Magnesium in PDB 8g9l: Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase

All present enzymatic activity of Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase:
2.7.7.7;

The structure of Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Magnesium atom in the Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase (pdb code 8g9l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase, PDB code: 8g9l:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1502 b:61.8 occ:1.00 OD1 A:ASP859 1.9 66.9 1.0 OD2 A:ASP1000 2.1 64.4 1.0 O1G A:DGT1501 2.1 53.4 1.0 O2B A:DGT1501 2.2 57.3 1.0 O1A A:DGT1501 2.2 65.3 1.0 O A:PHE860 2.2 58.1 1.0 CG A:ASP859 3.0 72.8 1.0 PB A:DGT1501 3.2 43.4 1.0 CG A:ASP1000 3.3 61.4 1.0 OD2 A:ASP859 3.4 76.8 1.0 PA A:DGT1501 3.4 67.0 1.0 PG A:DGT1501 3.4 55.0 1.0 C A:PHE860 3.4 58.9 1.0 O3A A:DGT1501 3.6 44.3 1.0 O3B A:DGT1501 3.6 46.8 1.0 H5'A A:DGT1501 3.7 53.7 1.0 H A:PHE860 3.8 59.4 1.0 OD1 A:ASP1000 3.8 64.2 1.0 N A:PHE860 4.0 57.5 1.0 H A:SER862 4.1 58.1 1.0 HA A:ASN861 4.1 63.9 1.0 H5' A:DGT1501 4.2 54.1 1.0 CA A:PHE860 4.2 59.2 1.0 C5' A:DGT1501 4.2 52.1 1.0 O5' A:DGT1501 4.3 56.1 1.0 CB A:ASP859 4.3 67.5 1.0 HB2 A:PHE860 4.3 60.1 1.0 HB2 A:ASP1000 4.4 62.8 1.0 H A:LEU863 4.4 56.2 1.0 HB3 A:ASP859 4.4 67.5 1.0 O3G A:DGT1501 4.4 60.1 1.0 CB A:ASP1000 4.4 62.6 1.0 O2G A:DGT1501 4.4 47.9 1.0 N A:ASN861 4.5 62.6 1.0 HB2 A:LEU863 4.5 55.1 1.0 C A:ASP859 4.6 67.4 1.0 O2A A:DGT1501 4.6 61.4 1.0 N A:SER862 4.6 58.9 1.0 O1B A:DGT1501 4.6 61.0 1.0 CA A:ASN861 4.7 62.2 1.0 CB A:PHE860 4.7 62.5 1.0 HB3 A:ASP1000 4.7 62.6 1.0 HB3 A:PHE860 4.8 58.8 1.0 CA A:ASP859 4.9 65.5 1.0 HA A:ASP859 4.9 67.5 1.0 HB2 A:ASP859 5.0 67.2 1.0

Magnesium binding site 2 out of 2 in the Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:127.7 occ:1.00 O1A D:GTP1 2.1 80.5 1.0 O1G D:GTP1 2.1 89.6 1.0 O2B D:GTP1 2.1 91.5 1.0 PB D:GTP1 3.2 94.6 1.0 PA D:GTP1 3.3 83.4 1.0 PG D:GTP1 3.3 94.5 1.0 O3B D:GTP1 3.5 87.9 1.0 O3A D:GTP1 3.5 83.7 1.0 O2G D:GTP1 4.3 88.0 1.0 HH21 B:ARG312 4.3 82.8 1.0 O2A D:GTP1 4.3 88.9 1.0 O5' D:GTP1 4.4 83.7 1.0 O3G D:GTP1 4.5 93.5 1.0 O1B D:GTP1 4.5 91.4 1.0 H8 D:GTP1 4.5 85.2 1.0 HH22 B:ARG312 4.8 83.1 1.0 NH2 B:ARG312 4.9 85.5 1.0 HH B:TYR351 5.0 83.5 1.0

E.A.Mullins, L.E.Salay, C.L.Durie, J.E.Jackman, M.D.Ohi, W.J.Chazin, B.F.Eichman. A Mechanistic Model of Primer Synthesis From Catalytic Structures of Dna Polymerase Alpha-Primase. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 36993335
DOI: 10.1101/2023.03.16.533013