Fluorine 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
Zinc (Zn) 4 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-DNA1 Conformation (pdb code 8vaq). 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-DNA1 Conformation, PDB code: 8vaq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 8vaq

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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-DNA1 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-DNA1 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:72.1
occ:1.00
 F1 C:BEF401 0.0 72.1 1.0
BE C:BEF401 1.5 72.1 1.0
NH2 C:ARG169 2.2 40.2 1.0
MG B:MG403 2.3 72.1 1.0
O3B B:ADP402 2.4 72.1 1.0
O1B B:ADP402 2.4 72.1 1.0
F2 C:BEF401 2.6 72.1 1.0
F3 C:BEF401 2.6 72.1 1.0
PB B:ADP402 2.9 72.1 1.0
NH2 B:ARG215 3.0 46.1 1.0
CZ C:ARG169 3.3 40.2 1.0
NH1 C:ARG169 3.5 40.2 1.0
O3A B:ADP402 3.8 72.1 1.0
CZ B:ARG215 4.0 46.1 1.0
O2A B:ADP402 4.0 72.1 1.0
OE2 B:GLU127 4.1 41.3 1.0
O2B B:ADP402 4.2 72.1 1.0
NH1 B:ARG215 4.2 46.1 1.0
OG1 B:THR52 4.3 49.5 1.0
NE C:ARG169 4.5 40.2 1.0
PA B:ADP402 4.6 72.1 1.0
OG1 C:THR165 4.9 41.0 1.0
CB B:THR52 5.0 49.5 1.0
NZ B:LYS51 5.0 48.7 1.0

Fluorine binding site 2 out of 9 in 8vaq

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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-DNA1 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-DNA1 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:72.1
occ:1.00
 F2 C:BEF401 0.0 72.1 1.0
BE C:BEF401 1.5 72.1 1.0
NH2 B:ARG215 2.4 46.1 1.0
O3B B:ADP402 2.4 72.1 1.0
F3 C:BEF401 2.6 72.1 1.0
F1 C:BEF401 2.6 72.1 1.0
NH1 C:ARG169 2.6 40.2 1.0
OG1 C:THR165 2.9 41.0 1.0
NH2 C:ARG169 3.3 40.2 1.0
CZ C:ARG169 3.3 40.2 1.0
CZ B:ARG215 3.4 46.1 1.0
CB C:THR165 3.9 41.0 1.0
NE B:ARG215 3.9 46.1 1.0
PB B:ADP402 3.9 72.1 1.0
N B:GLY48 4.1 49.5 1.0
CB B:ARG47 4.2 47.5 1.0
NH1 B:ARG215 4.3 46.1 1.0
O1B B:ADP402 4.4 72.1 1.0
CA B:ARG47 4.4 47.5 1.0
O3A B:ADP402 4.6 72.1 1.0
NE C:ARG169 4.6 40.2 1.0
MG B:MG403 4.7 72.1 1.0
NZ B:LYS51 4.7 48.7 1.0
CA C:THR165 4.8 41.0 1.0
C B:ARG47 4.8 47.5 1.0
O2B B:ADP402 4.8 72.1 1.0
CG2 C:THR165 4.9 41.0 1.0
CD1 C:LEU140 5.0 42.7 1.0

Fluorine binding site 3 out of 9 in 8vaq

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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-DNA1 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-DNA1 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:72.1
occ:1.00
 F3 C:BEF401 0.0 72.1 1.0
BE C:BEF401 1.6 72.1 1.0
O3B B:ADP402 2.5 72.1 1.0
F2 C:BEF401 2.6 72.1 1.0
F1 C:BEF401 2.6 72.1 1.0
OE2 B:GLU127 3.1 41.3 1.0
MG B:MG403 3.3 72.1 1.0
NZ B:LYS51 3.4 48.7 1.0
PB B:ADP402 3.6 72.1 1.0
OG1 B:THR157 3.6 46.8 1.0
O1B B:ADP402 3.6 72.1 1.0
CE B:LYS51 3.8 48.7 1.0
O2B B:ADP402 4.0 72.1 1.0
CD B:GLU127 4.2 41.3 1.0
NH2 B:ARG215 4.3 46.1 1.0
NH2 C:ARG169 4.3 40.2 1.0
OE1 B:GLU127 4.5 41.3 1.0
OG1 C:THR165 4.7 41.0 1.0
NH1 C:ARG169 4.7 40.2 1.0
O3A B:ADP402 5.0 72.1 1.0
CB B:THR157 5.0 46.8 1.0
CZ C:ARG169 5.0 40.2 1.0

