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Fluorine in PDB 3gli: Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide

Enzymatic activity of Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide

All present enzymatic activity of Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide, PDB code: 3gli was solved by K.R.Simonetta, A.J.Cantor, J.Kuriyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.03 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.690, 217.180, 275.320, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 25.7

Other elements in 3gli:

The structure of Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Zinc (Zn) 8 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide (pdb code 3gli). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide, PDB code: 3gli:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in 3gli

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Fluorine binding site 1 out of 18 in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:97.1
occ:1.00
 F1 B:BEF401 0.0 97.1 1.0
BE B:BEF401 1.6 96.9 1.0
MG B:MG412 2.1 86.0 1.0
O1B B:ADP400 2.4 92.8 1.0
O3B B:ADP400 2.6 92.4 1.0
F2 B:BEF401 2.6 96.9 1.0
F3 B:BEF401 2.6 96.0 1.0
NH2 C:ARG169 2.9 84.4 1.0
PB B:ADP400 3.0 93.5 1.0
OE2 B:GLU127 3.2 96.1 1.0
NH2 B:ARG215 3.3 89.0 1.0
NH1 B:ARG215 3.5 91.0 1.0
OE2 C:GLU144 3.7 92.3 1.0
O3A B:ADP400 3.8 95.2 1.0
CZ B:ARG215 3.9 90.4 1.0
CZ C:ARG169 3.9 84.3 1.0
O2A B:ADP400 4.1 95.6 1.0
NH1 C:ARG169 4.2 84.5 1.0
O2B B:ADP400 4.2 94.2 1.0
CD C:GLU144 4.4 93.7 1.0
OE1 C:GLU144 4.4 95.1 1.0
CD B:GLU127 4.4 95.3 1.0
OG1 B:THR52 4.6 0.3 1.0
PA B:ADP400 4.7 96.6 1.0
N B:GLY48 4.8 90.6 1.0
NZ B:LYS51 4.9 99.0 1.0
OD2 B:ASP126 4.9 88.5 1.0
NE C:ARG169 5.0 84.3 1.0

Fluorine binding site 2 out of 18 in 3gli

Go back to Fluorine Binding Sites List in 3gli
Fluorine binding site 2 out of 18 in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:96.9
occ:1.00
 F2 B:BEF401 0.0 96.9 1.0
BE B:BEF401 1.5 96.9 1.0
O3B B:ADP400 2.5 92.4 1.0
F3 B:BEF401 2.6 96.0 1.0
NH2 B:ARG215 2.6 89.0 1.0
F1 B:BEF401 2.6 97.1 1.0
CA B:ARG47 3.2 89.7 1.0
N B:GLY48 3.2 90.6 1.0
CZ B:ARG215 3.5 90.4 1.0
NH1 C:ARG169 3.6 84.5 1.0
CB B:ARG47 3.7 89.5 1.0
C B:ARG47 3.7 91.3 1.0
NH2 C:ARG169 3.8 84.4 1.0
NH1 B:ARG215 3.9 91.0 1.0
PB B:ADP400 3.9 93.5 1.0
CG2 C:THR165 3.9 85.5 1.0
CZ C:ARG169 4.1 84.3 1.0
NZ B:LYS51 4.2 99.0 1.0
N B:ARG47 4.3 89.7 1.0
O1B B:ADP400 4.3 92.8 1.0
CA B:GLY48 4.3 92.3 1.0
OG C:SER168 4.5 0.8 1.0
O3A B:ADP400 4.5 95.2 1.0
MG B:MG412 4.6 86.0 1.0
OE2 B:GLU127 4.6 96.1 1.0
NE B:ARG215 4.6 91.4 1.0
CB C:THR165 4.8 84.8 1.0
CE B:LYS51 4.8 98.0 1.0
O2B B:ADP400 4.8 94.2 1.0
O B:ARG47 4.8 92.5 1.0
CA C:THR165 4.9 86.0 1.0

