Magnesium in PDB 8g9o: Complete Dna Elongation Subcomplex of Xenopus Laevis Dna Polymerase Alpha-Primase

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

The structure of Complete Dna Elongation 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 Complete Dna Elongation Subcomplex of Xenopus Laevis Dna Polymerase Alpha-Primase (pdb code 8g9o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Complete Dna Elongation Subcomplex of Xenopus Laevis Dna Polymerase Alpha-Primase, PDB code: 8g9o:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Complete Dna Elongation 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 Complete Dna Elongation Subcomplex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1502 b:119.0 occ:1.00 OD2 A:ASP1000 2.1 126.2 1.0 O1A A:DGT1501 2.1 112.4 1.0 O1G A:DGT1501 2.1 112.4 1.0 O2B A:DGT1501 2.2 112.4 1.0 OD1 A:ASP859 2.3 129.3 1.0 O A:PHE860 2.3 120.8 1.0 PB A:DGT1501 3.1 112.4 1.0 CG A:ASP1000 3.2 126.2 1.0 PA A:DGT1501 3.3 112.4 1.0 O3A A:DGT1501 3.3 112.4 1.0 CG A:ASP859 3.3 129.3 1.0 PG A:DGT1501 3.4 112.4 1.0 C A:PHE860 3.5 120.8 1.0 O3B A:DGT1501 3.5 112.4 1.0 H5' A:DGT1501 3.6 112.4 1.0 OD1 A:ASP1000 3.7 126.2 1.0 OD2 A:ASP859 3.7 129.3 1.0 H A:SER862 3.7 120.4 1.0 H A:PHE860 3.8 120.8 1.0 H5'A A:DGT1501 3.9 112.4 1.0 O3G A:DGT1501 4.1 112.4 1.0 C5' A:DGT1501 4.1 112.4 1.0 HA A:ASN861 4.1 122.9 1.0 O5' A:DGT1501 4.1 112.4 1.0 N A:PHE860 4.2 120.8 1.0 H A:LEU863 4.2 118.2 1.0 CA A:PHE860 4.3 120.8 1.0 N A:SER862 4.3 120.4 1.0 HB2 A:ASP1000 4.4 126.2 1.0 HB2 A:PHE860 4.4 120.8 1.0 CB A:ASP1000 4.4 126.2 1.0 O2A A:DGT1501 4.5 112.4 1.0 N A:ASN861 4.5 122.9 1.0 O1B A:DGT1501 4.6 112.4 1.0 O2G A:DGT1501 4.6 112.4 1.0 CB A:ASP859 4.7 129.3 1.0 CA A:ASN861 4.7 122.9 1.0 HB3 A:ASP1000 4.7 126.2 1.0 HB3 A:ASP859 4.7 129.3 1.0 HB2 A:LEU863 4.8 118.2 1.0 CB A:PHE860 4.8 120.8 1.0 HA A:SER862 4.9 120.4 1.0 C A:ASN861 4.9 122.9 1.0 HB3 A:PHE860 4.9 120.8 1.0 C A:ASP859 5.0 129.3 1.0 N A:LEU863 5.0 118.2 1.0

Magnesium binding site 2 out of 2 in the Complete Dna Elongation 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 Complete Dna Elongation Subcomplex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:237.3 occ:1.00 O1A D:GTP1 2.0 174.6 1.0 O2B D:GTP1 2.1 174.6 1.0 O1G D:GTP1 2.1 174.6 1.0 PB D:GTP1 3.1 174.6 1.0 PA D:GTP1 3.2 174.6 1.0 PG D:GTP1 3.3 174.6 1.0 O3A D:GTP1 3.5 174.6 1.0 O3B D:GTP1 3.5 174.6 1.0 O2A D:GTP1 4.1 174.6 1.0 HH21 B:ARG312 4.1 237.7 1.0 H8 D:GTP1 4.2 174.6 1.0 O3G D:GTP1 4.3 174.6 1.0 HH22 B:ARG312 4.4 237.7 1.0 O1B D:GTP1 4.4 174.6 1.0 O2G D:GTP1 4.4 174.6 1.0 O5' D:GTP1 4.5 174.6 1.0 NH2 B:ARG312 4.6 237.7 1.0 N7 D:GTP1 4.8 174.6 1.0 C8 D:GTP1 4.8 174.6 1.0 HH B:TYR351 4.9 274.4 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