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Fluorine in PDB 8vap: Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Fully-Open Conformation

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

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

Other elements in 8vap:

The structure of Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Fully-Open 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 Fully-Open Conformation (pdb code 8vap). 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 Fully-Open Conformation, PDB code: 8vap:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 8vap

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

b:83.0
occ:1.00
 F1 B:BEF402 0.0 83.0 1.0
BE B:BEF402 1.6 82.5 1.0
MG B:MG403 2.1 48.1 1.0
O1B B:ADP401 2.4 63.9 1.0
O3B B:ADP401 2.5 74.8 1.0
F2 B:BEF402 2.6 88.8 1.0
F3 B:BEF402 2.6 90.4 1.0
PB B:ADP401 3.0 86.5 1.0
NH2 B:ARG215 3.0 73.4 1.0
NH2 C:ARG169 3.3 77.6 1.0
NH1 B:ARG215 3.5 70.7 1.0
CZ B:ARG215 3.7 70.5 1.0
O3A B:ADP401 3.8 64.0 1.0
OG1 C:THR165 4.0 76.2 1.0
O2A B:ADP401 4.0 60.9 1.0
O2B B:ADP401 4.2 65.5 1.0
OE2 B:GLU127 4.5 72.4 1.0
N B:GLY48 4.5 65.7 1.0
CZ C:ARG169 4.6 77.0 1.0
PA B:ADP401 4.6 55.5 1.0
CD2 C:LEU140 4.8 61.3 1.0
OD2 B:ASP126 4.8 61.9 1.0
NE B:ARG215 5.0 72.3 1.0

Fluorine binding site 2 out of 9 in 8vap

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

b:88.8
occ:1.00
 F2 B:BEF402 0.0 88.8 1.0
BE B:BEF402 1.5 82.5 1.0
O3B B:ADP401 2.5 74.8 1.0
F3 B:BEF402 2.6 90.4 1.0
F1 B:BEF402 2.6 83.0 1.0
NH1 B:ARG215 2.7 70.7 1.0
OG1 C:THR165 2.9 76.2 1.0
CA B:ARG47 3.1 70.6 1.0
CB B:ARG47 3.1 66.9 1.0
N B:GLY48 3.2 65.7 1.0
CB C:THR165 3.5 54.0 1.0
C B:ARG47 3.6 74.6 1.0
CZ B:ARG215 3.7 70.5 1.0
CA C:THR165 3.9 47.0 1.0
NH2 B:ARG215 3.9 73.4 1.0
PB B:ADP401 4.0 86.5 1.0
NH2 C:ARG169 4.3 77.6 1.0
N B:ARG47 4.3 76.6 1.0
O1B B:ADP401 4.4 63.9 1.0
CA B:GLY48 4.4 64.9 1.0
CG B:ARG47 4.4 66.1 1.0
O C:THR165 4.4 69.5 1.0
MG B:MG403 4.6 48.1 1.0
C C:THR165 4.6 61.5 1.0
O3A B:ADP401 4.6 64.0 1.0
O B:THR46 4.8 74.4 1.0
O B:ARG47 4.8 83.1 1.0
O2B B:ADP401 4.8 65.5 1.0
NE B:ARG215 4.9 72.3 1.0
CG2 C:THR165 5.0 54.8 1.0

Fluorine binding site 3 out of 9 in 8vap

Go back to Fluorine Binding Sites List in 8vap
Fluorine binding site 3 out of 9 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Fully-Open 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 Fully-Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:90.4
occ:1.00
 F3 B:BEF402 0.0 90.4 1.0
BE B:BEF402 1.6 82.5 1.0
F2 B:BEF402 2.6 88.8 1.0
F1 B:BEF402 2.6 83.0 1.0
O3B B:ADP401 2.6 74.8 1.0
OG1 B:THR157 3.2 78.2 1.0
NZ B:LYS51 3.3 55.0 1.0
OE2 B:GLU127 3.5 72.4 1.0
MG B:MG403 3.6 48.1 1.0
PB B:ADP401 3.6 86.5 1.0
O1B B:ADP401 3.6 63.9 1.0
CA B:ARG47 3.7 70.6 1.0
O B:THR46 3.9 74.4 1.0
O2B B:ADP401 4.0 65.5 1.0
OG1 C:THR165 4.1 76.2 1.0
N B:ARG47 4.2 76.6 1.0
CB B:ARG47 4.3 66.9 1.0
C B:THR46 4.4 73.5 1.0
N B:GLY48 4.4 65.7 1.0
CB B:THR157 4.4 66.7 1.0
CE B:LYS51 4.5 62.8 1.0
CG2 B:THR157 4.6 59.4 1.0
C B:ARG47 4.6 74.6 1.0
CD B:GLU127 4.6 72.9 1.0
CB C:THR165 4.7 54.0 1.0
CD B:LYS51 4.8 63.8 1.0
NH1 B:ARG215 4.9 70.7 1.0
CA B:THR157 5.0 63.0 1.0
O3A B:ADP401 5.0 64.0 1.0

