Magnesium in PDB 8vaq: Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA1 Conformation

All present enzymatic activity of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA1 Conformation:
2.7.7.7;

The structure of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA1 Conformation also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Fluorine	(F)	9 atoms

The binding sites of Magnesium atom in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA1 Conformation (pdb code 8vaq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA1 Conformation, PDB code: 8vaq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA1 Conformation


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 E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA1 Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:72.1 occ:1.00 O1B B:ADP402 2.0 72.1 1.0 OG1 B:THR52 2.2 49.5 1.0 F1 C:BEF401 2.3 72.1 1.0 CB B:THR52 3.2 49.5 1.0 OD2 B:ASP126 3.3 42.4 1.0 BE C:BEF401 3.3 72.1 1.0 PB B:ADP402 3.3 72.1 1.0 F3 C:BEF401 3.3 72.1 1.0 OD1 B:ASP126 3.5 42.4 1.0 OE2 B:GLU127 3.6 41.3 1.0 O3B B:ADP402 3.7 72.1 1.0 CG B:ASP126 3.8 42.4 1.0 NH2 C:ARG169 4.0 40.2 1.0 CG2 B:THR52 4.0 49.5 1.0 O2B B:ADP402 4.2 72.1 1.0 O2A B:ADP402 4.2 72.1 1.0 CA B:THR52 4.4 49.5 1.0 N B:THR52 4.5 49.5 1.0 O3A B:ADP402 4.5 72.1 1.0 F2 C:BEF401 4.7 72.1 1.0 CD B:GLU127 4.8 41.3 1.0 NZ C:LYS141 4.9 42.2 1.0 PA B:ADP402 5.0 72.1 1.0

Magnesium binding site 2 out of 3 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA1 Conformation


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 E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA1 Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg405 b:72.1 occ:1.00 F1 C:BEF404 1.8 72.1 1.0 OG1 C:THR52 1.9 46.0 1.0 O1B C:ADP403 2.2 72.1 1.0 CB C:THR52 3.0 46.0 1.0 BE C:BEF404 3.2 72.1 1.0 PB C:ADP403 3.5 72.1 1.0 O3B C:ADP403 3.8 72.1 1.0 F2 C:BEF404 3.9 72.1 1.0 N C:THR52 4.0 46.0 1.0 CG2 C:THR52 4.0 46.0 1.0 O2A C:ADP403 4.0 72.1 1.0 OE2 C:GLU127 4.1 43.6 1.0 OE1 D:GLU144 4.1 44.7 1.0 CA C:THR52 4.1 46.0 1.0 F3 C:BEF404 4.3 72.1 1.0 NH2 D:ARG169 4.4 36.8 1.0 OD1 C:ASP126 4.5 42.7 1.0 O2B C:ADP403 4.5 72.1 1.0 C C:LYS51 4.7 43.6 1.0 NH2 C:ARG215 4.7 41.1 1.0 O3A C:ADP403 4.7 72.1 1.0 CG C:ASP126 4.8 42.7 1.0 CD D:GLU144 4.9 44.7 1.0 CB C:LYS51 4.9 43.6 1.0 NZ C:LYS51 4.9 43.6 1.0 PA C:ADP403 5.0 72.1 1.0 OE2 D:GLU144 5.0 44.7 1.0

Magnesium binding site 3 out of 3 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA1 Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA1 Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg403 b:72.1 occ:1.00 O1B D:ADP401 1.8 72.1 1.0 OG1 D:THR52 2.1 49.8 1.0 F1 D:BEF402 2.1 72.1 1.0 CB D:THR52 3.0 49.8 1.0 OD2 D:ASP126 3.2 43.0 1.0 PB D:ADP401 3.3 72.1 1.0 BE D:BEF402 3.4 72.1 1.0 O2A D:ADP401 3.6 72.1 1.0 CG2 D:THR52 3.8 49.8 1.0 O3B D:ADP401 3.8 72.1 1.0 OE1 E:GLU133 3.8 56.3 1.0 OD1 D:ASP126 3.9 43.0 1.0 CG D:ASP126 3.9 43.0 1.0 F2 D:BEF402 4.0 72.1 1.0 CA D:THR52 4.2 49.8 1.0 N D:THR52 4.2 49.8 1.0 O2B D:ADP401 4.2 72.1 1.0 OE2 E:GLU133 4.3 56.3 1.0 O3A D:ADP401 4.4 72.1 1.0 OE2 D:GLU127 4.5 43.5 1.0 CD E:GLU133 4.5 56.3 1.0 PA D:ADP401 4.6 72.1 1.0 NH1 D:ARG215 4.6 59.3 1.0 F3 D:BEF402 4.6 72.1 1.0 NH2 E:ARG158 4.8 50.4 1.0 NH2 D:ARG215 4.9 59.3 1.0

J.T.Landeck, J.Pajak, E.K.Norman, E.L.Sedivy, B.A.Kelch. Differences Between Bacteria and Eukaryotes in Clamp Loader Mechanism, A Conserved Process Underlying Dna Replication. J.Biol.Chem. 07166 2024.
ISSN: ESSN 1083-351X
PubMed: 38490435
DOI: 10.1016/J.JBC.2024.107166