Zinc in PDB 8vam: Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Semi-Open Conformation

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

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

Other elements in 8vam:

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

Zinc binding site 1 out of 4 in 8vam

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

b:171.3
occ:1.00
 SG B:CYS76 2.3 146.3 1.0
SG B:CYS73 2.3 143.9 1.0
SG B:CYS79 2.3 146.4 1.0
SG B:CYS64 2.3 133.6 1.0
CB B:CYS79 3.2 146.4 1.0
CB B:CYS76 3.2 146.3 1.0
CB B:CYS64 3.7 133.6 1.0
CB B:CYS73 3.9 143.9 1.0
N B:CYS79 3.9 146.4 1.0
N B:CYS73 4.0 143.9 1.0
N B:GLY74 4.0 142.1 1.0
N B:CYS76 4.0 146.3 1.0
CA B:CYS79 4.1 146.4 1.0
CA B:CYS76 4.2 146.3 1.0
N B:GLU65 4.2 130.6 1.0
CA B:CYS64 4.3 133.6 1.0
CA B:CYS73 4.4 143.9 1.0
C B:CYS73 4.7 143.9 1.0
N B:VAL75 4.7 144.5 1.0
C B:CYS76 4.8 146.3 1.0
C B:CYS64 4.8 133.6 1.0
CG2 B:THR66 4.8 129.2 1.0
CA B:GLY74 4.8 142.1 1.0
O B:CYS76 4.9 146.3 1.0
C B:PRO72 4.9 129.3 1.0
C B:ASN78 5.0 136.7 1.0

Zinc binding site 2 out of 4 in 8vam

Go back to Zinc Binding Sites List in 8vam
Zinc binding site 2 out of 4 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Semi-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 Semi-Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn404

b:199.6
occ:1.00
 CB C:CYS64 1.8 97.5 1.0
SG C:CYS73 2.3 108.6 1.0
SG C:CYS64 2.3 97.5 1.0
SG C:CYS76 2.3 107.4 1.0
SG C:CYS79 2.3 98.2 1.0
CB C:CYS73 2.5 108.6 1.0
CB C:CYS76 2.8 107.4 1.0
CA C:CYS64 3.2 97.5 1.0
O C:LYS60 3.7 71.5 1.0
O C:CYS64 3.7 97.5 1.0
C C:CYS64 3.8 97.5 1.0
CB C:CYS79 3.9 98.2 1.0
CA C:CYS73 3.9 108.6 1.0
O C:CYS73 4.2 108.6 1.0
N C:CYS64 4.2 97.5 1.0
C C:CYS73 4.3 108.6 1.0
CA C:CYS76 4.3 107.4 1.0
N C:CYS73 4.8 108.6 1.0
C C:LYS60 4.8 71.5 1.0
N C:GLU65 4.9 100.2 1.0
O C:ASN63 4.9 80.4 1.0
C C:ASN63 4.9 80.4 1.0

Zinc binding site 3 out of 4 in 8vam

Go back to Zinc Binding Sites List in 8vam
Zinc binding site 3 out of 4 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Semi-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 Semi-Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn404

b:61.7
occ:1.00
 SG D:CYS73 2.3 38.3 1.0
SG D:CYS64 2.3 34.9 1.0
SG D:CYS79 2.3 47.9 1.0
SG D:CYS76 2.3 44.5 1.0
CB D:CYS76 3.4 44.5 1.0
CB D:CYS79 3.4 47.9 1.0
N D:CYS73 3.6 38.3 1.0
CB D:CYS73 3.6 38.3 1.0
N D:GLY74 3.7 37.0 1.0
CB D:CYS64 3.8 34.9 1.0
OE1 D:GLU65 3.9 42.6 1.0
CA D:CYS73 4.0 38.3 1.0
N D:CYS79 4.2 47.9 1.0
N D:CYS76 4.2 44.5 1.0
C D:CYS73 4.4 38.3 1.0
CA D:CYS79 4.4 47.9 1.0
CA D:CYS76 4.4 44.5 1.0
CA D:CYS64 4.5 34.9 1.0
C D:PRO72 4.6 33.5 1.0
OE2 D:GLU65 4.6 42.6 1.0
CD D:GLU65 4.7 42.6 1.0
CA D:GLY74 4.7 37.0 1.0
CA D:PRO72 4.8 33.5 1.0
N D:VAL75 4.9 37.6 1.0
CB D:PRO72 5.0 33.5 1.0

Zinc binding site 4 out of 4 in 8vam

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

b:207.9
occ:1.00
 CB E:CYS59 2.0 109.0 1.0
SG E:CYS65 2.3 98.8 1.0
SG E:CYS59 2.3 109.0 1.0
SG E:CYS62 2.3 107.5 1.0
SG E:CYS50 2.3 71.1 1.0
CB E:CYS65 3.3 98.8 1.0
CA E:CYS59 3.4 109.0 1.0
CB E:CYS62 3.7 107.5 1.0
N E:CYS65 3.8 98.8 1.0
N E:CYS59 3.9 109.0 1.0
CB E:CYS50 3.9 71.1 1.0
CA E:CYS65 4.1 98.8 1.0
N E:CYS62 4.1 107.5 1.0
CA E:CYS62 4.3 107.5 1.0
O E:CYS62 4.4 107.5 1.0
C E:CYS59 4.4 109.0 1.0
C E:SER58 4.5 86.1 1.0
CA E:CYS50 4.6 71.1 1.0
C E:HIS61 4.6 114.8 1.0
C E:CYS62 4.6 107.5 1.0
N E:GLY60 4.7 111.0 1.0
O E:SER58 4.7 86.1 1.0
C E:CYS65 4.8 98.8 1.0
N E:HIS61 4.9 114.8 1.0
C E:GLY64 4.9 95.4 1.0
O E:HIS61 5.0 114.8 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 12:43:20 2024

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