Fluorine binding site 3 out of 18 in 3gli

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Fluorine binding site 3 out of 18 in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:96.0
occ:1.00
 F3 B:BEF401 0.0 96.0 1.0
BE B:BEF401 1.5 96.9 1.0
O3B B:ADP400 2.5 92.4 1.0
F2 B:BEF401 2.6 96.9 1.0
F1 B:BEF401 2.6 97.1 1.0
CE B:LYS51 3.0 98.0 1.0
NZ B:LYS51 3.1 99.0 1.0
OE2 B:GLU127 3.3 96.1 1.0
OG1 B:THR157 3.5 84.3 1.0
PB B:ADP400 3.5 93.5 1.0
O1B B:ADP400 3.6 92.8 1.0
MG B:MG412 3.6 86.0 1.0
O2B B:ADP400 4.0 94.2 1.0
OE1 B:GLU127 4.0 94.8 1.0
CD B:GLU127 4.1 95.3 1.0
CD B:LYS51 4.3 98.8 1.0
CA B:ARG47 4.4 89.7 1.0
CG2 C:THR165 4.5 85.5 1.0
CB B:THR157 4.5 84.6 1.0
CG2 B:THR157 4.6 85.4 1.0
N B:GLY48 4.6 90.6 1.0
NH2 C:ARG169 4.7 84.4 1.0
NH2 B:ARG215 4.8 89.0 1.0
CB B:LYS51 4.8 0.5 1.0
N B:THR157 4.8 84.7 1.0
N B:ARG47 4.9 89.7 1.0
CA B:THR157 4.9 85.1 1.0
O3A B:ADP400 4.9 95.2 1.0
CG B:LYS51 5.0 0.5 1.0

Fluorine binding site 4 out of 18 in 3gli

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Fluorine binding site 4 out of 18 in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F403

b:85.4
occ:1.00
 F1 C:BEF403 0.0 85.4 1.0
BE C:BEF403 1.5 86.7 1.0
MG C:MG413 2.1 84.0 1.0
O1B C:ADP402 2.4 87.2 1.0
O3B C:ADP402 2.5 88.4 1.0
F3 C:BEF403 2.6 86.7 1.0
F2 C:BEF403 2.6 87.1 1.0
PB C:ADP402 3.0 88.6 1.0
OE2 C:GLU127 3.0 0.1 1.0
OG1 C:THR52 3.4 84.2 1.0
NZ C:LYS51 3.7 91.6 1.0
NH2 D:ARG169 3.8 94.1 1.0
O2B C:ADP402 3.8 89.3 1.0
CD C:GLU127 4.0 0.5 1.0
O3A C:ADP402 4.3 90.1 1.0
OE1 C:GLU127 4.3 0.8 1.0
CE C:LYS51 4.3 90.6 1.0
CB C:THR52 4.4 85.3 1.0
OD2 C:ASP126 4.5 95.1 1.0
NH2 C:ARG215 4.5 87.9 1.0
CG C:LYS51 4.6 91.9 1.0
O2A C:ADP402 4.7 88.9 1.0
CZ D:ARG169 4.8 93.4 1.0
N C:THR52 4.8 86.8 1.0
NH1 D:ARG169 4.8 92.8 1.0

Fluorine binding site 5 out of 18 in 3gli

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Fluorine binding site 5 out of 18 in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F403

b:87.1
occ:1.00
 F2 C:BEF403 0.0 87.1 1.0
BE C:BEF403 1.5 86.7 1.0
O3B C:ADP402 2.5 88.4 1.0
F3 C:BEF403 2.5 86.7 1.0
F1 C:BEF403 2.6 85.4 1.0
NH1 C:ARG215 2.7 88.8 1.0
NH2 C:ARG215 2.8 87.9 1.0
NH2 D:ARG169 2.8 94.1 1.0
NH1 D:ARG169 2.8 92.8 1.0
CZ C:ARG215 3.1 88.8 1.0
CZ D:ARG169 3.2 93.4 1.0
MG C:MG413 3.4 84.0 1.0
O1B C:ADP402 3.5 87.2 1.0
PB C:ADP402 3.5 88.6 1.0
N C:GLY48 4.0 93.9 1.0
O3A C:ADP402 4.0 90.1 1.0
CB C:ARG47 4.4 90.6 1.0
NE D:ARG169 4.4 93.6 1.0
CA C:ARG47 4.4 90.6 1.0
NE C:ARG215 4.4 89.9 1.0
OE2 C:GLU127 4.5 0.1 1.0
O2A C:ADP402 4.6 88.9 1.0
CG2 D:THR165 4.6 80.9 1.0
C C:ARG47 4.7 92.0 1.0
OE1 D:GLU144 4.7 0.4 1.0
CA C:GLY48 4.7 95.2 1.0
O2B C:ADP402 4.8 89.3 1.0
NZ C:LYS51 4.9 91.6 1.0
PA C:ADP402 5.0 90.3 1.0

