A:PRP601 4.2 16.6 1.0 O A:HOH863 4.2 21.2 1.0 C4 A:PRP601 4.3 15.1 1.0 H32 A:GOL603 4.3 36.5 1.0 OD1 A:ASP331 4.3 17.1 1.0 OD2 A:ASP331 4.3 15.7 1.0 OD1 A:ASP332 4.3 16.2 1.0 H31 A:GOL603 4.3 36.5 1.0 O2B A:PRP601 4.3 20.0 1.0 O A:VAL238 4.4 15.3 1.0 H4 A:PRP601 4.5 18.2 1.0 O3B A:PRP601 4.5 20.3 1.0 CA A:GLY239 4.6 17.7 1.0 HO1 A:GOL603 4.6 32.7 1.0 H12 A:GOL603 4.7 29.4 1.0 OD2 A:ASP332 4.7 17.4 1.0 CG A:ASP331 4.7 15.8 1.0 O2A A:PRP601 4.8 18.5 1.0 H A:HIS240 4.8 20.9 1.0 CG A:ASP332 4.9 19.9 1.0 CD2 A:TYR237 5.0 14.6 1.0

Y.Yu, Q.Chen, H.Pu. A Toxin-Antitoxin System Provides Phage Defense Via Dna Damage and Repair Nat Commun 2025.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-025-58540-9