Magnesium in PDB 8val: Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Open-Dnap/T Conformation

All present enzymatic activity of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Open-Dnap/T Conformation:
2.7.7.7;

The structure of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Open-Dnap/T 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 Open-Dnap/T Conformation (pdb code 8val). 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 Open-Dnap/T Conformation, PDB code: 8val:
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 Open-Dnap/T 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 Open-Dnap/T Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:72.3 occ:1.00 F1 B:BEF403 1.5 72.3 1.0 OG1 B:THR52 1.8 52.0 1.0 O1B B:ADP402 1.8 72.3 1.0 BE B:BEF403 2.5 72.3 1.0 CB B:THR52 2.8 52.0 1.0 PB B:ADP402 3.3 72.3 1.0 F3 B:BEF403 3.5 72.3 1.0 F2 B:BEF403 3.7 72.3 1.0 N B:THR52 3.8 52.0 1.0 CG2 B:THR52 3.8 52.0 1.0 CA B:THR52 3.8 52.0 1.0 O2A B:ADP402 3.9 72.3 1.0 O3B B:ADP402 4.1 72.3 1.0 O2B B:ADP402 4.1 72.3 1.0 NZ B:LYS51 4.3 51.3 1.0 OE1 C:GLU144 4.4 51.1 1.0 O3A B:ADP402 4.5 72.3 1.0 NH2 C:ARG169 4.6 43.9 1.0 OE2 B:GLU127 4.6 46.0 1.0 PA B:ADP402 4.7 72.3 1.0 CE B:LYS51 4.7 51.3 1.0 OE2 C:GLU144 4.8 51.1 1.0 OD2 B:ASP126 4.8 46.8 1.0 C B:LYS51 4.9 51.3 1.0 CB B:ALA155 4.9 45.2 1.0 CD C:GLU144 5.0 51.1 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 Open-Dnap/T 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 Open-Dnap/T Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg404 b:72.3 occ:1.00 OG1 C:THR52 1.8 45.3 1.0 F1 C:BEF403 2.1 72.3 1.0 O1B C:ADP402 2.6 72.3 1.0 OD2 C:ASP126 2.6 46.5 1.0 CB C:THR52 2.7 45.3 1.0 OE2 D:GLU144 3.3 42.0 1.0 CG2 C:THR52 3.4 45.3 1.0 BE C:BEF403 3.4 72.3 1.0 OE1 D:GLU144 3.5 42.0 1.0 CG C:ASP126 3.6 46.5 1.0 CD D:GLU144 3.8 42.0 1.0 O2A C:ADP402 3.8 72.3 1.0 OD1 C:ASP126 3.9 46.5 1.0 CA C:THR52 4.1 45.3 1.0 PB C:ADP402 4.1 72.3 1.0 F2 C:BEF403 4.2 72.3 1.0 N C:THR52 4.3 45.3 1.0 NH2 D:ARG169 4.6 39.1 1.0 F3 C:BEF403 4.6 72.3 1.0 CE D:LYS141 4.7 42.0 1.0 OE2 C:GLU127 4.8 45.1 1.0 NH2 C:ARG215 4.9 43.3 1.0 PA C:ADP402 4.9 72.3 1.0 O3B C:ADP402 4.9 72.3 1.0 O2B C:ADP402 5.0 72.3 1.0 CB C:ASP126 5.0 46.5 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 Open-Dnap/T 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 Open-Dnap/T Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg404 b:72.3 occ:1.00 OG1 D:THR52 1.8 48.1 1.0 F1 D:BEF403 2.5 72.3 1.0 O1B D:ADP402 2.7 72.3 1.0 CB D:THR52 2.9 48.1 1.0 CG2 D:THR52 3.6 48.1 1.0 BE D:BEF403 3.7 72.3 1.0 NH2 E:ARG158 3.8 53.4 1.0 OE1 E:GLU133 3.9 54.2 1.0 O2A D:ADP402 4.2 72.3 1.0 CA D:THR52 4.2 48.1 1.0 PB D:ADP402 4.2 72.3 1.0 F2 D:BEF403 4.3 72.3 1.0 N D:THR52 4.5 48.1 1.0 CD E:GLU133 4.7 54.2 1.0 OE2 E:GLU133 4.7 54.2 1.0 CG D:ASP126 4.7 49.6 1.0 OD2 D:ASP126 4.8 49.6 1.0 NH2 D:ARG215 4.9 58.3 1.0 CB D:ASP126 4.9 49.6 1.0 O2B D:ADP402 4.9 72.3 1.0 OE2 D:GLU127 4.9 46.8 1.0 F3 D:BEF403 5.0 72.3 1.0 O3B D:ADP402 5.0 72.3 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