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

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

The structure of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Fully-Open 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 Fully-Open Conformation (pdb code 8vap). 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 Fully-Open Conformation, PDB code: 8vap:
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 Fully-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 Fully-Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:48.1 occ:1.00 F1 B:BEF402 2.1 83.0 1.0 O1B B:ADP401 2.1 63.9 1.0 OD2 B:ASP126 3.2 61.9 1.0 BE B:BEF402 3.3 82.5 1.0 OG1 B:THR52 3.4 69.2 1.0 OD1 B:ASP126 3.5 70.9 1.0 PB B:ADP401 3.5 86.5 1.0 F3 B:BEF402 3.6 90.4 1.0 CG B:ASP126 3.7 64.2 1.0 O3B B:ADP401 3.9 74.8 1.0 O2A B:ADP401 4.1 60.9 1.0 OE2 B:GLU127 4.1 72.4 1.0 NH2 B:ARG215 4.3 73.4 1.0 NH2 C:ARG169 4.3 77.6 1.0 CB B:THR52 4.5 60.3 1.0 O2B B:ADP401 4.6 65.5 1.0 NZ B:LYS51 4.6 55.0 1.0 F2 B:BEF402 4.6 88.8 1.0 O3A B:ADP401 4.6 64.0 1.0 CD2 C:LEU140 4.9 61.3 1.0 PA B:ADP401 5.0 55.5 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 Fully-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 Fully-Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:65.7 occ:1.00 O1B C:ADP401 1.7 75.3 1.0 F1 D:BEF401 1.8 71.5 1.0 OG1 C:THR52 1.8 60.6 1.0 CB C:THR52 3.0 52.0 1.0 PB C:ADP401 3.0 81.7 1.0 BE D:BEF401 3.2 72.0 1.0 O3B C:ADP401 3.6 76.7 1.0 O2A C:ADP401 3.8 73.9 1.0 N C:THR52 3.8 58.8 1.0 O2B C:ADP401 3.9 77.3 1.0 CA C:THR52 4.0 48.1 1.0 CG2 C:THR52 4.0 57.0 1.0 F2 D:BEF401 4.0 73.4 1.0 O3A C:ADP401 4.3 61.8 1.0 F3 D:BEF401 4.4 79.0 1.0 NH2 D:ARG169 4.5 63.4 1.0 PA C:ADP401 4.6 69.8 1.0 NH2 C:ARG215 4.6 62.9 1.0 OE2 D:GLU144 4.7 91.0 1.0 OD1 C:ASP126 4.8 85.5 1.0 C C:LYS51 5.0 55.5 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 Fully-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 Fully-Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg404 b:58.5 occ:1.00 OG1 D:THR52 1.7 60.2 1.0 O1B D:ADP402 2.1 64.8 1.0 F1 D:BEF403 2.6 68.1 1.0 CB D:THR52 3.1 56.6 1.0 OD2 D:ASP126 3.1 82.3 1.0 PB D:ADP402 3.6 75.1 1.0 O2A D:ADP402 3.8 66.3 1.0 CG D:ASP126 3.9 79.1 1.0 OD1 D:ASP126 3.9 82.6 1.0 N D:THR52 3.9 65.2 1.0 CG2 D:THR52 4.0 60.5 1.0 BE D:BEF403 4.0 72.4 1.0 CA D:THR52 4.0 55.2 1.0 OE1 E:GLU133 4.2 86.3 1.0 NH2 E:ARG158 4.3 65.6 1.0 O3B D:ADP402 4.4 67.5 1.0 O2B D:ADP402 4.4 68.1 1.0 OE2 E:GLU133 4.5 91.2 1.0 NH2 D:ARG215 4.6 68.3 1.0 O3A D:ADP402 4.7 62.1 1.0 F2 D:BEF403 4.7 76.4 1.0 PA D:ADP402 4.8 57.5 1.0 CD E:GLU133 4.8 89.6 1.0 CE D:LYS51 5.0 63.5 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