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Fluorine in PDB 8var: Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation

Enzymatic activity of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation

All present enzymatic activity of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation:
2.7.7.7;

Other elements in 8var:

The structure of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Magnesium (Mg) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation (pdb code 8var). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation, PDB code: 8var:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 8var

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Fluorine binding site 1 out of 9 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:71.6
occ:1.00
 F1 B:BEF403 0.0 71.6 1.0
BE B:BEF403 1.6 71.6 1.0
MG B:MG404 1.8 71.6 1.0
O1B B:ADP402 2.4 71.6 1.0
O3B B:ADP402 2.5 71.6 1.0
F2 B:BEF403 2.6 71.6 1.0
F3 B:BEF403 2.6 71.6 1.0
NH2 B:ARG215 2.7 39.8 1.0
PB B:ADP402 3.0 71.6 1.0
NH2 C:ARG169 3.6 34.5 1.0
CZ B:ARG215 3.6 39.8 1.0
NH1 B:ARG215 3.7 39.8 1.0
O3A B:ADP402 3.8 71.6 1.0
OG1 B:THR52 3.9 37.9 1.0
O2A B:ADP402 4.0 71.6 1.0
OE1 C:GLU144 4.0 40.1 1.0
NH1 C:ARG169 4.2 34.5 1.0
O2B B:ADP402 4.2 71.6 1.0
CZ C:ARG169 4.4 34.5 1.0
OE2 B:GLU127 4.4 38.6 1.0
CD C:GLU144 4.6 40.1 1.0
PA B:ADP402 4.6 71.6 1.0
CB B:THR52 4.8 37.9 1.0
OE2 C:GLU144 4.8 40.1 1.0
NE B:ARG215 4.9 39.8 1.0
CA B:GLY48 4.9 42.1 1.0
N B:GLY48 5.0 42.1 1.0

Fluorine binding site 2 out of 9 in 8var

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Fluorine binding site 2 out of 9 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:71.6
occ:1.00
 F2 B:BEF403 0.0 71.6 1.0
BE B:BEF403 1.5 71.6 1.0
NH2 B:ARG215 2.1 39.8 1.0
O3B B:ADP402 2.5 71.6 1.0
F3 B:BEF403 2.6 71.6 1.0
F1 B:BEF403 2.6 71.6 1.0
NH2 C:ARG169 3.0 34.5 1.0
N B:GLY48 3.0 42.1 1.0
CZ B:ARG215 3.4 39.8 1.0
OG1 C:THR165 3.5 36.0 1.0
CA B:GLY48 3.5 42.1 1.0
C B:ARG47 3.9 41.5 1.0
PB B:ADP402 4.0 71.6 1.0
NE B:ARG215 4.1 39.8 1.0
MG B:MG404 4.1 71.6 1.0
CA B:ARG47 4.2 41.5 1.0
NH1 B:ARG215 4.2 39.8 1.0
CZ C:ARG169 4.2 34.5 1.0
O1B B:ADP402 4.4 71.6 1.0
CB C:THR165 4.5 36.0 1.0
O3A B:ADP402 4.6 71.6 1.0
N B:ARG47 4.8 41.5 1.0
CE B:LYS51 4.8 38.4 1.0
NH1 C:ARG169 4.8 34.5 1.0
O2B B:ADP402 4.8 71.6 1.0
O B:ARG47 4.9 41.5 1.0
C B:GLY48 5.0 42.1 1.0
NZ B:LYS51 5.0 38.4 1.0

Fluorine binding site 3 out of 9 in 8var

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Fluorine binding site 3 out of 9 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:71.6
occ:1.00
 F3 B:BEF403 0.0 71.6 1.0
BE B:BEF403 1.6 71.6 1.0
F2 B:BEF403 2.6 71.6 1.0
F1 B:BEF403 2.6 71.6 1.0
O3B B:ADP402 2.6 71.6 1.0
MG B:MG404 3.0 71.6 1.0
CE B:LYS51 3.1 38.4 1.0
O1B B:ADP402 3.6 71.6 1.0
PB B:ADP402 3.6 71.6 1.0
OE2 B:GLU127 3.8 38.6 1.0
OG1 B:THR157 3.8 39.3 1.0
NZ B:LYS51 3.9 38.4 1.0
O2B B:ADP402 4.0 71.6 1.0
NH2 B:ARG215 4.2 39.8 1.0
CD B:LYS51 4.2 38.4 1.0
N B:GLY48 4.4 42.1 1.0
OG1 B:THR52 4.8 37.9 1.0
NH2 C:ARG169 4.8 34.5 1.0
OG1 C:THR165 4.8 36.0 1.0
CD B:GLU127 4.9 38.6 1.0
CB B:LYS51 4.9 38.4 1.0
CA B:GLY48 5.0 42.1 1.0
O3A B:ADP402 5.0 71.6 1.0

