Magnesium in PDB 8v1q: Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna in Both Open/Closed Conformations

All present enzymatic activity of Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna in Both Open/Closed Conformations:
2.7.7.7;

The binding sites of Magnesium atom in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna in Both Open/Closed Conformations (pdb code 8v1q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna in Both Open/Closed Conformations, PDB code: 8v1q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna in Both Open/Closed Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna in Both Open/Closed Conformations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1301 b:47.7 occ:1.00 OD1 A:ASP368 2.8 37.3 1.0 O A:ILE369 3.6 26.4 1.0 CG A:ASP368 3.9 36.9 1.0 OD1 A:ASP471 4.2 33.8 1.0 OD2 A:ASP368 4.4 38.8 1.0 CD2 A:PHE470 4.6 26.7 1.0 CE2 A:PHE470 4.7 23.6 1.0 OD2 A:ASP581 4.7 48.0 1.0 C A:ILE369 4.8 19.3 1.0 OD2 A:ASP471 4.8 30.8 1.0 OE2 A:GLU370 4.9 39.3 1.0 CG A:ASP471 4.9 30.9 1.0 OE1 A:GLU370 5.0 38.2 1.0

Magnesium binding site 2 out of 2 in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna in Both Open/Closed Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna in Both Open/Closed Conformations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1302 b:28.2 occ:1.00 O A:TYR465 3.0 28.0 1.0 O A:PHE367 3.0 21.3 1.0 N A:TYR465 3.1 19.7 1.0 OD1 A:ASP368 3.5 37.3 1.0 CG2 A:ILE467 3.6 14.7 1.0 CB A:ASP368 3.6 22.0 1.0 CA A:ASP368 3.7 19.0 1.0 OD2 A:ASP471 3.7 30.8 1.0 C A:TYR465 3.7 19.3 1.0 CA A:GLY464 3.8 15.0 1.0 C A:GLY464 3.9 19.4 1.0 CA A:TYR465 3.9 15.8 1.0 CG A:ASP368 3.9 36.9 1.0 C A:PHE367 4.0 18.6 1.0 CG A:ASP471 4.0 30.9 1.0 OD1 A:ASP471 4.0 33.8 1.0 CB A:TYR465 4.3 18.5 1.0 N A:ASP368 4.3 20.4 1.0 N A:ASN466 4.9 23.3 1.0 N A:ILE467 4.9 20.8 1.0 CB A:ILE467 4.9 18.1 1.0 C A:ASP368 4.9 18.3 1.0 O A:GLY464 5.0 27.3 1.0

S.Shankar, J.Pan, P.Yang, Y.Bian, G.Oroszlan, Z.Yu, P.Mukherjee, D.J.Filman, J.Hogle, M.Shekhar, D.M.Coen, J.Abraham. Viral Dna Polymerase Structures Reveal Mechanisms For Drug Selectivity Cell(Cambridge,Mass.) 2024.
ISSN: ISSN 0092-8674
DOI: 10.1016/J.CELL.2024.07.048