Fluorine 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
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 Semi-Open Conformation (pdb code 8vam). 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 Semi-Open Conformation, PDB code: 8vam:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 8vam

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

b:134.4
occ:1.00
 F1 B:BEF403 0.0 134.4 1.0
BE B:BEF403 1.5 134.4 1.0
MG B:MG404 2.1 134.8 1.0
O1B B:ADP402 2.4 133.7 1.0
O3B B:ADP402 2.5 133.7 1.0
F2 B:BEF403 2.6 134.4 1.0
F3 B:BEF403 2.6 134.4 1.0
PB B:ADP402 3.0 133.7 1.0
OG1 B:THR52 3.8 131.1 1.0
O3A B:ADP402 3.8 133.7 1.0
O2A B:ADP402 4.0 133.7 1.0
O2B B:ADP402 4.2 133.7 1.0
OD2 B:ASP126 4.3 140.9 1.0
NH1 B:ARG215 4.5 124.0 1.0
OE2 B:GLU127 4.6 132.6 1.0
PA B:ADP402 4.6 133.7 1.0
CB B:THR52 4.8 131.1 1.0
CD B:ARG215 4.8 124.0 1.0
CZ B:ARG215 4.9 124.0 1.0

Fluorine binding site 2 out of 9 in 8vam

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

b:134.4
occ:1.00
 F2 B:BEF403 0.0 134.4 1.0
BE B:BEF403 1.5 134.4 1.0
O3B B:ADP402 2.5 133.7 1.0
F3 B:BEF403 2.6 134.4 1.0
F1 B:BEF403 2.6 134.4 1.0
NE B:ARG47 3.1 127.3 1.0
CD B:ARG47 3.3 127.3 1.0
CG B:ARG47 3.7 127.3 1.0
C B:ARG47 3.8 127.3 1.0
CA B:ARG47 3.9 127.3 1.0
O B:ARG47 4.0 127.3 1.0
PB B:ADP402 4.0 133.7 1.0
CD B:ARG215 4.1 124.0 1.0
N B:GLY48 4.1 125.6 1.0
CZ B:ARG47 4.3 127.3 1.0
O1B B:ADP402 4.4 133.7 1.0
CB B:ARG47 4.4 127.3 1.0
MG B:MG404 4.6 134.8 1.0
CA B:GLY48 4.6 125.6 1.0
NH2 B:ARG47 4.6 127.3 1.0
NE B:ARG215 4.6 124.0 1.0
O3A B:ADP402 4.6 133.7 1.0
O2B B:ADP402 4.8 133.7 1.0

Fluorine binding site 3 out of 9 in 8vam

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

b:134.4
occ:1.00
 F3 B:BEF403 0.0 134.4 1.0
BE B:BEF403 1.6 134.4 1.0
F2 B:BEF403 2.6 134.4 1.0
OE2 B:GLU127 2.6 132.6 1.0
F1 B:BEF403 2.6 134.4 1.0
O3B B:ADP402 2.6 133.7 1.0
CD B:GLU127 3.5 132.6 1.0
MG B:MG404 3.6 134.8 1.0
O1B B:ADP402 3.6 133.7 1.0
PB B:ADP402 3.6 133.7 1.0
OG1 B:THR157 3.6 117.6 1.0
O2B B:ADP402 4.0 133.7 1.0
O B:ARG47 4.0 127.3 1.0
OE1 B:GLU127 4.2 132.6 1.0
CG B:GLU127 4.3 132.6 1.0
CE B:LYS51 4.3 129.2 1.0
NZ B:LYS51 4.4 129.2 1.0
C B:ARG47 4.4 127.3 1.0
CA B:ARG47 4.4 127.3 1.0
OD1 B:ASP126 4.4 140.9 1.0
OD2 B:ASP126 4.7 140.9 1.0
CD B:ARG47 4.8 127.3 1.0
CG B:ASP126 4.9 140.9 1.0
O3A B:ADP402 5.0 133.7 1.0

