Magnesium in PDB 8exx: Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Foscarnet (Pre-Translocation State)

All present enzymatic activity of Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Foscarnet (Pre-Translocation State):
2.7.7.7;

The binding sites of Magnesium atom in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Foscarnet (Pre-Translocation State) (pdb code 8exx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Foscarnet (Pre-Translocation State), PDB code: 8exx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Foscarnet (Pre-Translocation State)


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 Foscarnet (Pre-Translocation State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1301 b:31.2 occ:1.00 OD2 A:ASP888 2.1 36.7 1.0 OP1 P:DOC0 2.3 74.8 1.0 O1 A:PPF1304 2.3 85.0 1.0 O4 A:PPF1304 2.4 71.8 1.0 OD1 A:ASP717 2.8 47.6 1.0 O5' P:DOC0 2.9 77.1 1.0 O A:PHE718 3.0 13.9 1.0 P P:DOC0 3.1 92.8 1.0 C1 A:PPF1304 3.3 78.6 1.0 CG A:ASP888 3.3 31.5 1.0 OD2 A:ASP717 3.3 39.1 1.0 P1 A:PPF1304 3.4 92.9 1.0 CG A:ASP717 3.5 48.6 1.0 OP2 P:DOC0 3.6 74.8 1.0 OD1 A:ASP888 3.9 30.9 1.0 N A:SER720 4.0 46.2 1.0 C A:PHE718 4.2 18.2 1.0 C5' P:DOC0 4.3 71.3 1.0 O2 A:PPF1304 4.4 85.1 1.0 O3' P:DT-1 4.4 71.6 1.0 CB A:ASP888 4.4 24.3 1.0 O5 A:PPF1304 4.5 79.8 1.0 O3 A:PPF1304 4.5 82.6 1.0 CA A:SER720 4.6 45.0 1.0 NZ A:LYS811 4.8 55.3 1.0 N A:LEU721 4.9 26.4 1.0 C4' P:DOC0 4.9 70.8 1.0 CA A:ALA719 4.9 29.7 1.0 CB A:ASP717 5.0 40.7 1.0 C A:ALA719 5.0 36.0 1.0

Magnesium binding site 2 out of 3 in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Foscarnet (Pre-Translocation State)


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 Foscarnet (Pre-Translocation State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1302 b:39.9 occ:1.00 O3 A:PPF1304 2.5 82.6 1.0 O2 A:PPF1304 2.6 85.1 1.0 P1 A:PPF1304 2.7 92.9 1.0 O1 A:PPF1304 2.9 85.0 1.0 OE1 A:GLU927 3.1 67.6 1.0 OE1 A:GLU925 3.5 49.1 1.0 OD2 A:ASP717 3.5 39.1 1.0 CG A:ASP717 3.8 48.6 1.0 CB A:GLU927 3.9 52.9 1.0 CD A:GLU927 4.2 62.1 1.0 CB A:ASP717 4.2 40.7 1.0 OD1 A:ASP717 4.3 47.6 1.0 NH2 A:ARG789 4.4 64.8 1.0 CG A:GLU927 4.4 53.6 1.0 C1 A:PPF1304 4.6 78.6 1.0 CD A:GLU925 4.7 48.4 1.0 NH1 A:ARG789 4.8 63.0 1.0 O A:PHE718 5.0 13.9 1.0

Magnesium binding site 3 out of 3 in the Herpes Simplex Virus 1 Polymerase Holoenzyme Bound to Dna and Foscarnet (Pre-Translocation State)


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 Foscarnet (Pre-Translocation State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1303 b:12.9 occ:1.00 OD1 A:ASP471 2.9 33.2 1.0 O A:TYR465 3.1 31.5 1.0 OD2 A:ASP471 3.1 27.2 1.0 OD1 A:ASP368 3.4 50.0 1.0 CG A:ASP471 3.4 27.8 1.0 CG A:ASP368 4.2 44.9 1.0 C A:TYR465 4.3 29.2 1.0 CB A:ASN466 4.5 27.2 1.0 CD2 A:PHE470 4.5 40.5 1.0 O A:ASN466 4.6 35.1 1.0 N A:ILE369 4.7 28.7 1.0 O A:ILE369 4.7 37.5 1.0 CB A:ASP471 4.9 21.0 1.0 C A:ASN466 4.9 19.9 1.0 OD2 A:ASP368 4.9 38.6 1.0 CA A:ASP368 4.9 32.3 1.0 CB A:ASP368 5.0 36.7 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