Magnesium in PDB 8v1r: Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Dttp in Closed Conformation

All present enzymatic activity of Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Dttp in Closed Conformation:
2.7.7.7;

The binding sites of Magnesium atom in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Dttp in Closed Conformation (pdb code 8v1r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Dttp in Closed Conformation, PDB code: 8v1r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Dttp in Closed Conformation


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 and Dttp in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1301 b:4.3 occ:1.00 O1B A:TTP1306 1.8 15.4 1.0 OD2 A:ASP888 1.9 27.8 1.0 O A:PHE718 2.2 14.8 1.0 OD1 A:ASP717 2.5 32.4 1.0 O2A A:TTP1306 2.6 21.7 1.0 O3G A:TTP1306 2.7 28.4 1.0 CG A:ASP888 3.1 25.5 1.0 PB A:TTP1306 3.3 28.8 1.0 CG A:ASP717 3.3 34.4 1.0 C A:PHE718 3.4 15.1 1.0 MG A:MG1303 3.6 37.4 1.0 PA A:TTP1306 3.7 20.4 1.0 OD1 A:ASP888 3.7 38.0 1.0 PG A:TTP1306 3.8 24.7 1.0 O3A A:TTP1306 3.9 25.6 1.0 OD2 A:ASP717 4.0 44.5 1.0 O3B A:TTP1306 4.0 9.6 1.0 CB A:ASP888 4.1 19.5 1.0 N A:PHE718 4.1 19.1 1.0 CB A:ASP717 4.1 24.8 1.0 MG A:MG1302 4.3 38.0 1.0 CA A:PHE718 4.3 14.2 1.0 C5' A:TTP1306 4.3 21.2 1.0 O1G A:TTP1306 4.3 27.8 1.0 O2B A:TTP1306 4.3 19.1 1.0 O5' A:TTP1306 4.4 13.7 1.0 N A:ALA719 4.4 18.1 1.0 C A:ASP717 4.5 13.9 1.0 CA A:ALA719 4.5 12.7 1.0 N A:SER720 4.6 17.9 1.0 CB A:PHE718 4.8 13.7 1.0 O1A A:TTP1306 4.9 26.4 1.0 N A:LEU721 4.9 8.7 1.0 CA A:ASP717 4.9 19.9 1.0 C A:ALA719 4.9 17.6 1.0 CB A:LEU721 5.0 8.8 1.0 O2G A:TTP1306 5.0 21.8 1.0

Magnesium binding site 2 out of 5 in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Dttp in Closed Conformation


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 and Dttp in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1302 b:38.0 occ:1.00 OD2 A:ASP717 2.3 44.5 1.0 OE2 A:GLU925 2.9 44.6 1.0 CG A:ASP717 3.3 34.4 1.0 OE1 A:GLU927 3.5 49.8 1.0 CG A:GLU925 3.5 24.8 1.0 OD1 A:ASP717 3.6 32.4 1.0 O A:ASP717 3.6 23.1 1.0 CD A:GLU925 3.7 43.4 1.0 O A:PHE718 3.8 14.8 1.0 O3G A:TTP1306 3.9 28.4 1.0 CA A:ALA719 4.0 12.7 1.0 C A:PHE718 4.0 15.1 1.0 N A:ALA719 4.1 18.1 1.0 C A:ASP717 4.2 13.9 1.0 MG A:MG1301 4.3 4.3 1.0 CB A:ALA719 4.3 17.9 1.0 O1G A:TTP1306 4.4 27.8 1.0 CD A:GLU927 4.5 47.7 1.0 CB A:ASP717 4.6 24.8 1.0 CB A:GLU927 4.6 33.5 1.0 O A:GLU925 4.8 36.8 1.0 PG A:TTP1306 4.8 24.7 1.0 N A:PHE718 4.8 19.1 1.0 CA A:ASP717 4.9 19.9 1.0 OE1 A:GLU925 4.9 36.4 1.0 CB A:GLU925 4.9 30.7 1.0 CA A:PHE718 5.0 14.2 1.0