Fluorine binding site 4 out of 9 in 8vaq

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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-DNA1 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-DNA1 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F404

b:72.1
occ:1.00
 F1 C:BEF404 0.0 72.1 1.0
BE C:BEF404 1.6 72.1 1.0
MG C:MG405 1.8 72.1 1.0
O1B C:ADP403 2.3 72.1 1.0
O3B C:ADP403 2.4 72.1 1.0
F3 C:BEF404 2.5 72.1 1.0
F2 C:BEF404 2.7 72.1 1.0
PB C:ADP403 2.8 72.1 1.0
NZ C:LYS51 3.2 43.6 1.0
OG1 C:THR52 3.4 46.0 1.0
NH2 D:ARG169 3.7 36.8 1.0
CE C:LYS51 3.7 43.6 1.0
O2B C:ADP403 3.7 72.1 1.0
OE2 C:GLU127 3.8 43.6 1.0
CB C:LYS51 4.2 43.6 1.0
O3A C:ADP403 4.2 72.1 1.0
CB C:THR52 4.4 46.0 1.0
O2A C:ADP403 4.4 72.1 1.0
N C:THR52 4.5 46.0 1.0
NH2 C:ARG215 4.5 41.1 1.0
CZ D:ARG169 4.7 36.8 1.0
NH1 C:ARG215 4.8 41.1 1.0
N C:LYS51 4.8 43.6 1.0
CA C:LYS51 4.9 43.6 1.0
CD C:GLU127 4.9 43.6 1.0
C C:LYS51 4.9 43.6 1.0
NH1 D:ARG169 4.9 36.8 1.0
CD C:LYS51 5.0 43.6 1.0
CG C:LYS51 5.0 43.6 1.0

Fluorine binding site 5 out of 9 in 8vaq

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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-DNA1 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-DNA1 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F404

b:72.1
occ:1.00
 F2 C:BEF404 0.0 72.1 1.0
BE C:BEF404 1.6 72.1 1.0
NH1 C:ARG215 2.2 41.1 1.0
O3B C:ADP403 2.5 72.1 1.0
F3 C:BEF404 2.5 72.1 1.0
NH2 D:ARG169 2.7 36.8 1.0
F1 C:BEF404 2.7 72.1 1.0
CZ C:ARG215 2.9 41.1 1.0
NH2 C:ARG215 3.0 41.1 1.0
CZ D:ARG169 3.2 36.8 1.0
NH1 D:ARG169 3.5 36.8 1.0
PB C:ADP403 3.6 72.1 1.0
O1B C:ADP403 3.6 72.1 1.0
MG C:MG405 3.9 72.1 1.0
NE D:ARG169 4.0 36.8 1.0
NZ C:LYS51 4.0 43.6 1.0
NE C:ARG215 4.1 41.1 1.0
O3A C:ADP403 4.1 72.1 1.0
N C:GLY48 4.3 41.2 1.0
CG2 D:THR165 4.4 36.2 1.0
O2A C:ADP403 4.4 72.1 1.0
CA C:GLY48 4.7 41.2 1.0
CD C:ARG215 4.8 41.1 1.0
OE1 D:GLU144 4.8 44.7 1.0
O2B C:ADP403 4.8 72.1 1.0
PA C:ADP403 5.0 72.1 1.0

Fluorine binding site 6 out of 9 in 8vaq

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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-DNA1 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-DNA1 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F404

b:72.1
occ:1.00
 F3 C:BEF404 0.0 72.1 1.0
BE C:BEF404 1.6 72.1 1.0
NZ C:LYS51 2.3 43.6 1.0
F2 C:BEF404 2.5 72.1 1.0
F1 C:BEF404 2.5 72.1 1.0
O3B C:ADP403 2.6 72.1 1.0
CE C:LYS51 3.1 43.6 1.0
NH2 D:ARG169 3.4 36.8 1.0
CG2 D:THR165 3.8 36.2 1.0
PB C:ADP403 4.0 72.1 1.0
N C:GLY48 4.1 41.2 1.0
CA C:ARG47 4.2 39.2 1.0
MG C:MG405 4.3 72.1 1.0
O1B C:ADP403 4.3 72.1 1.0
OE2 C:GLU127 4.3 43.6 1.0
OG1 C:THR157 4.4 42.1 1.0
CD C:LYS51 4.5 43.6 1.0
NH1 C:ARG215 4.5 41.1 1.0
CZ D:ARG169 4.6 36.8 1.0
O2B C:ADP403 4.6 72.1 1.0
CB C:ARG47 4.6 39.2 1.0
C C:ARG47 4.7 39.2 1.0