Fluorine binding site 4 out of 9 in 8var

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Fluorine binding site 4 out of 9 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:71.6
occ:1.00
 F1 D:BEF401 0.0 71.6 1.0
BE D:BEF401 1.6 71.6 1.0
O1B C:ADP402 2.3 71.6 1.0
O3B C:ADP402 2.5 71.6 1.0
F3 D:BEF401 2.6 71.6 1.0
MG C:MG403 2.6 71.6 1.0
F2 D:BEF401 2.7 71.6 1.0
PB C:ADP402 2.9 71.6 1.0
NH2 D:ARG169 3.7 35.9 1.0
O2B C:ADP402 3.7 71.6 1.0
OG1 C:THR52 3.7 38.3 1.0
OE2 C:GLU127 3.8 37.8 1.0
NH1 D:ARG169 4.2 35.9 1.0
O3A C:ADP402 4.2 71.6 1.0
CZ D:ARG169 4.3 35.9 1.0
O2A C:ADP402 4.4 71.6 1.0
CG C:LYS51 4.7 38.3 1.0
NH1 C:ARG215 4.8 40.6 1.0
CB C:THR52 4.8 38.3 1.0
CD C:LYS51 4.9 38.3 1.0
CD C:GLU127 4.9 37.8 1.0

Fluorine binding site 5 out of 9 in 8var

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Fluorine binding site 5 out of 9 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:71.6
occ:1.00
 F2 D:BEF401 0.0 71.6 1.0
BE D:BEF401 1.6 71.6 1.0
NH2 C:ARG215 2.3 40.6 1.0
NH1 D:ARG169 2.4 35.9 1.0
F3 D:BEF401 2.5 71.6 1.0
O3B C:ADP402 2.5 71.6 1.0
NH1 C:ARG215 2.7 40.6 1.0
CZ C:ARG215 2.7 40.6 1.0
F1 D:BEF401 2.7 71.6 1.0
CZ D:ARG169 2.8 35.9 1.0
NH2 D:ARG169 3.1 35.9 1.0
O1B C:ADP402 3.6 71.6 1.0
PB C:ADP402 3.6 71.6 1.0
NE D:ARG169 3.7 35.9 1.0
NE C:ARG215 3.8 40.6 1.0
N C:GLY48 4.1 38.2 1.0
O3A C:ADP402 4.1 71.6 1.0
CD D:ARG169 4.3 35.9 1.0
O2A C:ADP402 4.4 71.6 1.0
CA C:GLY48 4.5 38.2 1.0
MG C:MG403 4.6 71.6 1.0
OG D:SER168 4.6 37.9 1.0
O2B C:ADP402 4.8 71.6 1.0
CD C:ARG215 4.9 40.6 1.0
CB C:ARG47 4.9 39.4 1.0
PA C:ADP402 5.0 71.6 1.0

Fluorine binding site 6 out of 9 in 8var

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Fluorine binding site 6 out of 9 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:71.6
occ:1.00
 F3 D:BEF401 0.0 71.6 1.0
BE D:BEF401 1.5 71.6 1.0
F2 D:BEF401 2.5 71.6 1.0
F1 D:BEF401 2.6 71.6 1.0
O3B C:ADP402 2.7 71.6 1.0
NH1 D:ARG169 3.5 35.9 1.0
CB C:ARG47 3.6 39.4 1.0
CA C:ARG47 3.7 39.4 1.0
CG2 D:THR165 3.7 38.2 1.0
N C:GLY48 3.8 38.2 1.0
NH2 C:ARG215 4.0 40.6 1.0
PB C:ADP402 4.0 71.6 1.0
C C:ARG47 4.3 39.4 1.0
O1B C:ADP402 4.3 71.6 1.0
CB D:THR165 4.3 38.2 1.0
CZ D:ARG169 4.4 35.9 1.0
NH2 D:ARG169 4.4 35.9 1.0
OG1 C:THR157 4.4 40.6 1.0
O2B C:ADP402 4.6 71.6 1.0
OE2 C:GLU127 4.6 37.8 1.0
NZ C:LYS51 4.7 38.3 1.0
NH1 C:ARG215 4.8 40.6 1.0
CZ C:ARG215 4.8 40.6 1.0
N C:ARG47 4.9 39.4 1.0
CG C:ARG47 4.9 39.4 1.0
CA C:GLY48 4.9 38.2 1.0

