Fluorine in PDB 3u5z: Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog

The structure of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog, PDB code: 3u5z was solved by B.A.Kelch, D.L.Makino, M.O'donnell, J.Kuriyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.19 / 3.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.702, 239.177, 247.672, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 27.9

The structure of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog (pdb code 3u5z). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog, PDB code: 3u5z:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:F700 b:72.2 occ:1.00 F1 B:08T700 0.0 72.2 1.0 BE B:08T700 1.4 71.9 1.0 O1B B:08T700 2.3 72.7 1.0 F3 B:08T700 2.3 71.8 1.0 F2 B:08T700 2.3 71.4 1.0 O3B B:08T700 2.3 72.1 1.0 MG B:MG800 2.4 71.4 1.0 OE2 B:GLU108 2.5 72.2 1.0 PB B:08T700 2.8 72.6 1.0 CD B:GLU108 3.5 72.0 1.0 CG2 B:THR57 3.6 70.4 1.0 CE B:LYS56 3.7 70.0 1.0 NH2 C:ARG151 3.7 68.3 1.0 O2B B:08T700 3.7 73.1 1.0 OE1 B:GLU108 3.8 71.7 1.0 NH2 B:ARG205 3.9 68.6 1.0 NZ B:LYS56 3.9 69.9 1.0 O3A B:08T700 4.1 72.6 1.0 OG1 B:THR57 4.3 70.4 1.0 CG2 B:THR137 4.5 70.6 1.0 ND2 B:ASN139 4.6 68.7 1.0 CB B:THR57 4.6 70.7 1.0 OD1 B:ASN139 4.6 68.6 1.0 CZ C:ARG151 4.7 67.9 1.0 NH1 C:ARG151 4.7 67.7 1.0 N B:GLY53 4.7 68.8 1.0 CG B:GLU108 4.8 72.1 1.0 CZ B:ARG205 4.9 68.3 1.0 NH1 B:ARG205 5.0 68.1 1.0 N B:THR57 5.0 71.0 1.0

Fluorine binding site 2 out of 18 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:F700 b:71.4 occ:1.00 F2 B:08T700 0.0 71.4 1.0 BE B:08T700 1.4 71.9 1.0 F3 B:08T700 2.3 71.8 1.0 F1 B:08T700 2.3 72.2 1.0 O3B B:08T700 2.3 72.1 1.0 NH2 B:ARG205 2.7 68.6 1.0 NH1 C:ARG151 2.9 67.7 1.0 NH1 B:ARG205 3.0 68.1 1.0 NH2 C:ARG151 3.1 68.3 1.0 CZ B:ARG205 3.3 68.3 1.0 CZ C:ARG151 3.4 67.9 1.0 PB B:08T700 3.5 72.6 1.0 O1B B:08T700 3.6 72.7 1.0 N B:GLY53 3.6 68.8 1.0 MG B:MG800 3.8 71.4 1.0 CB B:PRO52 4.0 67.8 1.0 O3A B:08T700 4.1 72.6 1.0 CA B:PRO52 4.2 68.3 1.0 OE2 B:GLU108 4.3 72.2 1.0 C B:PRO52 4.4 68.5 1.0 CA B:GLY53 4.4 69.0 1.0 NE B:ARG205 4.6 68.3 1.0 ND2 B:ASN139 4.6 68.7 1.0 NE C:ARG151 4.7 67.7 1.0 CB C:PRO147 4.7 67.2 1.0 O2B B:08T700 4.8 73.1 1.0 NZ B:LYS56 4.8 69.9 1.0 CD B:GLU108 4.9 72.0 1.0 O C:PRO147 4.9 66.8 1.0 OE1 B:GLU108 4.9 71.7 1.0 OD1 B:ASN139 4.9 68.6 1.0