Fluorine binding site 6 out of 18 in 3gli

Go back to Fluorine Binding Sites List in 3gli
Fluorine binding site 6 out of 18 in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F403

b:86.7
occ:1.00
 F3 C:BEF403 0.0 86.7 1.0
BE C:BEF403 1.5 86.7 1.0
F2 C:BEF403 2.5 87.1 1.0
F1 C:BEF403 2.6 85.4 1.0
O3B C:ADP402 2.6 88.4 1.0
NZ C:LYS51 3.0 91.6 1.0
CA C:ARG47 3.3 90.6 1.0
CG2 D:THR165 3.5 80.9 1.0
OG1 C:THR157 3.7 0.4 1.0
CB C:ARG47 3.7 90.6 1.0
PB C:ADP402 4.0 88.6 1.0
N C:GLY48 4.0 93.9 1.0
CE C:LYS51 4.1 90.6 1.0
N C:ARG47 4.1 91.3 1.0
C C:ARG47 4.2 92.0 1.0
NH1 D:ARG169 4.3 92.8 1.0
OE2 C:GLU127 4.3 0.1 1.0
O1B C:ADP402 4.3 87.2 1.0
NH2 D:ARG169 4.5 94.1 1.0
MG C:MG413 4.5 84.0 1.0
OE1 C:GLU127 4.5 0.8 1.0
O2B C:ADP402 4.6 89.3 1.0
C C:THR46 4.7 91.3 1.0
NH1 C:ARG215 4.7 88.8 1.0
CB C:THR157 4.8 0.0 1.0
O C:THR46 4.8 91.5 1.0
CB D:THR165 4.9 80.1 1.0
CD C:GLU127 4.9 0.5 1.0
CZ D:ARG169 4.9 93.4 1.0
CG2 C:THR157 4.9 0.8 1.0

Fluorine binding site 7 out of 18 in 3gli

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Fluorine binding site 7 out of 18 in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F405

b:82.7
occ:1.00
 F1 D:BEF405 0.0 82.7 1.0
BE D:BEF405 1.6 82.9 1.0
MG D:MG414 2.1 84.0 1.0
O1B D:ADP404 2.5 85.7 1.0
F3 D:BEF405 2.5 81.8 1.0
O3B D:ADP404 2.6 85.0 1.0
F2 D:BEF405 2.7 83.3 1.0
OE2 D:GLU127 2.8 88.3 1.0
PB D:ADP404 3.0 86.0 1.0
NH2 E:ARG158 3.7 95.2 1.0
O2B D:ADP404 3.9 85.7 1.0
CD D:GLU127 3.9 87.5 1.0
CE D:LYS51 4.0 89.9 1.0
NH2 D:ARG215 4.0 0.4 1.0
OG1 D:THR52 4.2 92.2 1.0
NH1 E:ARG158 4.3 94.2 1.0
O3A D:ADP404 4.4 87.8 1.0
NZ D:LYS51 4.4 90.5 1.0
OE1 D:GLU127 4.4 86.7 1.0
CZ E:ARG158 4.5 94.6 1.0
OD2 D:ASP126 4.7 1.0 1.0
OD1 D:ASP126 4.8 0.9 1.0
O2A D:ADP404 4.9 89.1 1.0
CB D:THR52 4.9 93.9 1.0
CG2 E:THR154 4.9 95.8 1.0

Fluorine binding site 8 out of 18 in 3gli

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Fluorine binding site 8 out of 18 in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F405

b:83.3
occ:1.00
 F2 D:BEF405 0.0 83.3 1.0
BE D:BEF405 1.5 82.9 1.0
O3B D:ADP404 2.5 85.0 1.0
F3 D:BEF405 2.5 81.8 1.0
NH1 E:ARG158 2.5 94.2 1.0
F1 D:BEF405 2.7 82.7 1.0
NH2 D:ARG215 2.7 0.4 1.0
NH1 D:ARG215 3.3 0.5 1.0
CZ D:ARG215 3.4 0.2 1.0
CG2 E:THR154 3.4 95.8 1.0
CZ E:ARG158 3.4 94.6 1.0
NH2 E:ARG158 3.5 95.2 1.0
N D:GLY48 3.7 1.0 1.0
PB D:ADP404 3.9 86.0 1.0
CA D:ARG47 4.0 85.4 1.0
O1B D:ADP404 4.1 85.7 1.0
CB D:ARG47 4.2 85.3 1.0
CB E:THR154 4.2 95.1 1.0
MG D:MG414 4.2 84.0 1.0
C D:ARG47 4.3 87.0 1.0
CA D:GLY48 4.5 0.8 1.0
O3A D:ADP404 4.5 87.8 1.0
OE2 D:GLU127 4.6 88.3 1.0
NE E:ARG158 4.7 94.7 1.0
NE D:ARG215 4.7 0.9 1.0
OG E:SER157 4.7 87.4 1.0
CA E:THR154 4.8 95.0 1.0
O2B D:ADP404 4.9 85.7 1.0
O E:THR154 4.9 96.4 1.0
NZ D:LYS51 4.9 90.5 1.0