Fluorine binding site 4 out of 9 in 8vap

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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 Fully-Open 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 Fully-Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:71.5
occ:1.00
 F1 D:BEF401 0.0 71.5 1.0
BE D:BEF401 1.6 72.0 1.0
MG C:MG402 1.8 65.7 1.0
O1B C:ADP401 2.3 75.3 1.0
O3B C:ADP401 2.5 76.7 1.0
F3 D:BEF401 2.6 79.0 1.0
F2 D:BEF401 2.7 73.4 1.0
PB C:ADP401 2.9 81.7 1.0
OG1 C:THR52 3.6 60.6 1.0
NH2 D:ARG169 3.6 63.4 1.0
O2B C:ADP401 3.7 77.3 1.0
O3A C:ADP401 4.2 61.8 1.0
NH2 C:ARG215 4.4 62.9 1.0
O2A C:ADP401 4.4 73.9 1.0
NZ C:LYS51 4.5 45.7 1.0
CE C:LYS51 4.6 55.0 1.0
CB C:THR52 4.7 52.0 1.0
OG1 D:THR165 4.8 72.8 1.0
CZ D:ARG169 4.8 61.2 1.0

Fluorine binding site 5 out of 9 in 8vap

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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 Fully-Open 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 Fully-Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:73.4
occ:1.00
 F2 D:BEF401 0.0 73.4 1.0
BE D:BEF401 1.6 72.0 1.0
NH2 D:ARG169 2.2 63.4 1.0
F3 D:BEF401 2.5 79.0 1.0
O3B C:ADP401 2.5 76.7 1.0
F1 D:BEF401 2.7 71.5 1.0
NH2 C:ARG215 2.8 62.9 1.0
OG1 D:THR165 3.5 72.8 1.0
CZ D:ARG169 3.5 61.2 1.0
N C:GLY48 3.6 60.2 1.0
O1B C:ADP401 3.6 75.3 1.0
PB C:ADP401 3.6 81.7 1.0
CZ C:ARG215 3.7 62.8 1.0
MG C:MG402 4.0 65.7 1.0
NE D:ARG169 4.1 63.0 1.0
O3A C:ADP401 4.1 61.8 1.0
CA C:GLY48 4.2 61.6 1.0
OG D:SER168 4.2 65.9 1.0
CB C:ARG47 4.3 62.5 1.0
NE C:ARG215 4.4 51.2 1.0
CA C:ARG47 4.4 62.3 1.0
NH1 C:ARG215 4.4 68.3 1.0
O2A C:ADP401 4.4 73.9 1.0
NH1 D:ARG169 4.4 57.2 1.0
C C:ARG47 4.4 58.3 1.0
CB D:THR165 4.7 62.6 1.0
O2B C:ADP401 4.8 77.3 1.0
PA C:ADP401 5.0 69.8 1.0
O D:THR165 5.0 77.1 1.0

Fluorine binding site 6 out of 9 in 8vap

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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 Fully-Open 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 Fully-Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:79.0
occ:1.00
 F3 D:BEF401 0.0 79.0 1.0
BE D:BEF401 1.5 72.0 1.0
F2 D:BEF401 2.5 73.4 1.0
F1 D:BEF401 2.6 71.5 1.0
O3B C:ADP401 2.7 76.7 1.0
CA C:ARG47 3.3 62.3 1.0
OG1 D:THR165 3.3 72.8 1.0
CB C:ARG47 3.5 62.5 1.0
N C:GLY48 3.7 60.2 1.0
NZ C:LYS51 3.9 45.7 1.0
NH2 D:ARG169 3.9 63.4 1.0
PB C:ADP401 4.0 81.7 1.0
C C:ARG47 4.1 58.3 1.0
CB D:THR165 4.1 62.6 1.0
N C:ARG47 4.3 63.0 1.0
O1B C:ADP401 4.3 75.3 1.0
MG C:MG402 4.4 65.7 1.0
O C:THR46 4.5 59.8 1.0
CE C:LYS51 4.6 55.0 1.0
OG1 C:THR157 4.6 60.3 1.0
O2B C:ADP401 4.6 77.3 1.0
C C:THR46 4.7 56.4 1.0
CG C:ARG47 4.9 61.4 1.0
CA C:GLY48 4.9 61.6 1.0

