Magnesium in PDB 8ucv: Complete Dna Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase

All present enzymatic activity of Complete Dna Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase:
2.7.7.7;

The structure of Complete Dna Termination Subcomplex 1 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 Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase (pdb code 8ucv). 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 Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase, PDB code: 8ucv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Complete Dna Termination Subcomplex 1 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 Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1502 b:114.7 occ:1.00 OD2 A:ASP859 1.9 113.2 1.0 OD2 A:ASP1000 2.1 116.8 1.0 O1G A:DGT1501 2.1 108.4 1.0 O2B A:DGT1501 2.1 108.4 1.0 O1A A:DGT1501 2.2 108.4 1.0 O A:PHE860 2.3 112.0 1.0 CG A:ASP859 2.9 113.2 1.0 PB A:DGT1501 3.2 108.4 1.0 CG A:ASP1000 3.2 116.8 1.0 OD1 A:ASP859 3.3 113.2 1.0 PG A:DGT1501 3.4 108.4 1.0 PA A:DGT1501 3.4 108.4 1.0 C A:PHE860 3.5 112.0 1.0 O3B A:DGT1501 3.5 108.4 1.0 O3A A:DGT1501 3.5 108.4 1.0 H5'A A:DGT1501 3.5 108.4 1.0 OD1 A:ASP1000 3.9 116.8 1.0 HA A:ASN861 4.0 111.2 1.0 H A:PHE860 4.0 112.0 1.0 N A:PHE860 4.1 112.0 1.0 H A:SER862 4.1 107.5 1.0 C5' A:DGT1501 4.2 108.4 1.0 O5' A:DGT1501 4.2 108.4 1.0 H5' A:DGT1501 4.2 108.4 1.0 CB A:ASP859 4.2 113.2 1.0 HB2 A:ASP1000 4.3 116.8 1.0 CA A:PHE860 4.3 112.0 1.0 O2G A:DGT1501 4.3 108.4 1.0 HB3 A:ASP859 4.3 113.2 1.0 CB A:ASP1000 4.4 116.8 1.0 H A:LEU863 4.4 109.6 1.0 O3G A:DGT1501 4.4 108.4 1.0 N A:ASN861 4.5 111.2 1.0 HB2 A:PHE860 4.5 112.0 1.0 HB2 A:LEU863 4.5 109.6 1.0 O2A A:DGT1501 4.6 108.4 1.0 C A:ASP859 4.6 113.2 1.0 O1B A:DGT1501 4.6 108.4 1.0 N A:SER862 4.6 107.5 1.0 CA A:ASN861 4.7 111.2 1.0 HB3 A:ASP1000 4.7 116.8 1.0 HB3 A:PHE860 4.8 112.0 1.0 CB A:PHE860 4.8 112.0 1.0 CA A:ASP859 4.9 113.2 1.0 HA A:ASP859 4.9 113.2 1.0 HB2 A:ASP859 4.9 113.2 1.0

Magnesium binding site 2 out of 2 in the Complete Dna Termination Subcomplex 1 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 Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:87.4 occ:1.00 O2B D:GTP1 2.1 86.6 1.0 O1G D:GTP1 2.1 86.6 1.0 O1A D:GTP1 2.1 86.6 1.0 H8 D:GTP1 2.2 86.6 1.0 N7 D:GTP1 2.5 86.6 1.0 C8 D:GTP1 2.6 86.6 1.0 HH22 B:ARG312 2.7 124.6 1.0 PB D:GTP1 3.1 86.6 1.0 PG D:GTP1 3.2 86.6 1.0 PA D:GTP1 3.4 86.6 1.0 NH2 B:ARG312 3.4 124.6 1.0 O3B D:GTP1 3.4 86.6 1.0 O3A D:GTP1 3.5 86.6 1.0 HH21 B:ARG312 3.5 124.6 1.0 HB2 B:HIS309 3.5 108.2 1.0 O2G D:GTP1 3.7 86.6 1.0 C5 D:GTP1 3.9 86.6 1.0 N9 D:GTP1 3.9 86.6 1.0 O5' D:GTP1 4.3 86.6 1.0 CB B:HIS309 4.4 108.2 1.0 O1B D:GTP1 4.4 86.6 1.0 HH12 B:ARG312 4.5 124.6 1.0 O2A D:GTP1 4.5 86.6 1.0 O3G D:GTP1 4.5 86.6 1.0 C4 D:GTP1 4.6 86.6 1.0 CZ B:ARG312 4.6 124.6 1.0 HB3 B:HIS309 4.6 108.2 1.0 O4' D:GTP1 4.6 86.6 1.0 H B:HIS309 4.7 108.2 1.0 C6 D:GTP1 4.9 86.6 1.0 C1' D:GTP1 4.9 86.6 1.0 O6 D:GTP1 4.9 86.6 1.0 NH1 B:ARG312 4.9 124.6 1.0

E.A.Mullins, L.E.Salay, C.L.Durie, N.P.Bradley, 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