Fluorine in PDB 8unf: Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna

The structure of Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Fluorine atom in the Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna (pdb code 8unf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna, PDB code: 8unf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in the Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:F401 b:60.9 occ:1.00 F1 D:08T401 0.0 60.9 1.0 BE D:08T401 1.5 56.6 1.0 MG D:MG402 2.0 22.0 1.0 O1B D:08T401 2.2 55.8 1.0 F2 D:08T401 2.4 53.0 1.0 O3B D:08T401 2.4 54.9 1.0 F3 D:08T401 2.5 58.8 1.0 OE2 D:GLU108 2.6 35.6 1.0 PB D:08T401 2.8 46.0 1.0 O2B D:08T401 3.5 58.4 1.0 CD D:GLU108 3.6 40.5 1.0 CE D:LYS56 3.7 30.4 1.0 NH1 E:ARG151 3.9 36.6 1.0 OG1 D:THR57 4.0 26.8 1.0 NH2 E:ARG151 4.1 35.5 1.0 OE1 D:GLU108 4.2 41.2 1.0 O3A D:08T401 4.2 52.0 1.0 NZ D:LYS56 4.2 30.5 1.0 NH2 D:ARG205 4.4 51.2 1.0 CZ E:ARG151 4.4 28.8 1.0 O2A D:08T401 4.5 48.3 1.0 CG D:GLU108 4.7 45.2 1.0 OD1 D:ASN139 4.8 40.9 1.0 NH1 D:ARG205 4.8 53.4 1.0 OE1 E:GLU126 4.9 40.3 1.0 ND2 D:ASN139 5.0 34.1 1.0 CB D:THR57 5.0 17.1 1.0

Fluorine binding site 2 out of 9 in the Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:F401 b:53.0 occ:1.00 F2 D:08T401 0.0 53.0 1.0 BE D:08T401 1.4 56.6 1.0 NH1 E:ARG151 2.3 36.6 1.0 NH2 D:ARG205 2.4 51.2 1.0 F3 D:08T401 2.4 58.8 1.0 F1 D:08T401 2.4 60.9 1.0 O3B D:08T401 2.5 54.9 1.0 CZ E:ARG151 3.2 28.8 1.0 CZ D:ARG205 3.5 46.7 1.0 CB D:PRO52 3.6 34.2 1.0 NH2 E:ARG151 3.7 35.5 1.0 O1B D:08T401 3.8 55.8 1.0 PB D:08T401 3.8 46.0 1.0 NH1 D:ARG205 3.8 53.4 1.0 N D:GLY53 4.1 32.5 1.0 MG D:MG402 4.1 22.0 1.0 CA D:PRO52 4.1 25.5 1.0 NE E:ARG151 4.2 15.4 1.0 OE2 D:GLU108 4.3 35.6 1.0 CB E:PRO147 4.3 20.8 1.0 CD E:ARG151 4.5 17.1 1.0 OD1 D:ASN139 4.6 40.9 1.0 C D:PRO52 4.6 35.7 1.0 NE D:ARG205 4.6 44.1 1.0 O3A D:08T401 4.7 52.0 1.0 CA E:PRO147 4.8 14.5 1.0 ND2 D:ASN139 4.8 34.1 1.0 CD D:GLU108 4.8 40.5 1.0 O2B D:08T401 4.8 58.4 1.0 O E:PRO147 5.0 43.9 1.0 CG D:PRO52 5.0 25.2 1.0 OE1 D:GLU108 5.0 41.2 1.0 NZ D:LYS56 5.0 30.5 1.0