Fluorine binding site 4 out of 9 in 8vam

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

b:66.8
occ:1.00
 F1 C:BEF402 0.0 66.8 1.0
BE C:BEF402 1.6 66.8 1.0
MG C:MG403 2.1 66.8 1.0
O1B C:ADP401 2.3 66.8 1.0
O3B C:ADP401 2.5 66.8 1.0
F3 C:BEF402 2.6 66.8 1.0
F2 C:BEF402 2.7 66.8 1.0
NZ C:LYS51 2.8 45.9 1.0
PB C:ADP401 2.9 66.8 1.0
NH2 D:ARG169 3.3 29.6 1.0
OG1 D:THR165 3.7 33.0 1.0
O2B C:ADP401 3.7 66.8 1.0
CE C:LYS51 3.8 45.9 1.0
NH1 C:ARG215 4.2 38.2 1.0
O3A C:ADP401 4.2 66.8 1.0
O2A C:ADP401 4.4 66.8 1.0
N C:GLY48 4.5 37.4 1.0
CZ D:ARG169 4.5 29.6 1.0
CZ C:ARG215 4.7 38.2 1.0
CB D:THR165 4.8 33.0 1.0
OG1 C:THR52 4.8 47.3 1.0
NH2 C:ARG215 4.8 38.2 1.0

Fluorine binding site 5 out of 9 in 8vam

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

b:66.8
occ:1.00
 F2 C:BEF402 0.0 66.8 1.0
BE C:BEF402 1.6 66.8 1.0
CZ C:ARG215 2.3 38.2 1.0
NH1 C:ARG215 2.4 38.2 1.0
F3 C:BEF402 2.5 66.8 1.0
O3B C:ADP401 2.5 66.8 1.0
NH2 C:ARG215 2.6 38.2 1.0
F1 C:BEF402 2.7 66.8 1.0
NE C:ARG215 2.9 38.2 1.0
NH2 D:ARG169 3.6 29.6 1.0
O1B C:ADP401 3.6 66.8 1.0
PB C:ADP401 3.6 66.8 1.0
CD C:ARG215 3.6 38.2 1.0
OG1 D:THR165 3.7 33.0 1.0
N C:GLY48 3.8 37.4 1.0
MG C:MG403 3.8 66.8 1.0
O3A C:ADP401 4.1 66.8 1.0
CA C:GLY48 4.1 37.4 1.0
O D:THR165 4.2 33.0 1.0
CB D:SER168 4.2 34.7 1.0
CZ D:ARG169 4.3 29.6 1.0
NE D:ARG169 4.4 29.6 1.0
O2A C:ADP401 4.4 66.8 1.0
CB D:THR165 4.6 33.0 1.0
CB C:ARG47 4.7 36.6 1.0
CB C:ARG215 4.7 38.2 1.0
CA D:THR165 4.7 33.0 1.0
CG C:ARG215 4.7 38.2 1.0
C C:ARG47 4.8 36.6 1.0
O2B C:ADP401 4.8 66.8 1.0
C D:THR165 4.9 33.0 1.0
PA C:ADP401 5.0 66.8 1.0
CA C:ARG47 5.0 36.6 1.0

Fluorine binding site 6 out of 9 in 8vam

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

b:66.8
occ:1.00
 F3 C:BEF402 0.0 66.8 1.0
BE C:BEF402 1.5 66.8 1.0
F2 C:BEF402 2.5 66.8 1.0
F1 C:BEF402 2.6 66.8 1.0
O3B C:ADP401 2.7 66.8 1.0
CB C:ARG47 2.7 36.6 1.0
OG1 D:THR165 2.9 33.0 1.0
CA C:ARG47 3.1 36.6 1.0
N C:GLY48 3.2 37.4 1.0
CB D:THR165 3.3 33.0 1.0
C C:ARG47 3.6 36.6 1.0
NZ C:LYS51 3.7 45.9 1.0
CG C:ARG47 3.8 36.6 1.0
CA D:THR165 3.8 33.0 1.0
PB C:ADP401 4.0 66.8 1.0
NH2 C:ARG215 4.1 38.2 1.0
O1B C:ADP401 4.3 66.8 1.0
CA C:GLY48 4.3 37.4 1.0
N C:ARG47 4.4 36.6 1.0
CZ C:ARG215 4.5 38.2 1.0
NH2 D:ARG169 4.6 29.6 1.0
MG C:MG403 4.6 66.8 1.0
O2B C:ADP401 4.6 66.8 1.0
O D:THR165 4.6 33.0 1.0
NH1 C:ARG215 4.7 38.2 1.0
C D:THR165 4.7 33.0 1.0
CG2 D:THR165 4.7 33.0 1.0
O C:ARG47 4.8 36.6 1.0
N D:THR165 4.9 33.0 1.0
CE C:LYS51 5.0 45.9 1.0