Magnesium binding site 3 out of 5 in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Dttp in Closed Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Dttp in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1303 b:37.4 occ:1.00 O2A A:TTP1306 2.6 21.7 1.0 OD1 A:ASP717 2.9 32.4 1.0 OD1 A:ASP888 3.3 38.0 1.0 MG A:MG1301 3.6 4.3 1.0 OD2 A:ASP888 3.7 27.8 1.0 PA A:TTP1306 3.9 20.4 1.0 CG A:ASP888 3.9 25.5 1.0 CG A:ASP717 3.9 34.4 1.0 C3' P:DOC-1 4.0 8.9 1.0 O1A A:TTP1306 4.1 26.4 1.0 O5' P:DOC-1 4.3 8.5 1.0 CB A:ASP717 4.3 24.8 1.0 OE2 A:GLU927 4.4 49.7 1.0 C4' P:DOC-1 4.4 1.8 1.0 O5' A:TTP1306 4.7 13.7 1.0 O3G A:TTP1306 4.7 28.4 1.0 C5' P:DOC-1 4.7 8.8 1.0 O1B A:TTP1306 4.7 15.4 1.0 CB A:SER889 4.7 27.1 1.0 OE1 A:GLU927 4.8 49.8 1.0 OD2 A:ASP717 4.9 44.5 1.0 C2' P:DOC-1 4.9 4.4 1.0

Magnesium binding site 4 out of 5 in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Dttp in Closed Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Dttp in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1304 b:31.9 occ:1.00 OD1 A:ASP368 2.0 40.6 1.0 O A:ILE369 2.8 29.4 1.0 MG A:MG1305 2.9 32.0 1.0 CG A:ASP368 3.1 42.2 1.0 OD1 A:ASP471 3.3 29.6 1.0 OD2 A:ASP368 3.6 41.9 1.0 OD2 A:ASP471 3.9 33.7 1.0 C A:ILE369 4.0 18.6 1.0 N A:ILE369 4.0 22.2 1.0 CG A:ASP471 4.0 24.9 1.0 CB A:ASP368 4.2 30.4 1.0 C A:ASP368 4.4 21.9 1.0 CA A:ASP368 4.4 19.9 1.0 CD2 A:PHE470 4.5 26.4 1.0 OE1 A:GLU370 4.6 42.9 1.0 CA A:ILE369 4.6 28.2 1.0 CE2 A:PHE470 4.6 20.5 1.0 CG1 A:ILE369 4.8 24.7 1.0

Magnesium binding site 5 out of 5 in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Dttp in Closed Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Dttp in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1305 b:32.0 occ:1.00 O A:TYR465 2.3 33.2 1.0 OD2 A:ASP471 2.6 33.7 1.0 MG A:MG1304 2.9 31.9 1.0 OD1 A:ASP471 3.1 29.6 1.0 CG A:ASP471 3.1 24.9 1.0 OD1 A:ASP368 3.4 40.6 1.0 C A:TYR465 3.5 15.2 1.0 O A:ASN466 4.1 28.2 1.0 C A:ASN466 4.2 16.9 1.0 CB A:ASN466 4.3 17.0 1.0 N A:TYR465 4.4 20.3 1.0 CA A:TYR465 4.4 11.0 1.0 N A:ASN466 4.4 16.3 1.0 CA A:ASN466 4.5 17.6 1.0 CG A:ASP368 4.5 42.2 1.0 CB A:ASP471 4.5 12.2 1.0 N A:ILE467 4.6 17.4 1.0 CB A:TYR465 4.6 16.6 1.0 CG2 A:ILE467 4.8 17.5 1.0 CA A:ILE467 4.9 10.8 1.0 CD2 A:PHE470 4.9 26.4 1.0 CB A:ASP368 5.0 30.4 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