Fluorine binding site 3 out of 9 in the Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:F401 b:58.8 occ:1.00 F3 D:08T401 0.0 58.8 1.0 BE D:08T401 1.5 56.6 1.0 F2 D:08T401 2.4 53.0 1.0 F1 D:08T401 2.5 60.9 1.0 O3B D:08T401 2.6 54.9 1.0 NZ D:LYS56 2.8 30.5 1.0 ND2 D:ASN139 2.9 34.1 1.0 CE D:LYS56 3.2 30.4 1.0 CA D:PRO52 3.3 25.5 1.0 CB D:PRO52 3.5 34.2 1.0 OD1 D:ASN139 3.5 40.9 1.0 CG D:ASN139 3.6 30.4 1.0 PB D:08T401 3.8 46.0 1.0 N D:GLY53 3.9 32.5 1.0 OE2 D:GLU108 4.0 35.6 1.0 O2B D:08T401 4.1 58.4 1.0 C D:PRO52 4.1 35.7 1.0 O1B D:08T401 4.2 55.8 1.0 N D:PRO52 4.3 21.3 1.0 NH1 E:ARG151 4.4 36.6 1.0 NH2 D:ARG205 4.4 51.2 1.0 MG D:MG402 4.5 22.0 1.0 OE1 D:GLU108 4.5 41.2 1.0 CD D:LYS56 4.7 25.1 1.0 CD D:GLU108 4.7 40.5 1.0 O D:SER51 4.7 35.8 1.0 CG D:PRO52 4.8 25.2 1.0 C D:SER51 4.9 30.1 1.0 CB D:ASN139 5.0 26.1 1.0 O D:SER49 5.0 35.0 1.0

Fluorine binding site 4 out of 9 in the Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:F401 b:60.6 occ:1.00 F1 C:08T401 0.0 60.6 1.0 BE C:08T401 1.5 57.2 1.0 MG C:MG402 1.8 23.3 1.0 O1B C:08T401 2.1 53.7 1.0 F2 C:08T401 2.4 62.0 1.0 OE2 C:GLU108 2.5 35.1 1.0 O3B C:08T401 2.5 47.6 1.0 F3 C:08T401 2.5 56.4 1.0 PB C:08T401 2.9 41.0 1.0 NH2 D:ARG151 3.3 48.1 1.0 OG1 C:THR57 3.5 33.7 1.0 CD C:GLU108 3.5 36.4 1.0 NZ C:LYS56 3.8 51.5 1.0 O2B C:08T401 3.9 62.9 1.0 CE C:LYS56 3.9 50.1 1.0 NH2 C:ARG205 4.0 54.5 1.0 O3A C:08T401 4.0 54.1 1.0 OE1 C:GLU108 4.1 36.8 1.0 CG2 C:THR137 4.3 23.6 1.0 CZ D:ARG151 4.4 48.6 1.0 OD1 C:ASP107 4.5 39.5 1.0 CG C:GLU108 4.5 30.5 1.0 CB C:THR57 4.6 29.2 1.0 OD1 C:ASN139 4.7 31.9 1.0 O1A C:08T401 4.7 46.5 1.0 NH1 D:ARG151 4.8 57.0 1.0 N C:THR57 4.8 31.4 1.0 PA C:08T401 5.0 41.7 1.0

Fluorine binding site 5 out of 9 in the Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:F401 b:62.0 occ:1.00 F2 C:08T401 0.0 62.0 1.0 BE C:08T401 1.4 57.2 1.0 F3 C:08T401 2.4 56.4 1.0 F1 C:08T401 2.4 60.6 1.0 NH2 D:ARG151 2.4 48.1 1.0 O3B C:08T401 2.5 47.6 1.0 NH2 C:ARG205 2.7 54.5 1.0 NH1 D:ARG151 2.8 57.0 1.0 CZ D:ARG151 3.0 48.6 1.0 NH1 C:ARG205 3.5 53.0 1.0 CZ C:ARG205 3.5 44.4 1.0 PB C:08T401 3.6 41.0 1.0 O1B C:08T401 3.6 53.7 1.0 CB C:PRO52 3.9 25.5 1.0 MG C:MG402 4.0 23.3 1.0 O3A C:08T401 4.2 54.1 1.0 N C:GLY53 4.2 31.4 1.0 OE2 C:GLU108 4.2 35.1 1.0 NE D:ARG151 4.2 42.7 1.0 CA C:PRO52 4.3 18.2 1.0 CB D:PRO147 4.5 22.7 1.0 OD1 C:ASN139 4.6 31.9 1.0 NZ C:LYS56 4.6 51.5 1.0 CD C:GLU108 4.8 36.4 1.0 NE C:ARG205 4.8 35.4 1.0 C C:PRO52 4.8 30.6 1.0 O D:PRO147 4.8 44.8 1.0 O2B C:08T401 4.9 62.9 1.0 CA D:PRO147 4.9 19.3 1.0 OE1 C:GLU108 5.0 36.8 1.0

