Magnesium in PDB 8d9d: Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template

All present enzymatic activity of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template:
2.7.7.102; 2.7.7.7;

The structure of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Zinc	(Zn)	3 atoms

The binding sites of Magnesium atom in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template (pdb code 8d9d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template, PDB code: 8d9d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1501 b:59.7 occ:1.00 OD1 C:ASP1004 2.2 63.1 1.0 O C:PHE861 2.5 53.6 1.0 OD2 C:ASP860 2.5 59.4 1.0 O2B C:DTP1504 2.7 75.5 1.0 CG C:ASP860 3.0 59.4 1.0 OD1 C:ASP860 3.1 59.4 1.0 O3G C:DTP1504 3.2 75.5 1.0 O1A C:DTP1504 3.2 75.5 1.0 CG C:ASP1004 3.4 63.1 1.0 O3B C:DTP1504 3.5 75.5 1.0 PB C:DTP1504 3.5 75.5 1.0 O3A C:DTP1504 3.6 75.5 1.0 C C:PHE861 3.6 53.6 1.0 N C:PHE861 3.9 53.6 1.0 PA C:DTP1504 4.0 75.5 1.0 PG C:DTP1504 4.0 75.5 1.0 CB C:ASP1004 4.2 63.1 1.0 CB C:ASP860 4.2 59.4 1.0 CA C:PHE861 4.3 53.6 1.0 OD2 C:ASP1004 4.4 63.1 1.0 C C:ASP860 4.6 59.4 1.0 N C:ASN862 4.7 58.7 1.0 CB C:PHE861 4.8 53.6 1.0 C5' C:DTP1504 4.8 75.5 1.0 CA C:ASP860 4.8 59.4 1.0 O5' C:DTP1504 4.9 75.5 1.0 O1B C:DTP1504 4.9 75.5 1.0 CA C:ASN862 5.0 58.7 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:72.0 occ:1.00 O1G E:GTP1 2.8 76.2 1.0 O1A E:GTP1 2.8 76.2 1.0 O2B E:GTP1 3.3 76.2 1.0 PA E:GTP1 4.1 76.2 1.0 PG E:GTP1 4.1 76.2 1.0 O3A E:GTP1 4.2 76.2 1.0 PB E:GTP1 4.3 76.2 1.0 O3G E:GTP1 4.6 76.2 1.0 O3B E:GTP1 4.7 76.2 1.0 N7 E:GTP1 4.8 76.2 1.0 O5' E:GTP1 4.9 76.2 1.0

Q.He, A.G.Baranovskiy, L.M.Morstadt, A.E.Lisova, N.D.Babayeva, B.L.Lusk, C.Lim, T.H.Tahirov. Structures of Human Primosome Elongation Complexes Nat.Struct.Mol.Biol. 2023.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-023-00971-3