Fluorine binding site 9 out of 18 in 3gli

Go back to Fluorine Binding Sites List in 3gli
Fluorine binding site 9 out of 18 in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F405

b:81.8
occ:1.00
 F3 D:BEF405 0.0 81.8 1.0
BE D:BEF405 1.5 82.9 1.0
O3B D:ADP404 2.5 85.0 1.0
F2 D:BEF405 2.5 83.3 1.0
F1 D:BEF405 2.5 82.7 1.0
NZ D:LYS51 2.6 90.5 1.0
CE D:LYS51 3.0 89.9 1.0
CA D:ARG47 3.4 85.4 1.0
CG2 E:THR154 3.6 95.8 1.0
N D:GLY48 3.7 1.0 1.0
PB D:ADP404 3.7 86.0 1.0
CG2 D:THR157 3.8 86.5 1.0
O2B D:ADP404 3.9 85.7 1.0
OG1 D:THR157 4.0 85.8 1.0
N D:ARG47 4.0 84.8 1.0
C D:ARG47 4.1 87.0 1.0
O1B D:ADP404 4.2 85.7 1.0
CB D:ARG47 4.2 85.3 1.0
C D:THR46 4.4 92.9 1.0
OE2 D:GLU127 4.4 88.3 1.0
O D:THR46 4.4 94.0 1.0
CB D:THR157 4.5 85.6 1.0
CD D:LYS51 4.5 90.2 1.0
MG D:MG414 4.6 84.0 1.0
NH2 D:ARG215 4.7 0.4 1.0
O D:GLY45 4.8 82.2 1.0
O3A D:ADP404 4.8 87.8 1.0
CA D:THR157 4.9 85.7 1.0
CA D:GLY48 4.9 0.8 1.0
NH1 E:ARG158 4.9 94.2 1.0
CB E:THR154 5.0 95.1 1.0

Fluorine binding site 10 out of 18 in 3gli

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Fluorine binding site 10 out of 18 in the Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of the E. Coli Clamp Loader Bound to Primer-Template Dna and Psi Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F407

b:95.0
occ:1.00
 F1 G:BEF407 0.0 95.0 1.0
BE G:BEF407 1.5 94.5 1.0
MG G:MG415 2.1 92.4 1.0
O1B G:ADP406 2.4 95.0 1.0
F3 G:BEF407 2.6 94.1 1.0
O3B G:ADP406 2.6 94.0 1.0
F2 G:BEF407 2.6 94.3 1.0
NH2 H:ARG169 2.8 0.2 1.0
PB G:ADP406 3.1 95.0 1.0
OE2 G:GLU127 3.1 0.3 1.0
NH2 G:ARG215 3.3 91.2 1.0
NH1 G:ARG215 3.6 92.7 1.0
OE2 H:GLU144 3.7 0.5 1.0
CZ H:ARG169 3.9 99.4 1.0
CZ G:ARG215 3.9 92.2 1.0
O3A G:ADP406 3.9 96.0 1.0
O2A G:ADP406 4.2 97.3 1.0
NH1 H:ARG169 4.2 99.0 1.0
O2B G:ADP406 4.3 95.5 1.0
CD G:GLU127 4.4 0.0 1.0
CD H:GLU144 4.4 0.9 1.0
OE1 H:GLU144 4.4 0.7 1.0
OG1 G:THR52 4.6 0.9 1.0
PA G:ADP406 4.7 97.5 1.0
N G:GLY48 4.9 0.7 1.0
OE1 G:GLU127 4.9 0.6 1.0
NE H:ARG169 5.0 98.2 1.0
NZ G:LYS51 5.0 96.5 1.0

Reference:

K.R.Simonetta, S.L.Kazmirski, E.R.Goedken, A.J.Cantor, B.A.Kelch, R.Mcnally, S.N.Seyedin, D.L.Makino, M.O'donnell, J.Kuriyan. The Mechanism of Atp-Dependent Primer-Template Recognition By A Clamp Loader Complex. Cell(Cambridge,Mass.) V. 137 659 2009.
ISSN: ISSN 0092-8674
PubMed: 19450514
DOI: 10.1016/J.CELL.2009.03.044
Page generated: Wed Jul 31 18:55:18 2024

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