Fluorine binding site 3 out of 18 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:F700 b:71.8 occ:1.00 F3 B:08T700 0.0 71.8 1.0 BE B:08T700 1.4 71.9 1.0 F2 B:08T700 2.3 71.4 1.0 F1 B:08T700 2.3 72.2 1.0 O3B B:08T700 2.3 72.1 1.0 ND2 B:ASN139 2.7 68.7 1.0 NZ B:LYS56 3.2 69.9 1.0 CE B:LYS56 3.2 70.0 1.0 CA B:PRO52 3.5 68.3 1.0 N B:GLY53 3.6 68.8 1.0 CG B:ASN139 3.6 68.7 1.0 OD1 B:ASN139 3.6 68.6 1.0 PB B:08T700 3.7 72.6 1.0 CB B:PRO52 4.0 67.8 1.0 O1B B:08T700 4.0 72.7 1.0 C B:PRO52 4.1 68.5 1.0 OE2 B:GLU108 4.1 72.2 1.0 OG B:SER49 4.2 69.5 1.0 O2B B:08T700 4.3 73.1 1.0 OE1 B:GLU108 4.3 71.7 1.0 O B:SER51 4.5 69.1 1.0 N B:PRO52 4.6 68.3 1.0 CD B:GLU108 4.7 72.0 1.0 MG B:MG800 4.7 71.4 1.0 CA B:GLY53 4.7 69.0 1.0 CD B:LYS56 4.7 70.5 1.0 NH2 B:ARG205 4.8 68.6 1.0 NH1 B:ARG205 4.8 68.1 1.0 NH1 C:ARG151 4.8 67.7 1.0 CB B:SER49 4.9 69.9 1.0 O3A B:08T700 4.9 72.6 1.0 NH2 C:ARG151 4.9 68.3 1.0 C B:SER51 4.9 68.7 1.0 CB B:ASN139 5.0 68.9 1.0

Fluorine binding site 4 out of 18 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:F700 b:64.4 occ:1.00 F1 C:08T700 0.0 64.4 1.0 BE C:08T700 1.4 64.2 1.0 O1B C:08T700 2.2 64.5 1.0 MG C:MG800 2.3 63.5 1.0 F3 C:08T700 2.3 64.2 1.0 F2 C:08T700 2.3 64.0 1.0 O3B C:08T700 2.3 64.1 1.0 OE2 C:GLU108 2.5 77.0 1.0 PB C:08T700 2.8 64.3 1.0 CG2 C:THR57 3.5 62.1 1.0 OG1 C:THR57 3.5 61.8 1.0 O2B C:08T700 3.6 64.5 1.0 CD C:GLU108 3.7 77.1 1.0 NH2 D:ARG151 3.8 61.1 1.0 CE C:LYS56 3.8 61.8 1.0 NH2 C:ARG205 4.0 60.8 1.0 O3A C:08T700 4.1 64.2 1.0 CB C:THR57 4.2 62.1 1.0 O2A C:08T700 4.3 64.2 1.0 OE1 C:GLU108 4.3 77.2 1.0 CG2 C:THR137 4.3 62.4 1.0 NZ C:LYS56 4.5 61.7 1.0 OD1 C:ASN139 4.6 61.5 1.0 N C:THR57 4.6 62.2 1.0 CZ D:ARG151 4.7 60.9 1.0 NH1 D:ARG151 4.7 60.8 1.0 N C:GLY53 4.7 60.9 1.0 CB C:LYS56 4.9 62.2 1.0 CG C:GLU108 4.9 77.3 1.0 PA C:08T700 4.9 63.5 1.0 CD C:LYS56 5.0 62.1 1.0

Fluorine binding site 5 out of 18 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:F700 b:64.0 occ:1.00 F2 C:08T700 0.0 64.0 1.0 BE C:08T700 1.4 64.2 1.0 F3 C:08T700 2.2 64.2 1.0 F1 C:08T700 2.3 64.4 1.0 O3B C:08T700 2.3 64.1 1.0 NH1 D:ARG151 2.8 60.8 1.0 NH2 C:ARG205 2.9 60.8 1.0 NH2 D:ARG151 3.0 61.1 1.0 NH1 C:ARG205 3.1 60.5 1.0 CZ D:ARG151 3.2 60.9 1.0 CZ C:ARG205 3.4 60.6 1.0 MG C:MG800 3.5 63.5 1.0 PB C:08T700 3.6 64.3 1.0 O1B C:08T700 3.7 64.5 1.0 N C:GLY53 3.8 60.9 1.0 OE2 C:GLU108 3.8 77.0 1.0 CB C:PRO52 4.1 60.8 1.0 CA C:PRO52 4.4 60.9 1.0 O2A C:08T700 4.4 64.2 1.0 NE D:ARG151 4.5 60.9 1.0 O3A C:08T700 4.5 64.2 1.0 OD1 C:ASN139 4.5 61.5 1.0 CA C:GLY53 4.6 60.8 1.0 C C:PRO52 4.6 60.8 1.0 O2B C:08T700 4.7 64.5 1.0 CB D:PRO147 4.7 61.0 1.0 NE C:ARG205 4.8 60.4 1.0 CD C:GLU108 4.8 77.1 1.0 O D:PRO147 4.9 60.5 1.0 OG1 C:THR57 5.0 61.8 1.0

