Magnesium in PDB 8vam: Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Semi-Open Conformation

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

The structure of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Semi-Open 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 Semi-Open Conformation (pdb code 8vam). 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 Semi-Open Conformation, PDB code: 8vam:
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 Semi-Open 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 Semi-Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:134.8 occ:1.00 OG1 B:THR52 2.0 131.1 1.0 F1 B:BEF403 2.1 134.4 1.0 O1B B:ADP402 2.1 133.7 1.0 OD2 B:ASP126 2.4 140.9 1.0 BE B:BEF403 3.3 134.4 1.0 CB B:THR52 3.3 131.1 1.0 CG B:ASP126 3.3 140.9 1.0 PB B:ADP402 3.5 133.7 1.0 F3 B:BEF403 3.6 134.4 1.0 OD1 B:ASP126 3.9 140.9 1.0 O3B B:ADP402 3.9 133.7 1.0 O2A B:ADP402 4.1 133.7 1.0 CG2 B:THR52 4.2 131.1 1.0 N B:THR52 4.2 131.1 1.0 CA B:THR52 4.3 131.1 1.0 CB B:ASP126 4.4 140.9 1.0 OE2 B:GLU127 4.5 132.6 1.0 O2B B:ADP402 4.6 133.7 1.0 F2 B:BEF403 4.6 134.4 1.0 O3A B:ADP402 4.6 133.7 1.0 PA B:ADP402 5.0 133.7 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 Semi-Open 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 Semi-Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:66.8 occ:1.00 F1 C:BEF402 2.1 66.8 1.0 O1B C:ADP401 2.1 66.8 1.0 NH2 D:ARG169 2.8 29.6 1.0 BE C:BEF402 3.3 66.8 1.0 OG1 C:THR52 3.5 47.3 1.0 PB C:ADP401 3.5 66.8 1.0 O2A C:ADP401 3.6 66.8 1.0 F2 C:BEF402 3.8 66.8 1.0 CZ D:ARG169 3.9 29.6 1.0 O3B C:ADP401 3.9 66.8 1.0 NH1 C:ARG215 4.1 38.2 1.0 NZ C:LYS51 4.2 45.9 1.0 NH1 D:ARG169 4.3 29.6 1.0 CB C:THR52 4.5 47.3 1.0 O3A C:ADP401 4.6 66.8 1.0 F3 C:BEF402 4.6 66.8 1.0 O2B C:ADP401 4.6 66.8 1.0 PA C:ADP401 4.7 66.8 1.0 CE C:LYS51 4.7 45.9 1.0 OG1 D:THR165 4.9 33.0 1.0 NE D:ARG169 4.9 29.6 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 Semi-Open 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 Semi-Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg403 b:66.8 occ:1.00 F1 D:BEF402 2.1 66.8 1.0 O1B D:ADP401 2.1 66.8 1.0 OG1 D:THR52 2.5 36.4 1.0 CB D:THR52 3.5 36.4 1.0 BE D:BEF402 3.5 66.8 1.0 PB D:ADP401 3.6 66.8 1.0 OE1 E:GLU133 3.8 33.8 1.0 NH2 E:ARG158 3.9 23.7 1.0 O2A D:ADP401 3.9 66.8 1.0 OE2 E:GLU133 3.9 33.8 1.0 F2 D:BEF402 4.0 66.8 1.0 O3B D:ADP401 4.1 66.8 1.0 NH2 D:ARG215 4.2 22.8 1.0 CD E:GLU133 4.2 33.8 1.0 CG2 D:THR52 4.3 36.4 1.0 OE2 D:GLU127 4.5 31.5 1.0 O2B D:ADP401 4.6 66.8 1.0 NH1 D:ARG215 4.6 22.8 1.0 N D:THR52 4.6 36.4 1.0 CA D:THR52 4.6 36.4 1.0 O3A D:ADP401 4.7 66.8 1.0 F3 D:BEF402 4.7 66.8 1.0 PA D:ADP401 4.9 66.8 1.0 CZ D:ARG215 4.9 22.8 1.0 CZ E:ARG158 4.9 23.7 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