Fluorine binding site 7 out of 9 in 8var

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Fluorine binding site 7 out of 9 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F404

b:71.6
occ:1.00
 F1 D:BEF404 0.0 71.6 1.0
BE D:BEF404 1.6 71.6 1.0
MG D:MG405 2.2 71.6 1.0
O1B D:ADP403 2.3 71.6 1.0
F3 D:BEF404 2.6 71.6 1.0
O3B D:ADP403 2.7 71.6 1.0
F2 D:BEF404 2.7 71.6 1.0
PB D:ADP403 3.0 71.6 1.0
CE D:LYS51 3.5 44.0 1.0
NZ D:LYS51 3.6 44.0 1.0
O2B D:ADP403 3.7 71.6 1.0
OE2 D:GLU127 3.7 43.1 1.0
NH2 E:ARG158 3.8 48.6 1.0
OG1 D:THR52 3.9 43.6 1.0
CB D:LYS51 4.1 44.0 1.0
O3A D:ADP403 4.3 71.6 1.0
OD1 D:ASP126 4.4 42.6 1.0
NH2 D:ARG215 4.5 50.9 1.0
N D:THR52 4.7 43.6 1.0
CD D:LYS51 4.7 44.0 1.0
N D:LYS51 4.7 44.0 1.0
O2A D:ADP403 4.7 71.6 1.0
OD2 D:ASP126 4.8 42.6 1.0
CG D:LYS51 4.9 44.0 1.0
CD D:GLU127 4.9 43.1 1.0
CA D:LYS51 4.9 44.0 1.0
OG1 D:THR157 5.0 48.1 1.0

Fluorine binding site 8 out of 9 in 8var

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Fluorine binding site 8 out of 9 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F404

b:71.6
occ:1.00
 F2 D:BEF404 0.0 71.6 1.0
BE D:BEF404 1.6 71.6 1.0
NH2 D:ARG215 2.3 50.9 1.0
O3B D:ADP403 2.5 71.6 1.0
F3 D:BEF404 2.6 71.6 1.0
F1 D:BEF404 2.7 71.6 1.0
NH2 E:ARG158 2.9 48.6 1.0
CZ D:ARG215 3.4 50.9 1.0
CZ E:ARG158 3.6 48.6 1.0
OG1 E:THR154 3.7 48.1 1.0
PB D:ADP403 3.7 71.6 1.0
O1B D:ADP403 3.8 71.6 1.0
NH1 E:ARG158 3.8 48.6 1.0
N D:GLY48 3.8 47.1 1.0
NH1 D:ARG215 3.9 50.9 1.0
MG D:MG405 4.2 71.6 1.0
CA D:ARG47 4.2 48.6 1.0
O3A D:ADP403 4.3 71.6 1.0
CB D:ARG47 4.5 48.6 1.0
NZ D:LYS51 4.5 44.0 1.0
NE D:ARG215 4.5 50.9 1.0
NE E:ARG158 4.5 48.6 1.0
C D:ARG47 4.6 48.6 1.0
O2B D:ADP403 4.7 71.6 1.0
CA D:GLY48 4.7 47.1 1.0
OE2 D:GLU127 4.8 43.1 1.0
CB E:THR154 4.8 48.1 1.0

Fluorine binding site 9 out of 9 in 8var

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Fluorine binding site 9 out of 9 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Closed-DNA2 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F404

b:71.6
occ:1.00
 F3 D:BEF404 0.0 71.6 1.0
BE D:BEF404 1.6 71.6 1.0
NZ D:LYS51 2.3 44.0 1.0
O3B D:ADP403 2.6 71.6 1.0
F1 D:BEF404 2.6 71.6 1.0
F2 D:BEF404 2.6 71.6 1.0
CE D:LYS51 2.9 44.0 1.0
CA D:ARG47 3.6 48.6 1.0
OG1 D:THR157 3.7 48.1 1.0
O D:THR46 3.8 44.0 1.0
PB D:ADP403 3.8 71.6 1.0
O2B D:ADP403 4.1 71.6 1.0
N D:GLY48 4.1 47.1 1.0
N D:ARG47 4.2 48.6 1.0
C D:THR46 4.2 44.0 1.0
O D:GLY45 4.2 43.2 1.0
O1B D:ADP403 4.3 71.6 1.0
C D:ARG47 4.3 48.6 1.0
CD D:LYS51 4.4 44.0 1.0
CB D:ARG47 4.4 48.6 1.0
CA D:THR157 4.4 48.1 1.0
CB D:THR157 4.4 48.1 1.0
NH2 D:ARG215 4.5 50.9 1.0
CG2 D:THR157 4.5 48.1 1.0
OE2 D:GLU127 4.5 43.1 1.0
OG1 E:THR154 4.6 48.1 1.0
MG D:MG405 4.8 71.6 1.0
N D:THR157 4.8 48.1 1.0
NH2 E:ARG158 4.9 48.6 1.0
CG D:LYS51 4.9 44.0 1.0
CB D:LYS51 4.9 44.0 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: Wed Jul 16 09:44:55 2025

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