Magnesium in PDB 9p8w: Anti-Phage Dgtpase From Shewanella Putrefaciens Cn-32

The structure of Anti-Phage Dgtpase From Shewanella Putrefaciens Cn-32, PDB code: 9p8w was solved by S.Yamaguchi, S.G.Fernandez, D.R.Wassarman, M.Luder, F.Schwede, P.J.Kranzusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.74 / 2.68
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	121.718, 121.718, 151.483, 90, 90, 120
R / Rfree (%)	20.8 / 26.6

The binding sites of Magnesium atom in the Anti-Phage Dgtpase From Shewanella Putrefaciens Cn-32 (pdb code 9p8w). 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 Anti-Phage Dgtpase From Shewanella Putrefaciens Cn-32, PDB code: 9p8w:

Magnesium binding site 1 out of 1 in the Anti-Phage Dgtpase From Shewanella Putrefaciens Cn-32


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Anti-Phage Dgtpase From Shewanella Putrefaciens Cn-32 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:27.7 occ:1.00 NE2 A:HIS100 2.0 43.6 1.0 OD1 A:ASP254 2.2 56.7 1.0 OD2 A:ASP101 2.2 54.9 1.0 NE2 A:HIS59 2.6 55.4 1.0 OH A:TYR258 2.7 67.3 1.0 CD2 A:HIS100 2.8 54.5 1.0 CG A:ASP254 3.0 61.0 1.0 CG A:ASP101 3.0 59.3 1.0 CE1 A:HIS100 3.1 49.5 1.0 OD2 A:ASP254 3.2 60.1 1.0 OD1 A:ASP101 3.2 61.3 1.0 CD2 A:HIS59 3.3 50.5 1.0 CZ A:TYR258 3.3 73.4 1.0 CE2 A:TYR258 3.5 67.6 1.0 CE1 A:HIS59 3.7 69.7 1.0 CG A:HIS100 4.0 50.7 1.0 ND1 A:HIS100 4.1 44.6 1.0 CE1 A:TYR258 4.3 90.6 1.0 CB A:ASP254 4.4 54.5 1.0 CB A:ASP101 4.4 52.0 1.0 CG A:HIS59 4.5 65.1 1.0 CD2 A:TYR258 4.7 78.5 1.0 ND1 A:HIS59 4.7 70.2 1.0 OE1 A:GLN43 5.0 89.5 1.0

S.Yamaguchi, S.G.Fernandez, D.R.Wassarman, M.Luders, F.Schwede, P.J.Kranzusch. Activating and Inhibiting Nucleotide Signals Coordinate Bacterial Anti-Phage Defense. Biorxiv 2025.
ISSN: ISSN 2692-8205
PubMed: 40672243
DOI: 10.1101/2025.07.09.663793