Fluorine binding site 7 out of 9 in 8vaq

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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-DNA1 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-DNA1 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F402

b:72.1
occ:1.00
 F1 D:BEF402 0.0 72.1 1.0
BE D:BEF402 1.6 72.1 1.0
MG D:MG403 2.1 72.1 1.0
O1B D:ADP401 2.4 72.1 1.0
F3 D:BEF402 2.5 72.1 1.0
O3B D:ADP401 2.6 72.1 1.0
F2 D:BEF402 2.7 72.1 1.0
PB D:ADP401 2.9 72.1 1.0
NZ D:LYS51 3.3 49.8 1.0
OG1 D:THR52 3.6 49.8 1.0
O2B D:ADP401 3.7 72.1 1.0
OE2 D:GLU127 3.8 43.5 1.0
CE D:LYS51 3.8 49.8 1.0
OD1 D:ASP126 4.3 43.0 1.0
NH2 E:ARG158 4.3 50.4 1.0
O3A D:ADP401 4.3 72.1 1.0
CG D:LYS51 4.4 49.8 1.0
NH1 D:ARG215 4.5 59.3 1.0
CB D:THR52 4.6 49.8 1.0
OD2 D:ASP126 4.6 43.0 1.0
O2A D:ADP401 4.7 72.1 1.0
CD D:LYS51 4.8 49.8 1.0
CG2 D:THR157 4.8 43.5 1.0
CG D:ASP126 4.9 43.0 1.0
N D:THR52 4.9 49.8 1.0
N D:GLY48 5.0 53.6 1.0

Fluorine binding site 8 out of 9 in 8vaq

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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-DNA1 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-DNA1 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F402

b:72.1
occ:1.00
 F2 D:BEF402 0.0 72.1 1.0
BE D:BEF402 1.6 72.1 1.0
O3B D:ADP401 2.4 72.1 1.0
F3 D:BEF402 2.6 72.1 1.0
F1 D:BEF402 2.7 72.1 1.0
NH1 D:ARG215 2.8 59.3 1.0
N D:GLY48 3.0 53.6 1.0
NH2 E:ARG158 3.4 50.4 1.0
PB D:ADP401 3.6 72.1 1.0
O1B D:ADP401 3.7 72.1 1.0
CA D:GLY48 3.8 53.6 1.0
CA D:ARG47 3.9 54.4 1.0
C D:ARG47 3.9 54.4 1.0
MG D:MG403 4.0 72.1 1.0
CZ D:ARG215 4.1 59.3 1.0
NE E:ARG158 4.2 50.4 1.0
CZ E:ARG158 4.2 50.4 1.0
CB D:ARG47 4.3 54.4 1.0
O3A D:ADP401 4.3 72.1 1.0
NZ D:LYS51 4.4 49.8 1.0
O2B D:ADP401 4.7 72.1 1.0
NH2 D:ARG215 4.8 59.3 1.0
OG1 E:THR154 4.9 50.6 1.0
NE D:ARG215 4.9 59.3 1.0
CD D:ARG215 4.9 59.3 1.0
C D:GLY48 5.0 53.6 1.0

Fluorine binding site 9 out of 9 in 8vaq

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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-DNA1 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-DNA1 Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F402

b:72.1
occ:1.00
 F3 D:BEF402 0.0 72.1 1.0
BE D:BEF402 1.6 72.1 1.0
NZ D:LYS51 2.1 49.8 1.0
O3B D:ADP401 2.5 72.1 1.0
F1 D:BEF402 2.5 72.1 1.0
F2 D:BEF402 2.6 72.1 1.0
O D:THR46 3.2 50.2 1.0
CE D:LYS51 3.2 49.8 1.0
CG2 D:THR157 3.2 43.5 1.0
CA D:ARG47 3.5 54.4 1.0
N D:GLY48 3.6 53.6 1.0
PB D:ADP401 3.8 72.1 1.0
C D:ARG47 3.9 54.4 1.0
C D:THR46 4.0 50.2 1.0
O2B D:ADP401 4.0 72.1 1.0
N D:ARG47 4.1 54.4 1.0
O1B D:ADP401 4.2 72.1 1.0
CD D:LYS51 4.4 49.8 1.0
CB D:ARG47 4.4 54.4 1.0
CB D:THR157 4.5 43.5 1.0
MG D:MG403 4.6 72.1 1.0
CG D:LYS51 4.7 49.8 1.0
CA D:GLY48 4.8 53.6 1.0
OE2 D:GLU127 4.8 43.5 1.0
N D:VAL49 4.9 52.6 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: Sat Aug 3 01:26:53 2024

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