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

Enzymatic activity of 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;

Other elements in 8vaq:

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

Magnesium Binding Sites:

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 8vaq

Go back to Magnesium Binding Sites List in 8vaq
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 8vaq

Go back to Magnesium Binding Sites List in 8vaq
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 8vaq

Go back to Magnesium Binding Sites List in 8vaq
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

Reference:

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
Page generated: Fri Oct 4 22:02:48 2024

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