Magnesium in PDB 8var: Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation

All present enzymatic activity of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation:
2.7.7.7;

The structure of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation (pdb code 8var). 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-DNA2 Conformation, PDB code: 8var:
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-DNA2 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-DNA2 Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:71.6 occ:1.00 F1 B:BEF403 1.8 71.6 1.0 O1B B:ADP402 1.9 71.6 1.0 OG1 B:THR52 2.2 37.9 1.0 BE B:BEF403 2.8 71.6 1.0 F3 B:BEF403 3.0 71.6 1.0 PB B:ADP402 3.1 71.6 1.0 CB B:THR52 3.4 37.9 1.0 O3B B:ADP402 3.4 71.6 1.0 OD2 B:ASP126 3.9 39.9 1.0 OE2 B:GLU127 4.0 38.6 1.0 OE1 C:GLU144 4.1 40.1 1.0 O2A B:ADP402 4.1 71.6 1.0 O2B B:ADP402 4.1 71.6 1.0 OD1 B:ASP126 4.1 39.9 1.0 F2 B:BEF403 4.1 71.6 1.0 N B:THR52 4.2 37.9 1.0 CG2 B:THR52 4.3 37.9 1.0 O3A B:ADP402 4.3 71.6 1.0 CA B:THR52 4.4 37.9 1.0 NH2 B:ARG215 4.4 39.8 1.0 CG B:ASP126 4.4 39.9 1.0 OE2 C:GLU144 4.7 40.1 1.0 CD C:GLU144 4.8 40.1 1.0 PA B:ADP402 4.9 71.6 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-DNA2 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-DNA2 Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:71.6 occ:1.00 OG1 C:THR52 2.1 38.3 1.0 O1B C:ADP402 2.6 71.6 1.0 F1 D:BEF401 2.6 71.6 1.0 CB C:THR52 3.1 38.3 1.0 CG2 C:THR52 3.6 38.3 1.0 OD1 C:ASP126 3.7 38.1 1.0 BE D:BEF401 4.0 71.6 1.0 PB C:ADP402 4.0 71.6 1.0 O2A C:ADP402 4.1 71.6 1.0 NH2 D:ARG169 4.1 35.9 1.0 CG C:ASP126 4.2 38.1 1.0 OD2 C:ASP126 4.4 38.1 1.0 OE2 C:GLU127 4.4 37.8 1.0 CA C:THR52 4.4 38.3 1.0 O3B C:ADP402 4.5 71.6 1.0 OE1 C:GLU127 4.5 37.8 1.0 F2 D:BEF401 4.6 71.6 1.0 N C:THR52 4.7 38.3 1.0 O2B C:ADP402 4.9 71.6 1.0 CD C:GLU127 4.9 37.8 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-DNA2 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-DNA2 Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg405 b:71.6 occ:1.00 F1 D:BEF404 2.2 71.6 1.0 OG1 D:THR52 2.3 43.6 1.0 O1B D:ADP403 2.6 71.6 1.0 OD2 D:ASP126 2.7 42.6 1.0 OD1 D:ASP126 3.1 42.6 1.0 CG D:ASP126 3.3 42.6 1.0 CB D:THR52 3.7 43.6 1.0 BE D:BEF404 3.7 71.6 1.0 NH2 E:ARG158 3.8 48.6 1.0 PB D:ADP403 4.0 71.6 1.0 OE2 D:GLU127 4.0 43.1 1.0 F2 D:BEF404 4.2 71.6 1.0 O2A D:ADP403 4.3 71.6 1.0 N D:THR52 4.3 43.6 1.0 O3B D:ADP403 4.4 71.6 1.0 CG2 D:THR52 4.5 43.6 1.0 OE1 E:GLU133 4.5 56.4 1.0 CA D:THR52 4.5 43.6 1.0 CB D:ASP126 4.7 42.6 1.0 F3 D:BEF404 4.8 71.6 1.0 O2B D:ADP403 4.9 71.6 1.0 OE2 E:GLU133 5.0 56.4 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