Zinc 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
Magnesium	(Mg)	3 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn401 b:105.8 occ:1.00 SG B:CYS73 2.3 83.7 1.0 SG B:CYS79 2.3 82.0 1.0 SG B:CYS76 2.3 87.4 1.0 SG B:CYS64 2.3 73.3 1.0 CB B:CYS76 3.5 87.4 1.0 CB B:CYS79 3.5 82.0 1.0 CB B:CYS64 3.5 73.3 1.0 CB B:CYS73 3.6 83.7 1.0 N B:CYS73 3.7 83.7 1.0 N B:GLY74 3.8 85.6 1.0 N B:GLU65 3.8 78.0 1.0 N B:CYS76 3.9 87.4 1.0 CA B:CYS64 3.9 73.3 1.0 CA B:CYS73 4.1 83.7 1.0 N B:CYS79 4.2 82.0 1.0 CA B:CYS76 4.2 87.4 1.0 C B:CYS64 4.4 73.3 1.0 C B:CYS73 4.4 83.7 1.0 CA B:CYS79 4.4 82.0 1.0 N B:VAL75 4.4 86.7 1.0 CA B:GLY74 4.7 85.6 1.0 O B:CYS76 4.7 87.4 1.0 C B:PRO72 4.8 77.4 1.0 C B:CYS76 4.8 87.4 1.0 CB B:GLU65 4.8 78.0 1.0 N B:THR66 4.9 73.6 1.0 CA B:GLU65 4.9 78.0 1.0 CG2 B:THR66 4.9 73.6 1.0 C B:GLY74 5.0 85.6 1.0 C B:VAL75 5.0 86.7 1.0

Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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:Zn401 b:103.6 occ:1.00 SG C:CYS64 2.3 61.5 1.0 SG C:CYS76 2.3 84.3 1.0 SG C:CYS79 2.3 82.5 1.0 CB C:CYS79 3.5 82.5 1.0 CB C:CYS76 3.5 84.3 1.0 N C:CYS76 3.6 84.3 1.0 CB C:CYS64 3.8 61.5 1.0 SG C:CYS73 3.8 80.5 1.0 O C:GLY74 3.9 81.8 1.0 N C:CYS73 4.0 80.5 1.0 O C:CYS73 4.0 80.5 1.0 CA C:CYS76 4.2 84.3 1.0 C C:CYS73 4.3 80.5 1.0 CA C:CYS64 4.3 61.5 1.0 C C:GLY74 4.5 81.8 1.0 C C:PRO72 4.5 69.0 1.0 C C:VAL75 4.6 85.8 1.0 CA C:CYS73 4.6 80.5 1.0 CB C:PRO72 4.7 69.0 1.0 CA C:PRO72 4.7 69.0 1.0 N C:GLU65 4.7 70.9 1.0 CA C:VAL75 4.7 85.8 1.0 CA C:CYS79 4.7 82.5 1.0 N C:CYS79 4.8 82.5 1.0 N C:VAL75 4.9 85.8 1.0 C C:CYS76 4.9 84.3 1.0 CB C:CYS73 4.9 80.5 1.0 O C:CYS76 5.0 84.3 1.0 N C:GLY74 5.0 81.8 1.0

Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn 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:Zn402 b:116.4 occ:1.00 SG D:CYS73 2.3 77.4 1.0 SG D:CYS76 2.3 89.4 1.0 SG D:CYS79 2.3 85.2 1.0 SG D:CYS64 2.3 75.7 1.0 CB D:CYS79 3.1 85.2 1.0 OE1 D:GLU65 3.3 84.8 1.0 CB D:CYS73 3.4 77.4 1.0 CB D:CYS76 3.5 89.4 1.0 CB D:CYS64 3.6 75.7 1.0 OD1 D:ASN78 3.9 81.8 1.0 CD D:GLU65 4.1 84.8 1.0 OE2 D:GLU65 4.1 84.8 1.0 CA D:CYS64 4.1 75.7 1.0 N D:CYS73 4.2 77.4 1.0 N D:CYS79 4.2 85.2 1.0 CA D:CYS79 4.3 85.2 1.0 N D:GLY74 4.3 79.0 1.0 CA D:CYS73 4.3 77.4 1.0 O D:GLY74 4.4 79.0 1.0 N D:GLU65 4.6 84.8 1.0 CA D:CYS76 4.6 89.4 1.0 N D:CYS76 4.8 89.4 1.0 C D:ASN78 4.8 81.8 1.0 C D:CYS73 4.9 77.4 1.0 C D:GLY74 4.9 79.0 1.0 C D:CYS64 5.0 75.7 1.0

Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn binding site number 4 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 E:Zn401 b:140.8 occ:1.00 SG E:CYS50 2.3 105.5 1.0 SG E:CYS62 2.3 115.2 1.0 SG E:CYS65 2.3 114.3 1.0 SG E:CYS59 2.3 114.9 1.0 O E:CYS59 2.9 114.9 1.0 CB E:CYS50 3.2 105.5 1.0 CB E:CYS65 3.6 114.3 1.0 C E:CYS59 3.6 114.9 1.0 CB E:CYS59 3.7 114.9 1.0 CB E:CYS62 3.8 115.2 1.0 N E:CYS65 3.8 114.3 1.0 O E:GLN51 3.9 112.5 1.0 N E:CYS59 3.9 114.9 1.0 CA E:CYS59 3.9 114.9 1.0 NH1 E:ARG46 4.1 89.9 1.0 CA E:CYS65 4.2 114.3 1.0 N E:GLN51 4.4 112.5 1.0 CA E:CYS50 4.5 105.5 1.0 N E:GLY60 4.7 118.4 1.0 C E:CYS50 4.7 105.5 1.0 C E:GLY64 4.7 111.2 1.0 CA E:CYS62 4.8 115.2 1.0 C E:GLN51 4.8 112.5 1.0 N E:CYS62 4.8 115.2 1.0 O E:CYS62 4.9 115.2 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