Magnesium in PDB 7kc0: Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp

All present enzymatic activity of Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp:
2.7.7.7;

The structure of Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Iron	(Fe)	4 atoms

The binding sites of Magnesium atom in the Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp (pdb code 7kc0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp, PDB code: 7kc0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:69.1 occ:1.00 C5' P:DC25 2.4 69.7 1.0 C3' P:DC25 2.4 69.7 1.0 OD1 A:ASP764 2.4 65.9 1.0 C4' P:DC25 2.5 69.7 1.0 OD2 A:ASP764 2.7 65.9 1.0 CG A:ASP764 2.9 65.9 1.0 O2A A:D3T1102 2.9 70.0 1.0 O5' P:DC25 3.3 69.7 1.0 C2' P:DC25 3.9 69.7 1.0 O4' P:DC25 3.9 69.7 1.0 O A:ASP762 4.0 63.8 1.0 PA A:D3T1102 4.3 70.0 1.0 CB A:ASP764 4.4 65.9 1.0 MG A:MG1103 4.4 68.1 1.0 P P:DC25 4.5 69.7 1.0 OG A:SER765 4.6 62.8 1.0 C1' P:DC25 4.6 69.7 1.0 CB A:SER765 4.7 62.8 1.0 O5' A:D3T1102 4.7 70.0 1.0 CB A:ASP762 4.8 63.8 1.0 OP2 P:DC25 4.8 69.7 1.0 O1A A:D3T1102 4.8 70.0 1.0 OP1 P:DC25 4.8 69.7 1.0 N A:SER765 4.9 62.8 1.0 C5' A:D3T1102 4.9 70.0 1.0 N A:ASP764 5.0 65.9 1.0 C A:ASP762 5.0 63.8 1.0

Magnesium binding site 2 out of 2 in the Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:68.1 occ:1.00 O2B A:D3T1102 2.4 70.0 1.0 OD2 A:ASP764 2.6 65.9 1.0 OD2 A:ASP608 2.8 65.5 1.0 PB A:D3T1102 2.8 70.0 1.0 O A:PHE609 2.9 61.1 1.0 O3B A:D3T1102 2.9 70.0 1.0 O2A A:D3T1102 3.1 70.0 1.0 O3A A:D3T1102 3.1 70.0 1.0 CG A:ASP764 3.6 65.9 1.0 PA A:D3T1102 3.6 70.0 1.0 CG A:ASP608 3.7 65.5 1.0 C A:PHE609 4.0 61.1 1.0 CB A:ASP764 4.1 65.9 1.0 CB A:ASP608 4.1 65.5 1.0 C5' A:D3T1102 4.1 70.0 1.0 PG A:D3T1102 4.2 70.0 1.0 N A:PHE609 4.2 61.1 1.0 O1B A:D3T1102 4.2 70.0 1.0 O5' A:D3T1102 4.4 70.0 1.0 MG P:MG101 4.4 69.1 1.0 O2G A:D3T1102 4.4 70.0 1.0 OD1 A:ASP764 4.5 65.9 1.0 CA A:PHE609 4.6 61.1 1.0 N A:SER611 4.8 63.0 1.0 OD1 A:ASP608 4.8 65.5 1.0 C A:ASP608 4.9 65.5 1.0 O1A A:D3T1102 4.9 70.0 1.0

F.Zheng, R.E.Georgescu, H.Li, M.E.O'donnell. Structure of Eukaryotic Dna Polymerase Delta Bound to the Pcna Clamp While Encircling Dna. Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
PubMed: 33203675
DOI: 10.1073/PNAS.2017637117