Magnesium 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:

Fluorine

(F)

9 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and Dna, PDB code: 8unf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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 E:Mg402 b:30.6 occ:1.00 O1A E:ADP401 2.2 49.5 1.0 O1B E:ADP401 2.4 60.9 1.0 OG1 E:THR57 2.5 38.0 1.0 CB E:THR57 3.2 27.7 1.0 PA E:ADP401 3.5 47.1 1.0 PB E:ADP401 3.5 63.8 1.0 OD2 E:ASP107 3.7 43.1 1.0 O3B E:ADP401 3.9 60.4 1.0 CG2 E:THR57 3.9 34.1 1.0 OD1 E:ASP107 4.0 42.3 1.0 O3A E:ADP401 4.0 48.9 1.0 OE2 E:GLU108 4.1 51.6 1.0 NZ E:LYS56 4.2 34.2 1.0 O2A E:ADP401 4.3 51.3 1.0 CG E:ASP107 4.3 37.2 1.0 CA E:THR57 4.5 24.2 1.0 N E:THR57 4.6 36.1 1.0 O5' E:ADP401 4.7 53.8 1.0 O2B E:ADP401 4.9 49.4 1.0

Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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:Mg402 b:22.0 occ:1.00 F1 D:08T401 2.0 60.9 1.0 O1B D:08T401 2.1 55.8 1.0 OG1 D:THR57 2.2 26.8 1.0 OE2 D:GLU108 2.5 35.6 1.0 OD2 D:ASP107 3.4 46.3 1.0 OD1 D:ASP107 3.4 44.1 1.0 CB D:THR57 3.4 17.1 1.0 BE D:08T401 3.4 56.6 1.0 PB D:08T401 3.5 46.0 1.0 CD D:GLU108 3.6 40.5 1.0 CG D:ASP107 3.8 37.5 1.0 OE1 E:GLU126 3.9 40.3 1.0 O3B D:08T401 3.9 54.9 1.0 NH2 E:ARG151 4.1 35.5 1.0 F2 D:08T401 4.1 53.0 1.0 N D:THR57 4.2 28.0 1.0 O2A D:08T401 4.2 48.3 1.0 OG1 D:THR137 4.2 35.0 1.0 O2B D:08T401 4.2 58.4 1.0 CG D:GLU108 4.2 45.2 1.0 CA D:THR57 4.3 13.8 1.0 CG2 D:THR57 4.4 22.3 1.0 F3 D:08T401 4.5 58.8 1.0 OE1 D:GLU108 4.6 41.2 1.0 O3A D:08T401 4.7 52.0 1.0 CE D:LYS56 4.8 30.4 1.0 CZ E:ARG151 4.9 28.8 1.0 NH1 E:ARG151 4.9 36.6 1.0 PA D:08T401 4.9 39.5 1.0 CD E:GLU126 4.9 40.0 1.0

Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg 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 C:Mg402 b:23.3 occ:1.00 F1 C:08T401 1.8 60.6 1.0 OG1 C:THR57 1.9 33.7 1.0 O1B C:08T401 2.2 53.7 1.0 OE2 C:GLU108 2.5 35.1 1.0 OD1 C:ASP107 2.9 39.5 1.0 CB C:THR57 3.2 29.2 1.0 BE C:08T401 3.3 57.2 1.0 CD C:GLU108 3.6 36.4 1.0 PB C:08T401 3.7 41.0 1.0 CG2 C:THR137 3.8 23.6 1.0 NH2 D:ARG151 3.8 48.1 1.0 CG C:ASP107 4.0 31.2 1.0 F2 C:08T401 4.0 62.0 1.0 O3B C:08T401 4.0 47.6 1.0 OE1 D:GLU126 4.0 42.5 1.0 CG C:GLU108 4.0 30.5 1.0 CG2 C:THR57 4.1 39.8 1.0 N C:THR57 4.1 31.4 1.0 CA C:THR57 4.2 20.0 1.0 F3 C:08T401 4.3 56.4 1.0 OD2 C:ASP107 4.3 36.4 1.0 O1A C:08T401 4.4 46.5 1.0 O2B C:08T401 4.5 62.9 1.0 OE1 C:GLU108 4.6 36.8 1.0 O3A C:08T401 4.7 54.1 1.0 NH2 C:ARG205 4.8 54.5 1.0 CB C:THR137 4.9 18.8 1.0 CD D:GLU126 4.9 37.1 1.0

Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg 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 B:Mg402 b:19.8 occ:1.00 F1 B:08T401 1.9 50.3 1.0 OE2 B:GLU108 2.0 30.4 1.0 OG1 B:THR57 2.1 31.7 1.0 O1B B:08T401 2.4 35.9 1.0 CD B:GLU108 3.1 37.9 1.0 OD2 B:ASP107 3.2 38.9 1.0 OD1 B:ASP107 3.3 38.1 1.0 BE B:08T401 3.4 40.0 1.0 CB B:THR57 3.4 27.8 1.0 CG B:ASP107 3.6 33.3 1.0 CG B:GLU108 3.7 37.3 1.0 NH2 C:ARG151 3.8 25.5 1.0 PB B:08T401 3.8 34.9 1.0 OG1 B:THR137 3.9 34.4 1.0 F2 B:08T401 4.0 37.7 1.0 O3B B:08T401 4.1 31.3 1.0 OE1 B:GLU108 4.1 37.7 1.0 OE1 C:GLU126 4.2 39.0 1.0 CG2 B:THR57 4.2 30.8 1.0 N B:THR57 4.3 23.8 1.0 F3 B:08T401 4.3 39.9 1.0 CA B:THR57 4.4 21.2 1.0 O1A B:08T401 4.5 33.3 1.0 O2B B:08T401 4.6 45.8 1.0 CB B:THR137 4.8 19.8 1.0 O3A B:08T401 4.9 37.9 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.