Fluorine binding site 6 out of 9 in the Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:F401 b:56.4 occ:1.00 F3 C:08T401 0.0 56.4 1.0 BE C:08T401 1.5 57.2 1.0 F2 C:08T401 2.4 62.0 1.0 F1 C:08T401 2.5 60.6 1.0 O3B C:08T401 2.6 47.6 1.0 OD1 C:ASN139 2.9 31.9 1.0 NZ C:LYS56 3.0 51.5 1.0 ND2 C:ASN139 3.1 34.8 1.0 CE C:LYS56 3.2 50.1 1.0 CG C:ASN139 3.3 29.8 1.0 OE2 C:GLU108 3.5 35.1 1.0 CA C:PRO52 3.9 18.2 1.0 OE1 C:GLU108 4.0 36.8 1.0 PB C:08T401 4.0 41.0 1.0 CB C:PRO52 4.0 25.5 1.0 CD C:GLU108 4.1 36.4 1.0 O1B C:08T401 4.1 53.7 1.0 MG C:MG402 4.3 23.3 1.0 NH2 D:ARG151 4.3 48.1 1.0 N C:GLY53 4.5 31.4 1.0 CD C:LYS56 4.7 45.0 1.0 O2B C:08T401 4.7 62.9 1.0 NH1 D:ARG151 4.7 57.0 1.0 CB C:ASN139 4.7 19.5 1.0 C C:PRO52 4.8 30.6 1.0 CB D:PRO147 4.8 22.7 1.0 N C:PRO52 4.9 20.1 1.0 NH2 C:ARG205 4.9 54.5 1.0 CG D:PRO147 5.0 26.0 1.0

Fluorine binding site 7 out of 9 in the Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:50.3 occ:1.00 F1 B:08T401 0.0 50.3 1.0 BE B:08T401 1.5 40.0 1.0 MG B:MG402 1.9 19.8 1.0 O1B B:08T401 2.2 35.9 1.0 OE2 B:GLU108 2.3 30.4 1.0 F2 B:08T401 2.4 37.7 1.0 O3B B:08T401 2.5 31.3 1.0 F3 B:08T401 2.5 39.9 1.0 PB B:08T401 2.9 34.9 1.0 CD B:GLU108 3.3 37.9 1.0 NH2 C:ARG151 3.4 25.5 1.0 OG1 B:THR57 3.6 31.7 1.0 OE1 B:GLU108 3.8 37.7 1.0 O2B B:08T401 3.9 45.8 1.0 CE B:LYS56 3.9 26.5 1.0 O3A B:08T401 4.1 37.9 1.0 NH2 B:ARG205 4.3 24.1 1.0 CG B:GLU108 4.4 37.3 1.0 CZ C:ARG151 4.5 26.1 1.0 NZ B:LYS56 4.5 30.1 1.0 OD1 B:ASN139 4.6 36.4 1.0 NH1 C:ARG151 4.6 31.1 1.0 ND2 B:ASN139 4.8 35.0 1.0 CB B:THR57 4.8 27.8 1.0 O1A B:08T401 4.8 33.3 1.0 N B:THR57 4.9 23.8 1.0 OD2 B:ASP107 5.0 38.9 1.0 OG1 B:THR137 5.0 34.4 1.0