Fluorine binding site 6 out of 18 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:F700 b:64.2 occ:1.00 F3 C:08T700 0.0 64.2 1.0 BE C:08T700 1.4 64.2 1.0 F2 C:08T700 2.2 64.0 1.0 F1 C:08T700 2.3 64.4 1.0 O3B C:08T700 2.3 64.1 1.0 OD1 C:ASN139 2.8 61.5 1.0 CE C:LYS56 3.3 61.8 1.0 N C:GLY53 3.4 60.9 1.0 CA C:PRO52 3.4 60.9 1.0 PB C:08T700 3.6 64.3 1.0 NZ C:LYS56 3.6 61.7 1.0 CB C:PRO52 3.8 60.8 1.0 OE2 C:GLU108 3.8 77.0 1.0 CG C:ASN139 3.8 61.7 1.0 O1B C:08T700 3.8 64.5 1.0 O2B C:08T700 3.9 64.5 1.0 C C:PRO52 3.9 60.8 1.0 ND2 C:ASN139 4.1 61.7 1.0 OG C:SER49 4.4 0.7 1.0 MG C:MG800 4.4 63.5 1.0 CA C:GLY53 4.6 60.8 1.0 N C:PRO52 4.6 61.0 1.0 CD C:GLU108 4.6 77.1 1.0 OE1 C:GLU108 4.7 77.2 1.0 NH1 D:ARG151 4.7 60.8 1.0 CB C:SER49 4.8 0.7 1.0 NH1 C:ARG205 4.8 60.5 1.0 CD C:LYS56 4.8 62.1 1.0 NH2 C:ARG205 4.8 60.8 1.0 NH2 D:ARG151 4.8 61.1 1.0 O C:SER51 4.8 63.0 1.0 O3A C:08T700 4.9 64.2 1.0

Fluorine binding site 7 out of 18 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:F700 b:64.4 occ:1.00 F1 D:08T700 0.0 64.4 1.0 BE D:08T700 1.4 64.7 1.0 F2 D:08T700 2.3 65.1 1.0 OE2 D:GLU108 2.3 89.7 1.0 F3 D:08T700 2.3 64.8 1.0 O3B D:08T700 2.4 64.5 1.0 O1B D:08T700 2.5 64.0 1.0 MG D:MG800 2.7 63.9 1.0 PB D:08T700 3.0 64.1 1.0 CE D:LYS56 3.4 60.7 1.0 CG2 D:THR57 3.4 70.7 1.0 CD D:GLU108 3.5 89.8 1.0 OG1 D:THR57 3.8 70.8 1.0 CG2 D:THR137 3.9 60.9 1.0 OE1 D:GLU108 4.0 89.8 1.0 O2B D:08T700 4.0 63.7 1.0 NZ D:LYS56 4.2 60.6 1.0 OD1 D:ASN139 4.2 67.3 1.0 NH2 E:ARG151 4.2 62.9 1.0 O3A D:08T700 4.3 64.3 1.0 CB D:THR57 4.3 70.6 1.0 CD D:LYS56 4.5 60.3 1.0 CB D:LYS56 4.6 60.2 1.0 N D:THR57 4.6 60.5 1.0 NH2 D:ARG205 4.6 62.3 1.0 CG D:GLU108 4.7 90.1 1.0 ND2 D:ASN139 4.8 67.8 1.0 CG D:ASN139 4.9 67.5 1.0 N D:GLY53 4.9 65.4 1.0

Fluorine binding site 8 out of 18 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:F700 b:65.1 occ:1.00 F2 D:08T700 0.0 65.1 1.0 BE D:08T700 1.4 64.7 1.0 F3 D:08T700 2.2 64.8 1.0 F1 D:08T700 2.3 64.4 1.0 O3B D:08T700 2.3 64.5 1.0 NH2 E:ARG151 2.3 62.9 1.0 MG D:MG800 2.8 63.9 1.0 NH1 E:ARG151 2.8 63.1 1.0 NH2 D:ARG205 2.9 62.3 1.0 CZ E:ARG151 3.0 63.2 1.0 OE2 D:GLU108 3.2 89.7 1.0 PB D:08T700 3.5 64.1 1.0 O1B D:08T700 3.6 64.0 1.0 CZ D:ARG205 3.8 62.6 1.0 NH1 D:ARG205 3.9 62.6 1.0 O3A D:08T700 4.1 64.3 1.0 CD D:GLU108 4.2 89.8 1.0 NE E:ARG151 4.3 63.8 1.0 OG1 D:THR57 4.4 70.8 1.0 OE1 E:GLU126 4.5 62.8 1.0 N D:GLY53 4.5 65.4 1.0 OD1 D:ASN139 4.8 67.3 1.0 OE1 D:GLU108 4.8 89.8 1.0 O2B D:08T700 4.8 63.7 1.0 OE2 E:GLU126 4.8 62.7 1.0 CG2 D:THR57 4.8 70.7 1.0 CD E:GLU126 4.9 63.0 1.0 CB D:PRO52 5.0 62.5 1.0

