Zinc 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
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 Fully-Open Conformation (pdb code 8vap). 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 Fully-Open Conformation, PDB code: 8vap:
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 Fully-Open 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 Fully-Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:164.9 occ:1.00 SG B:CYS76 2.3 106.6 1.0 SG B:CYS73 2.3 129.8 1.0 SG B:CYS79 2.3 109.8 1.0 SG B:CYS64 2.4 117.3 1.0 CB B:CYS76 3.3 109.2 1.0 CB B:CYS79 3.5 106.2 1.0 CB B:CYS64 3.6 104.3 1.0 CB B:CYS73 3.7 125.5 1.0 CB B:PRO72 3.8 130.2 1.0 N B:CYS73 4.2 128.5 1.0 N B:CYS79 4.2 110.1 1.0 OE1 B:GLU65 4.3 115.6 1.0 CA B:CYS73 4.4 125.2 1.0 CA B:CYS79 4.4 108.1 1.0 CA B:CYS76 4.5 112.5 1.0 CG B:PRO72 4.5 126.0 1.0 CA B:CYS64 4.6 104.5 1.0 C B:CYS73 4.6 123.8 1.0 N B:CYS76 4.7 111.8 1.0 C B:PRO72 4.7 130.5 1.0 O B:CYS73 4.7 120.6 1.0 OE2 B:GLU65 4.8 115.4 1.0 CD B:GLU65 4.9 115.4 1.0 CA B:PRO72 4.9 130.1 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 Fully-Open 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 Fully-Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn403 b:155.2 occ:1.00 SG C:CYS79 2.3 110.7 1.0 SG C:CYS76 2.3 121.2 1.0 N C:CYS76 3.0 112.6 1.0 O C:GLY74 3.1 106.3 1.0 SG C:CYS64 3.2 99.1 1.0 CB C:CYS64 3.3 92.3 1.0 CA C:CYS64 3.3 90.1 1.0 CB C:CYS76 3.4 109.3 1.0 CB C:CYS79 3.6 96.8 1.0 CA C:CYS76 3.8 107.5 1.0 N C:GLU65 3.8 81.9 1.0 CA C:VAL75 3.9 105.3 1.0 C C:VAL75 3.9 108.7 1.0 C C:GLY74 4.0 105.6 1.0 C C:CYS64 4.1 87.7 1.0 O C:CYS73 4.3 109.2 1.0 N C:CYS79 4.4 94.7 1.0 C C:CYS76 4.4 105.6 1.0 N C:VAL75 4.4 102.3 1.0 N C:CYS64 4.5 91.3 1.0 SG C:CYS73 4.6 126.4 1.0 O C:CYS76 4.6 107.4 1.0 CA C:CYS79 4.6 92.1 1.0 C C:CYS73 4.8 110.4 1.0 O C:ASN63 4.8 75.4 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 Fully-Open 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 Fully-Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn405 b:137.1 occ:1.00 SG D:CYS76 2.3 103.4 1.0 SG D:CYS79 2.3 102.1 1.0 SG D:CYS64 2.3 111.4 1.0 SG D:CYS73 2.3 97.8 1.0 CB D:CYS76 2.9 95.5 1.0 CB D:CYS79 3.4 90.5 1.0 CB D:CYS64 3.7 89.8 1.0 N D:CYS73 3.8 93.8 1.0 CB D:CYS73 3.8 93.1 1.0 N D:CYS76 4.0 98.3 1.0 N D:GLY74 4.0 83.0 1.0 CA D:CYS76 4.0 97.8 1.0 N D:CYS79 4.2 89.4 1.0 CA D:CYS73 4.3 93.3 1.0 CA D:CYS64 4.3 86.1 1.0 CA D:CYS79 4.4 86.2 1.0 OE1 D:GLU65 4.4 108.1 1.0 C D:CYS73 4.7 93.3 1.0 C D:PRO72 4.7 90.9 1.0 C D:CYS76 4.8 99.5 1.0 CG2 D:THR66 4.8 90.5 1.0 CA D:PRO72 4.9 85.0 1.0 N D:GLU65 4.9 104.0 1.0 CB D:PRO72 4.9 84.3 1.0 N D:VAL75 4.9 92.5 1.0 CA D:GLY74 5.0 81.7 1.0 OG1 D:THR66 5.0 94.8 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 Fully-Open 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 Fully-Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:231.7 occ:1.00 SG E:CYS59 2.3 164.1 1.0 CB E:CYS62 2.3 136.6 1.0 SG E:CYS50 2.3 137.9 1.0 SG E:CYS62 2.3 143.7 1.0 SG E:CYS65 2.3 129.7 1.0 CB E:CYS50 3.5 120.4 1.0 CA E:CYS62 3.7 137.2 1.0 CB E:CYS65 3.8 129.3 1.0 O E:CYS59 3.8 153.0 1.0 N E:CYS59 3.9 152.2 1.0 CB E:CYS59 3.9 153.5 1.0 CA E:CYS50 4.0 120.0 1.0 N E:CYS62 4.1 138.9 1.0 N E:GLN51 4.1 119.4 1.0 N E:CYS65 4.2 133.5 1.0 CA E:CYS59 4.2 153.3 1.0 C E:CYS59 4.3 153.3 1.0 C E:CYS50 4.4 122.1 1.0 O E:GLN52 4.5 128.9 1.0 CA E:CYS65 4.6 128.8 1.0 C E:CYS62 4.6 138.1 1.0 N E:GLN52 4.7 124.8 1.0 O E:CYS62 5.0 141.6 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