Zinc 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:

Magnesium (Mg) 3 atoms
Fluorine (F) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 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-DNA1 Conformation, PDB code: 8vaq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8vaq

Go back to Zinc Binding Sites List in 8vaq
Zinc binding site 1 out of 4 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 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-DNA1 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:127.8
occ:1.00
 SG B:CYS64 2.3 87.9 1.0
SG B:CYS76 2.3 102.1 1.0
SG B:CYS73 2.3 99.8 1.0
SG B:CYS79 2.3 95.9 1.0
CB B:CYS76 2.6 102.1 1.0
N B:CYS76 3.6 102.1 1.0
O B:CYS73 3.6 99.8 1.0
CA B:CYS76 3.7 102.1 1.0
CB B:CYS64 3.7 87.9 1.0
N B:CYS73 3.9 99.8 1.0
CB B:CYS73 3.9 99.8 1.0
OG1 B:THR66 3.9 89.0 1.0
CB B:CYS79 4.0 95.9 1.0
CA B:CYS64 4.1 87.9 1.0
C B:CYS73 4.2 99.8 1.0
N B:GLU65 4.2 93.7 1.0
CA B:CYS73 4.2 99.8 1.0
CG2 B:THR66 4.5 89.0 1.0
N B:THR66 4.5 89.0 1.0
C B:CYS64 4.6 87.9 1.0
C B:CYS76 4.8 102.1 1.0
CB B:THR66 4.8 89.0 1.0
C B:VAL75 4.8 101.0 1.0
C B:PRO72 4.8 88.7 1.0
N B:VAL75 4.9 101.0 1.0
N B:CYS79 5.0 95.9 1.0
O B:CYS76 5.0 102.1 1.0

Zinc binding site 2 out of 4 in 8vaq

Go back to Zinc Binding Sites List in 8vaq
Zinc binding site 2 out of 4 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 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-DNA1 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:154.5
occ:1.00
 SG C:CYS73 2.3 88.9 1.0
SG C:CYS64 2.3 75.3 1.0
SG C:CYS76 2.3 99.5 1.0
SG C:CYS79 2.3 89.7 1.0
CB C:CYS76 3.6 99.5 1.0
CB C:CYS79 3.6 89.7 1.0
CB C:CYS64 3.6 75.3 1.0
CB C:CYS73 3.8 88.9 1.0
O C:CYS73 3.9 88.9 1.0
N C:GLU65 4.1 80.8 1.0
N C:CYS73 4.1 88.9 1.0
CA C:CYS64 4.2 75.3 1.0
C C:CYS73 4.2 88.9 1.0
CA C:CYS73 4.3 88.9 1.0
N C:CYS76 4.3 99.5 1.0
N C:CYS79 4.3 89.7 1.0
CA C:CYS76 4.5 99.5 1.0
CA C:CYS79 4.6 89.7 1.0
C C:CYS64 4.6 75.3 1.0
O C:CYS76 4.8 99.5 1.0
C C:CYS76 4.9 99.5 1.0

Zinc binding site 3 out of 4 in 8vaq

Go back to Zinc Binding Sites List in 8vaq
Zinc binding site 3 out of 4 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 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-DNA1 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn404

b:115.4
occ:1.00
 CB D:CYS64 2.0 79.9 1.0
SG D:CYS76 2.3 91.3 1.0
SG D:CYS64 2.3 79.9 1.0
SG D:CYS73 2.3 88.3 1.0
CB D:CYS76 3.2 91.3 1.0
OG1 D:THR66 3.3 85.0 1.0
N D:CYS73 3.3 88.3 1.0
CA D:CYS64 3.4 79.9 1.0
O D:CYS73 3.6 88.3 1.0
SG D:CYS79 3.6 83.7 1.0
CB D:CYS73 3.7 88.3 1.0
C D:CYS64 3.8 79.9 1.0
CB D:THR66 3.8 85.0 1.0
CA D:CYS73 3.9 88.3 1.0
N D:THR66 4.1 85.0 1.0
N D:GLU65 4.2 87.3 1.0
C D:CYS73 4.2 88.3 1.0
C D:PRO72 4.3 73.0 1.0
CA D:PRO72 4.4 73.0 1.0
O D:CYS64 4.5 79.9 1.0
N D:CYS64 4.5 79.9 1.0
CA D:THR66 4.6 85.0 1.0
CA D:CYS76 4.6 91.3 1.0
OG1 D:THR69 4.6 69.6 1.0
O D:LYS60 4.8 60.9 1.0
N D:CYS76 4.9 91.3 1.0
CB D:PRO72 4.9 73.0 1.0

Zinc binding site 4 out of 4 in 8vaq

Go back to Zinc Binding Sites List in 8vaq
Zinc binding site 4 out of 4 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 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-DNA1 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:162.4
occ:1.00
 CB E:CYS59 2.0 130.4 1.0
O E:CYS59 2.3 130.4 1.0
SG E:CYS59 2.3 130.4 1.0
SG E:CYS62 2.3 129.5 1.0
SG E:CYS50 2.3 112.0 1.0
C E:CYS59 2.9 130.4 1.0
CA E:CYS59 2.9 130.4 1.0
CB E:CYS50 3.3 112.0 1.0
O E:GLN51 3.6 122.3 1.0
CB E:CYS62 4.0 129.5 1.0
N E:GLY60 4.1 131.5 1.0
N E:CYS59 4.2 130.4 1.0
N E:GLN51 4.4 122.3 1.0
N E:CYS65 4.6 125.8 1.0
CA E:CYS50 4.6 112.0 1.0
O E:GLY60 4.6 131.5 1.0
C E:GLN51 4.6 122.3 1.0
C E:CYS50 4.7 112.0 1.0
CB E:CYS65 4.8 125.8 1.0
C E:GLY60 4.8 131.5 1.0
CA E:GLY60 4.8 131.5 1.0
O E:ARG46 4.9 86.0 1.0
N E:CYS62 4.9 129.5 1.0
CA E:GLN51 5.0 122.3 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: Thu Oct 31 12:43:44 2024

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