Fluorine binding site 9 out of 18 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:F700 b:64.8 occ:1.00 F3 D:08T700 0.0 64.8 1.0 BE D:08T700 1.4 64.7 1.0 F2 D:08T700 2.2 65.1 1.0 O3B D:08T700 2.3 64.5 1.0 F1 D:08T700 2.3 64.4 1.0 OD1 D:ASN139 2.8 67.3 1.0 CA D:PRO52 3.5 61.9 1.0 N D:GLY53 3.5 65.4 1.0 CB D:PRO52 3.6 62.5 1.0 OE2 D:GLU108 3.7 89.7 1.0 PB D:08T700 3.7 64.1 1.0 CG D:ASN139 3.8 67.5 1.0 CE D:LYS56 3.8 60.7 1.0 ND2 D:ASN139 4.0 67.8 1.0 NZ D:LYS56 4.1 60.6 1.0 C D:PRO52 4.1 61.7 1.0 NH1 E:ARG151 4.1 63.1 1.0 O1B D:08T700 4.2 64.0 1.0 NH2 E:ARG151 4.3 62.9 1.0 O2B D:08T700 4.4 63.7 1.0 MG D:MG800 4.4 63.9 1.0 NH2 D:ARG205 4.4 62.3 1.0 CD D:GLU108 4.5 89.8 1.0 OE1 D:GLU108 4.5 89.8 1.0 NH1 D:ARG205 4.5 62.6 1.0 CA D:GLY53 4.7 65.3 1.0 CZ E:ARG151 4.7 63.2 1.0 CB E:PRO147 4.7 63.4 1.0 N D:PRO52 4.7 62.0 1.0 OG D:SER49 4.8 0.5 1.0 O3A D:08T700 4.8 64.3 1.0

Fluorine binding site 10 out of 18 in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ L:F700 b:71.9 occ:1.00 F1 L:08T700 0.0 71.9 1.0 BE L:08T700 1.4 71.8 1.0 F3 L:08T700 2.2 71.9 1.0 F2 L:08T700 2.3 71.3 1.0 O3B L:08T700 2.4 72.1 1.0 OE2 L:GLU108 2.4 0.1 1.0 O1B L:08T700 2.6 72.0 1.0 MG L:MG800 2.7 70.9 1.0 PB L:08T700 3.0 72.6 1.0 CD L:GLU108 3.3 99.9 1.0 OE1 L:GLU108 3.6 99.8 1.0 NH2 M:ARG151 3.7 67.9 1.0 CE L:LYS56 3.7 82.3 1.0 O2B L:08T700 3.8 73.0 1.0 CG2 L:THR57 3.9 81.0 1.0 NZ L:LYS56 3.9 82.3 1.0 NH2 L:ARG205 4.0 68.5 1.0 OD1 L:ASN139 4.3 68.6 1.0 NH1 M:ARG151 4.3 67.6 1.0 ND2 L:ASN139 4.3 69.0 1.0 O3A L:08T700 4.4 72.8 1.0 CZ M:ARG151 4.5 67.6 1.0 CG2 L:THR137 4.5 70.2 1.0 OG1 L:THR57 4.6 81.0 1.0 N L:GLY53 4.7 69.2 1.0 O2A L:08T700 4.7 72.3 1.0 CG L:GLU108 4.7 99.8 1.0 CG L:ASN139 4.7 68.9 1.0 NH1 L:ARG205 4.9 68.3 1.0 CZ L:ARG205 4.9 68.4 1.0 CB L:THR57 4.9 81.3 1.0

B.A.Kelch, D.L.Makino, M.O'donnell, J.Kuriyan. How A Dna Polymerase Clamp Loader Opens A Sliding Clamp. Science V. 334 1675 2011.
ISSN: ISSN 0036-8075
PubMed: 22194570
DOI: 10.1126/SCIENCE.1211884