Fluorine binding site 8 out of 9 in the Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:37.7 occ:1.00 F2 B:08T401 0.0 37.7 1.0 BE B:08T401 1.5 40.0 1.0 F3 B:08T401 2.4 39.9 1.0 F1 B:08T401 2.4 50.3 1.0 O3B B:08T401 2.5 31.3 1.0 NH1 C:ARG151 2.7 31.1 1.0 NH2 C:ARG151 2.7 25.5 1.0 CZ C:ARG151 3.0 26.1 1.0 NH2 B:ARG205 3.1 24.1 1.0 O1B B:08T401 3.6 35.9 1.0 PB B:08T401 3.6 34.9 1.0 NH1 B:ARG205 3.6 25.5 1.0 CZ B:ARG205 3.8 17.7 1.0 CB B:PRO52 3.9 24.6 1.0 N B:GLY53 4.0 28.9 1.0 MG B:MG402 4.0 19.8 1.0 OE2 B:GLU108 4.1 30.4 1.0 CA B:PRO52 4.2 22.5 1.0 O3A B:08T401 4.2 37.9 1.0 CB C:PRO147 4.3 25.3 1.0 NE C:ARG151 4.3 14.0 1.0 OD1 B:ASN139 4.4 36.4 1.0 CD B:GLU108 4.6 37.9 1.0 OE1 B:GLU108 4.6 37.7 1.0 C B:PRO52 4.6 32.7 1.0 CA C:PRO147 4.7 20.3 1.0 O C:PRO147 4.7 34.1 1.0 ND2 B:ASN139 4.8 35.0 1.0 CA B:GLY53 4.9 25.1 1.0 O2B B:08T401 4.9 45.8 1.0

Fluorine binding site 9 out of 9 in the Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:39.9 occ:1.00 F3 B:08T401 0.0 39.9 1.0 BE B:08T401 1.5 40.0 1.0 F2 B:08T401 2.4 37.7 1.0 F1 B:08T401 2.5 50.3 1.0 ND2 B:ASN139 2.5 35.0 1.0 O3B B:08T401 2.6 31.3 1.0 OD1 B:ASN139 2.9 36.4 1.0 CG B:ASN139 3.1 33.0 1.0 CE B:LYS56 3.2 26.5 1.0 NZ B:LYS56 3.2 30.1 1.0 CA B:PRO52 3.7 22.5 1.0 OE2 B:GLU108 3.7 30.4 1.0 OE1 B:GLU108 3.9 37.7 1.0 PB B:08T401 4.0 34.9 1.0 CB B:PRO52 4.0 24.6 1.0 O1B B:08T401 4.2 35.9 1.0 CD B:GLU108 4.2 37.9 1.0 N B:GLY53 4.2 28.9 1.0 MG B:MG402 4.3 19.8 1.0 C B:PRO52 4.5 32.7 1.0 CB B:ASN139 4.5 23.7 1.0 NH2 C:ARG151 4.6 25.5 1.0 N B:PRO52 4.7 22.1 1.0 CB C:PRO147 4.7 25.3 1.0 O2B B:08T401 4.7 45.8 1.0 CD B:LYS56 4.7 19.1 1.0 NH1 C:ARG151 4.7 31.1 1.0 O B:SER51 4.8 37.7 1.0 O B:SER49 4.9 27.6 1.0 CG C:PRO147 5.0 29.1 1.0

K.Marcus, Y.Huang, S.Subramanian, L.C.Gee, K.Gorday, S.Ghaffari-Kashani, R.X.Luo, L.Zhang, M.O'donnell, S.Subramanian, J.Kuriyan. Autoinhibition of A Clamp-Loader Atpase Revealed By Deep Mutagenesis and Cryo-Em Nature Structural & 2023MOLECULAR Biology.