Zinc in PDB 8val: Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Open-Dnap/T Conformation

Enzymatic activity of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Open-Dnap/T Conformation

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

Other elements in 8val:

The structure of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Open-Dnap/T Conformation also contains other interesting chemical elements:

Fluorine (F) 9 atoms
Magnesium (Mg) 3 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 Open-Dnap/T Conformation (pdb code 8val). 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 Open-Dnap/T Conformation, PDB code: 8val:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8val

Go back to Zinc Binding Sites List in 8val
Zinc binding site 1 out of 4 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Open-Dnap/T 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 Open-Dnap/T Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:148.8
occ:1.00
 SG B:CYS76 2.3 121.4 1.0
SG B:CYS73 2.3 119.0 1.0
SG B:CYS79 2.3 106.8 1.0
SG B:CYS64 2.3 89.0 1.0
CB B:CYS79 3.4 106.8 1.0
CB B:CYS64 3.6 89.0 1.0
CB B:CYS76 3.7 121.4 1.0
CB B:CYS73 3.8 119.0 1.0
N B:CYS73 3.9 119.0 1.0
N B:GLY74 3.9 122.2 1.0
OD1 B:ASN78 4.0 106.2 1.0
OE1 B:GLU65 4.2 91.8 1.0
N B:CYS76 4.3 121.4 1.0
CA B:CYS64 4.3 89.0 1.0
CA B:CYS73 4.3 119.0 1.0
N B:CYS79 4.5 106.8 1.0
CA B:CYS79 4.5 106.8 1.0
CA B:CYS76 4.5 121.4 1.0
C B:CYS73 4.7 119.0 1.0
N B:VAL75 4.8 123.8 1.0
CA B:GLY74 4.8 122.2 1.0
CD B:GLU65 4.9 91.8 1.0
C B:PRO72 4.9 102.1 1.0
OG1 B:THR66 4.9 88.1 1.0
OE2 B:GLU65 4.9 91.8 1.0
CB B:PRO72 4.9 102.1 1.0

Zinc binding site 2 out of 4 in 8val

Go back to Zinc Binding Sites List in 8val
Zinc binding site 2 out of 4 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Open-Dnap/T 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 Open-Dnap/T Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:112.6
occ:1.00
 CB C:CYS76 1.9 100.2 1.0
SG C:CYS64 2.3 75.9 1.0
SG C:CYS76 2.3 100.2 1.0
SG C:CYS79 2.3 92.3 1.0
SG C:CYS73 2.3 96.9 1.0
CA C:CYS76 3.4 100.2 1.0
CB C:CYS64 3.5 75.9 1.0
CA C:CYS64 3.8 75.9 1.0
O C:CYS73 3.8 96.9 1.0
CB C:CYS79 3.9 92.3 1.0
CB C:CYS73 3.9 96.9 1.0
N C:CYS76 3.9 100.2 1.0
N C:GLU65 4.0 78.1 1.0
N C:CYS73 4.0 96.9 1.0
CA C:CYS73 4.3 96.9 1.0
C C:CYS76 4.3 100.2 1.0
C C:CYS64 4.4 75.9 1.0
C C:CYS73 4.4 96.9 1.0
N C:CYS79 4.5 92.3 1.0
O C:CYS76 4.8 100.2 1.0
CA C:CYS79 4.8 92.3 1.0

Zinc binding site 3 out of 4 in 8val

Go back to Zinc Binding Sites List in 8val
Zinc binding site 3 out of 4 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Open-Dnap/T 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 Open-Dnap/T Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:105.6
occ:1.00
 SG D:CYS76 2.3 84.6 1.0
SG D:CYS64 2.3 64.2 1.0
SG D:CYS73 2.3 82.0 1.0
SG D:CYS79 2.3 76.9 1.0
CB D:CYS76 3.0 84.6 1.0
CB D:CYS79 3.2 76.9 1.0
CB D:CYS73 3.6 82.0 1.0
CB D:CYS64 3.7 64.2 1.0
N D:CYS76 3.7 84.6 1.0
N D:GLY74 3.8 81.4 1.0
N D:CYS73 3.9 82.0 1.0
CA D:CYS76 3.9 84.6 1.0
N D:CYS79 4.0 76.9 1.0
CA D:CYS79 4.2 76.9 1.0
CA D:CYS73 4.2 82.0 1.0
CA D:CYS64 4.3 64.2 1.0
C D:CYS73 4.5 82.0 1.0
N D:VAL75 4.5 83.8 1.0
C D:CYS76 4.6 84.6 1.0
CA D:GLY74 4.7 81.4 1.0
N D:GLU65 4.8 70.2 1.0
O D:CYS76 4.8 84.6 1.0
OG1 D:THR66 4.9 70.2 1.0
C D:PRO72 4.9 68.2 1.0
C D:VAL75 5.0 83.8 1.0
OE1 D:GLU65 5.0 70.2 1.0
C D:GLY74 5.0 81.4 1.0

Zinc binding site 4 out of 4 in 8val

Go back to Zinc Binding Sites List in 8val
Zinc binding site 4 out of 4 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Open-Dnap/T 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 Open-Dnap/T Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:124.5
occ:1.00
 SG E:CYS50 2.3 86.7 1.0
SG E:CYS62 2.3 105.4 1.0
SG E:CYS65 2.3 98.8 1.0
SG E:CYS59 2.3 111.1 1.0
CB E:CYS65 3.4 98.8 1.0
CB E:CYS62 3.5 105.4 1.0
CB E:CYS50 3.6 86.7 1.0
CB E:CYS59 3.6 111.1 1.0
N E:GLY60 3.7 108.9 1.0
N E:CYS59 3.8 111.1 1.0
N E:CYS62 3.8 105.4 1.0
CA E:CYS50 4.1 86.7 1.0
CA E:CYS59 4.1 111.1 1.0
CA E:CYS62 4.2 105.4 1.0
N E:CYS65 4.2 98.8 1.0
O E:GLN52 4.3 100.2 1.0
N E:HIS61 4.3 104.4 1.0
CA E:CYS65 4.3 98.8 1.0
C E:CYS59 4.4 111.1 1.0
N E:GLN51 4.5 85.2 1.0
O E:CYS62 4.6 105.4 1.0
CA E:GLY60 4.6 108.9 1.0
N E:GLN52 4.7 100.2 1.0
C E:CYS50 4.7 86.7 1.0
C E:CYS62 4.7 105.4 1.0
CB E:SER58 4.7 108.1 1.0
C E:GLN52 4.8 100.2 1.0
C E:SER58 4.8 108.1 1.0
C E:GLY60 4.9 108.9 1.0
C E:HIS61 4.9 104.4 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 12:42:44 2024

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