Magnesium in PDB 8v1t: Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Acyclovir Triphosphate in Closed Conformation

All present enzymatic activity of Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Acyclovir Triphosphate 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 Acyclovir Triphosphate in Closed Conformation (pdb code 8v1t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Acyclovir Triphosphate in Closed Conformation, PDB code: 8v1t:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Acyclovir Triphosphate 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 Acyclovir Triphosphate in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1301 b:7.8 occ:1.00 OD2 A:ASP888 2.1 33.0 1.0 O A:PHE718 2.1 19.1 1.0 O2G A:AVP1305 2.2 34.2 1.0 OD2 A:ASP717 2.5 33.8 1.0 O3A A:AVP1305 2.6 28.1 1.0 O1B A:AVP1305 3.0 39.9 1.0 CG A:ASP888 3.2 22.4 1.0 C A:PHE718 3.4 18.1 1.0 PB A:AVP1305 3.5 28.9 1.0 CG A:ASP717 3.5 33.7 1.0 PG A:AVP1305 3.5 26.2 1.0 MG A:MG1302 3.6 28.8 1.0 PA A:AVP1305 3.9 31.2 1.0 OD1 A:ASP888 3.9 35.9 1.0 O3B A:AVP1305 4.0 30.2 1.0 O1A A:AVP1305 4.0 37.1 1.0 N A:PHE718 4.1 19.5 1.0 CB A:ASP888 4.1 12.6 1.0 OD1 A:ASP717 4.2 38.9 1.0 CA A:PHE718 4.2 12.5 1.0 O5' A:AVP1305 4.3 39.5 1.0 C5' A:AVP1305 4.3 40.6 1.0 N A:ALA719 4.3 24.6 1.0 CB A:ASP717 4.3 28.7 1.0 O3G A:AVP1305 4.3 34.9 1.0 N A:SER720 4.4 14.8 1.0 CA A:ALA719 4.4 17.6 1.0 O1G A:AVP1305 4.4 32.9 1.0 C A:ASP717 4.5 17.6 1.0 N A:LEU721 4.6 12.9 1.0 CB A:LEU721 4.6 11.9 1.0 CB A:PHE718 4.7 14.0 1.0 C A:ALA719 4.8 17.4 1.0 O2B A:AVP1305 4.8 31.5 1.0

Magnesium binding site 2 out of 4 in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Acyclovir Triphosphate 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 Acyclovir Triphosphate in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1302 b:28.8 occ:1.00 OD1 A:ASP888 2.1 35.9 1.0 CG A:ASP888 2.7 22.4 1.0 OD2 A:ASP888 3.0 33.0 1.0 OD2 A:ASP717 3.2 33.8 1.0 C3' P:DOC-1 3.6 2.7 1.0 N A:SER889 3.6 19.7 1.0 MG A:MG1301 3.6 7.8 1.0 O1A A:AVP1305 3.8 37.1 1.0 CB A:SER889 3.8 25.9 1.0 CB A:ASP888 3.9 12.6 1.0 CB A:ASP717 4.0 28.7 1.0 CG A:ASP717 4.0 33.7 1.0 N A:ASP888 4.2 33.8 1.0 CA A:SER889 4.2 21.9 1.0 C A:ASP888 4.2 20.5 1.0 O5' A:AVP1305 4.2 39.5 1.0 CA A:ASP888 4.3 17.1 1.0 OG A:SER889 4.3 26.6 1.0 C5' P:DOC-1 4.3 6.6 1.0 C4' P:DOC-1 4.4 1.6 1.0 PA A:AVP1305 4.4 31.2 1.0 O3A A:AVP1305 4.5 28.1 1.0 C2' P:DOC-1 4.7 3.8 1.0 C5' A:AVP1305 4.9 40.6 1.0

Magnesium binding site 3 out of 4 in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Acyclovir Triphosphate 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 Acyclovir Triphosphate in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1303 b:44.3 occ:1.00 OD1 A:ASP581 2.6 47.9 1.0 CB A:ASP368 3.2 27.9 1.0 CG A:ASP368 3.3 36.3 1.0 CG A:ASP581 3.4 44.6 1.0 OD1 A:ASP368 3.4 39.4 1.0 CG2 A:VAL585 3.4 24.1 1.0 O A:PHE367 3.6 25.0 1.0 N A:TYR465 3.7 20.6 1.0 OD2 A:ASP581 3.8 41.8 1.0 OG A:SER582 3.9 41.3 1.0 OD2 A:ASP368 4.0 35.2 1.0 CA A:ASP368 4.1 21.0 1.0 O A:ASP581 4.2 32.2 1.0 CA A:GLY464 4.2 19.6 1.0 CB A:VAL585 4.2 20.8 1.0 CB A:TYR465 4.2 18.7 1.0 CA A:SER582 4.3 27.3 1.0 C A:ASP581 4.3 29.1 1.0 C A:PHE367 4.4 24.1 1.0 N A:SER582 4.4 23.4 1.0 C A:GLY464 4.4 14.2 1.0 CA A:TYR465 4.5 22.5 1.0 CB A:ASP581 4.6 36.8 1.0 O A:TYR465 4.6 32.1 1.0 N A:ASP368 4.6 30.3 1.0 CB A:SER582 4.7 27.9 1.0 CG1 A:VAL585 4.7 21.6 1.0 CD2 A:LEU540 4.7 31.6 1.0

Magnesium binding site 4 out of 4 in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Acyclovir Triphosphate 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 Acyclovir Triphosphate in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1304 b:37.6 occ:1.00 OD1 A:ASP471 2.3 34.2 1.0 O A:TYR465 2.7 32.1 1.0 CG A:ASP471 3.1 28.1 1.0 OD2 A:ASP471 3.3 34.0 1.0 O A:ASN466 3.5 31.4 1.0 CB A:ASN466 3.8 15.4 1.0 C A:ASN466 3.8 14.2 1.0 C A:TYR465 3.9 23.1 1.0 OD1 A:ASP368 3.9 39.4 1.0 CD2 A:PHE470 4.2 33.1 1.0 CA A:ASN466 4.3 18.3 1.0 CB A:PHE470 4.3 22.5 1.0 CB A:ASP471 4.5 18.5 1.0 N A:ILE467 4.5 12.1 1.0 ND2 A:ASN466 4.5 29.4 1.0 N A:ASN466 4.5 21.9 1.0 N A:ASP471 4.6 26.9 1.0 CG A:ASN466 4.7 28.9 1.0 CG A:PHE470 4.7 33.7 1.0 CA A:ILE467 4.8 21.6 1.0 CA A:TYR465 5.0 22.5 1.0 CA A:ASP471 5.0 22.2 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