Fluorine binding site 7 out of 9 in 8vap

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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 Fully-Open 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 Fully-Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F403

b:68.1
occ:1.00
 F1 D:BEF403 0.0 68.1 1.0
BE D:BEF403 1.6 72.4 1.0
O1B D:ADP402 2.3 64.8 1.0
F3 D:BEF403 2.6 80.4 1.0
MG D:MG404 2.6 58.5 1.0
O3B D:ADP402 2.7 67.5 1.0
F2 D:BEF403 2.7 76.4 1.0
PB D:ADP402 2.9 75.1 1.0
NZ D:LYS51 3.2 67.8 1.0
CE D:LYS51 3.6 63.5 1.0
O2B D:ADP402 3.7 68.1 1.0
NH2 E:ARG158 3.9 65.6 1.0
NH2 D:ARG215 4.1 68.3 1.0
OG1 D:THR52 4.2 60.2 1.0
OE2 D:GLU127 4.2 79.2 1.0
O3A D:ADP402 4.3 62.1 1.0
OD1 D:ASP126 4.4 82.6 1.0
OD2 D:ASP126 4.6 82.3 1.0
O2A D:ADP402 4.7 66.3 1.0
OG1 E:THR154 4.8 81.4 1.0
CZ E:ARG158 4.9 65.7 1.0
CG D:ASP126 4.9 79.1 1.0
NH1 E:ARG158 5.0 64.3 1.0
CD D:LYS51 5.0 61.2 1.0

Fluorine binding site 8 out of 9 in 8vap

Go back to Fluorine Binding Sites List in 8vap
Fluorine binding site 8 out of 9 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Fully-Open 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 Fully-Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F403

b:76.4
occ:1.00
 F2 D:BEF403 0.0 76.4 1.0
BE D:BEF403 1.6 72.4 1.0
O3B D:ADP402 2.5 67.5 1.0
F3 D:BEF403 2.6 80.4 1.0
F1 D:BEF403 2.7 68.1 1.0
NH2 D:ARG215 2.9 68.3 1.0
NH1 E:ARG158 3.3 64.3 1.0
OG1 E:THR154 3.3 81.4 1.0
NH2 E:ARG158 3.4 65.6 1.0
N D:GLY48 3.7 54.3 1.0
PB D:ADP402 3.7 75.1 1.0
CA D:ARG47 3.7 59.8 1.0
CZ E:ARG158 3.7 65.7 1.0
O1B D:ADP402 3.8 64.8 1.0
CB D:ARG47 3.8 55.2 1.0
CZ D:ARG215 3.8 68.7 1.0
NE D:ARG215 3.9 67.3 1.0
C D:ARG47 4.2 64.7 1.0
CB E:THR154 4.3 65.9 1.0
O3A D:ADP402 4.3 62.1 1.0
NZ D:LYS51 4.3 67.8 1.0
O2B D:ADP402 4.7 68.1 1.0
MG D:MG404 4.7 58.5 1.0
CA D:GLY48 4.7 46.5 1.0
N D:ARG47 4.9 52.8 1.0
CA E:THR154 4.9 68.0 1.0
NE E:ARG158 5.0 66.9 1.0

Fluorine binding site 9 out of 9 in 8vap

Go back to Fluorine Binding Sites List in 8vap
Fluorine binding site 9 out of 9 in the Structure of the E. Coli Clamp Loader Bound to the Beta Clamp in A Fully-Open 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 Fully-Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F403

b:80.4
occ:1.00
 F3 D:BEF403 0.0 80.4 1.0
BE D:BEF403 1.6 72.4 1.0
NZ D:LYS51 2.3 67.8 1.0
O3B D:ADP402 2.6 67.5 1.0
F1 D:BEF403 2.6 68.1 1.0
F2 D:BEF403 2.6 76.4 1.0
CA D:ARG47 3.2 59.8 1.0
CE D:LYS51 3.3 63.5 1.0
O D:THR46 3.3 73.0 1.0
N D:ARG47 3.7 52.8 1.0
C D:THR46 3.7 64.4 1.0
OG1 D:THR157 3.8 78.7 1.0
PB D:ADP402 3.8 75.1 1.0
CB D:ARG47 4.0 55.2 1.0
O2B D:ADP402 4.1 68.1 1.0
N D:GLY48 4.1 54.3 1.0
C D:ARG47 4.2 64.7 1.0
O1B D:ADP402 4.3 64.8 1.0
O D:GLY45 4.3 64.6 1.0
OG1 E:THR154 4.4 81.4 1.0
CD D:LYS51 4.6 61.2 1.0
CB D:THR157 4.8 73.0 1.0
OE2 D:GLU127 4.8 79.2 1.0
CG2 D:THR157 4.8 72.7 1.0
CB E:THR154 4.9 65.9 1.0
CA D:THR46 4.9 65.7 1.0
CA D:THR157 5.0 78.6 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: Wed Jul 16 09:43:09 2025

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