Zinc in PDB 8vas: Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in An Altered-Collar Conformation

Enzymatic activity of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in An Altered-Collar Conformation

All present enzymatic activity of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in An Altered-Collar Conformation:
2.7.7.7;

Other elements in 8vas:

The structure of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in An Altered-Collar 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 An Altered-Collar Conformation (pdb code 8vas). 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 An Altered-Collar Conformation, PDB code: 8vas:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8vas

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Zinc binding site 1 out of 4 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in An Altered-Collar 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 An Altered-Collar Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:126.7
occ:1.00
 SG B:CYS76 2.3 92.2 1.0
SG B:CYS73 2.3 77.1 1.0
SG B:CYS64 2.3 72.8 1.0
SG B:CYS79 2.3 89.2 1.0
CB B:CYS64 2.6 72.8 1.0
CB B:CYS73 2.7 77.1 1.0
CB B:CYS79 3.0 89.2 1.0
CA B:CYS64 3.3 72.8 1.0
O B:ASN63 3.5 55.9 1.0
OD1 B:ASN78 3.6 83.9 1.0
O B:LYS60 3.9 54.0 1.0
CB B:CYS76 4.0 92.2 1.0
CA B:CYS73 4.2 77.1 1.0
CA B:CYS79 4.2 89.2 1.0
N B:CYS64 4.2 72.8 1.0
N B:CYS79 4.3 89.2 1.0
C B:ASN63 4.3 55.9 1.0
N B:GLU65 4.4 81.3 1.0
C B:CYS64 4.4 72.8 1.0
CD B:LYS60 4.4 54.0 1.0
O B:CYS76 4.6 92.2 1.0
CG B:ASN78 4.7 83.9 1.0
NZ B:LYS60 4.8 54.0 1.0
CE B:LYS60 4.8 54.0 1.0
CA B:CYS76 4.9 92.2 1.0
N B:CYS73 5.0 77.1 1.0

Zinc binding site 2 out of 4 in 8vas

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

b:157.4
occ:1.00
 SG C:CYS76 2.3 89.3 1.0
SG C:CYS73 2.3 81.1 1.0
SG C:CYS79 2.3 78.0 1.0
SG C:CYS64 2.3 62.1 1.0
CB C:CYS79 3.3 78.0 1.0
CB C:CYS64 3.4 62.1 1.0
CB C:CYS76 3.4 89.3 1.0
CA C:CYS64 3.7 62.1 1.0
CB C:CYS73 3.8 81.1 1.0
O C:CYS73 3.8 81.1 1.0
N C:GLU65 3.8 71.3 1.0
N C:CYS73 4.0 81.1 1.0
CA C:CYS73 4.2 81.1 1.0
C C:CYS73 4.2 81.1 1.0
C C:CYS64 4.3 62.1 1.0
N C:CYS76 4.3 89.3 1.0
CA C:CYS76 4.4 89.3 1.0
N C:CYS79 4.4 78.0 1.0
CA C:CYS79 4.5 78.0 1.0
O C:CYS76 4.9 89.3 1.0
C C:CYS76 4.9 89.3 1.0
CB C:GLU65 5.0 71.3 1.0
N C:CYS64 5.0 62.1 1.0
CA C:GLU65 5.0 71.3 1.0

Zinc binding site 3 out of 4 in 8vas

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Zinc binding site 3 out of 4 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in An Altered-Collar 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 An Altered-Collar Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:78.9
occ:1.00
 CB D:CYS73 1.2 71.2 1.0
CA D:CYS73 1.8 71.2 1.0
N D:CYS73 2.0 71.2 1.0
SG D:CYS76 2.3 63.0 1.0
SG D:CYS64 2.3 48.7 1.0
SG D:CYS73 2.3 71.2 1.0
C D:CYS73 2.8 71.2 1.0
N D:GLY74 2.9 66.8 1.0
SG D:CYS79 3.1 56.9 1.0
C D:PRO72 3.3 57.8 1.0
CB D:CYS76 3.7 63.0 1.0
O D:CYS73 3.9 71.2 1.0
CB D:CYS64 3.9 48.7 1.0
N D:CYS76 4.0 63.0 1.0
CB D:CYS79 4.1 56.9 1.0
O D:PRO72 4.1 57.8 1.0
CA D:PRO72 4.2 57.8 1.0
CA D:GLY74 4.3 66.8 1.0
N D:VAL75 4.3 66.1 1.0
CA D:CYS76 4.5 63.0 1.0
C D:GLY74 4.7 66.8 1.0
CB D:PRO72 4.8 57.8 1.0
CA D:CYS64 4.9 48.7 1.0
OG1 D:THR66 4.9 58.7 1.0
OE1 D:GLU65 4.9 56.0 1.0

Zinc binding site 4 out of 4 in 8vas

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Zinc binding site 4 out of 4 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in An Altered-Collar 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 An Altered-Collar Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:135.1
occ:1.00
 SG E:CYS65 2.3 93.0 1.0
SG E:CYS62 2.3 93.2 1.0
SG E:CYS50 2.3 65.9 1.0
SG E:CYS59 2.3 87.5 1.0
OG E:SER58 3.2 82.3 1.0
CB E:CYS62 3.4 93.2 1.0
CB E:CYS65 3.5 93.0 1.0
N E:GLY60 3.7 90.1 1.0
N E:CYS62 3.8 93.2 1.0
CB E:CYS50 3.8 65.9 1.0
CB E:CYS59 3.9 87.5 1.0
N E:CYS59 3.9 87.5 1.0
O E:GLN52 4.0 79.8 1.0
CA E:CYS62 4.1 93.2 1.0
N E:CYS65 4.1 93.0 1.0
O E:CYS62 4.2 93.2 1.0
CA E:CYS59 4.3 87.5 1.0
CA E:CYS65 4.3 93.0 1.0
N E:HIS61 4.4 90.6 1.0
C E:CYS59 4.5 87.5 1.0
CA E:GLY60 4.5 90.1 1.0
CA E:CYS50 4.5 65.9 1.0
CB E:SER58 4.6 82.3 1.0
C E:CYS62 4.6 93.2 1.0
C E:GLN52 4.7 79.8 1.0
C E:GLY60 4.8 90.1 1.0
C E:SER58 4.8 82.3 1.0
C E:HIS61 4.9 90.6 1.0
N E:GLN52 5.0 79.8 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 12:45:34 2024

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