Fluorine binding site 7 out of 9 in 8vam

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

b:66.8
occ:1.00
 F1 D:BEF402 0.0 66.8 1.0
BE D:BEF402 1.6 66.8 1.0
MG D:MG403 2.1 66.8 1.0
O1B D:ADP401 2.3 66.8 1.0
F3 D:BEF402 2.6 66.8 1.0
O3B D:ADP401 2.7 66.8 1.0
F2 D:BEF402 2.7 66.8 1.0
PB D:ADP401 3.0 66.8 1.0
O2B D:ADP401 3.7 66.8 1.0
OG1 D:THR52 3.9 36.4 1.0
NZ D:LYS51 3.9 25.8 1.0
CE D:LYS51 4.0 25.8 1.0
NH1 D:ARG215 4.3 22.8 1.0
O3A D:ADP401 4.3 66.8 1.0
NH2 E:ARG158 4.4 23.7 1.0
OE2 D:GLU127 4.5 31.5 1.0
O2A D:ADP401 4.7 66.8 1.0
NH1 E:ARG158 4.7 23.7 1.0
NH2 D:ARG215 4.8 22.8 1.0
CB D:THR52 4.9 36.4 1.0

Fluorine binding site 8 out of 9 in 8vam

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

b:66.8
occ:1.00
 F2 D:BEF402 0.0 66.8 1.0
BE D:BEF402 1.6 66.8 1.0
NH1 D:ARG215 2.5 22.8 1.0
O3B D:ADP401 2.5 66.8 1.0
F3 D:BEF402 2.6 66.8 1.0
F1 D:BEF402 2.7 66.8 1.0
NH1 E:ARG158 3.1 23.7 1.0
CZ D:ARG215 3.6 22.8 1.0
PB D:ADP401 3.7 66.8 1.0
N D:GLY48 3.7 26.2 1.0
O1B D:ADP401 3.8 66.8 1.0
CG2 E:THR154 3.9 28.1 1.0
MG D:MG403 4.0 66.8 1.0
CZ E:ARG158 4.1 23.7 1.0
NH2 D:ARG215 4.1 22.8 1.0
NH2 E:ARG158 4.2 23.7 1.0
CA D:ARG47 4.2 25.4 1.0
O3A D:ADP401 4.3 66.8 1.0
CB D:ARG47 4.4 25.4 1.0
C D:ARG47 4.5 25.4 1.0
CA D:GLY48 4.6 26.2 1.0
NE D:ARG215 4.6 22.8 1.0
O2B D:ADP401 4.7 66.8 1.0
NZ D:LYS51 4.8 25.8 1.0
CD D:ARG215 4.9 22.8 1.0

Fluorine binding site 9 out of 9 in 8vam

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

b:66.8
occ:1.00
 F3 D:BEF402 0.0 66.8 1.0
BE D:BEF402 1.6 66.8 1.0
O3B D:ADP401 2.6 66.8 1.0
F1 D:BEF402 2.6 66.8 1.0
F2 D:BEF402 2.6 66.8 1.0
NZ D:LYS51 2.6 25.8 1.0
CE D:LYS51 3.3 25.8 1.0
CA D:ARG47 3.7 25.4 1.0
O D:THR46 3.8 24.0 1.0
PB D:ADP401 3.8 66.8 1.0
O2B D:ADP401 4.1 66.8 1.0
N D:GLY48 4.1 26.2 1.0
OG1 D:THR157 4.2 31.8 1.0
O1B D:ADP401 4.3 66.8 1.0
N D:ARG47 4.3 25.4 1.0
C D:THR46 4.3 24.0 1.0
C D:ARG47 4.4 25.4 1.0
CB D:ARG47 4.5 25.4 1.0
O D:GLY45 4.5 26.0 1.0
CG2 D:THR157 4.5 31.8 1.0
MG D:MG403 4.7 66.8 1.0
CB D:THR157 4.7 31.8 1.0
CA D:THR157 4.8 31.8 1.0
CD D:LYS51 4.8 25.8 1.0
CG2 E:THR154 4.8 28.1 1.0
NH1 D:ARG215 5.0 22.8 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: Sat Aug 3 01:24:56 2024

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