Magnesium in PDB 8uh7: 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: 8uh7 was solved by C.L.Gee, K.Marcus, B.A.Kelch, D.L.Makino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.65 / 2.63
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	93.351, 118.325, 132.882, 90, 102.05, 90
R / Rfree (%)	19.3 / 24.5

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:

Fluorine

(F)

9 atoms

The binding sites of Magnesium atom in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog (pdb code 8uh7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of T4 Bacteriophage Clamp Loader Bound to the T4 Clamp, Primer-Template Dna, and Atp Analog, PDB code: 8uh7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg402 b:22.4 occ:1.00 F1 B:08T401 2.0 49.5 1.0 OG1 B:THR57 2.2 33.1 1.0 O2B B:08T401 2.5 24.9 1.0 OE2 B:GLU108 2.6 44.3 1.0 OD2 B:ASP107 3.4 45.8 1.0 CB B:THR57 3.5 26.2 1.0 BE B:08T401 3.5 39.5 1.0 OD1 B:ASP107 3.5 37.1 1.0 NH2 C:ARG151 3.6 40.5 1.0 CD B:GLU108 3.6 50.6 1.0 CG B:ASP107 3.9 44.0 1.0 PB B:08T401 3.9 28.8 1.0 O1A B:08T401 3.9 27.5 1.0 OE1 C:GLU126 4.0 42.1 1.0 F2 B:08T401 4.0 28.4 1.0 CG B:GLU108 4.0 43.0 1.0 O3B B:08T401 4.1 35.3 1.0 CG2 B:THR57 4.2 24.9 1.0 N B:THR57 4.4 26.3 1.0 NH2 B:ARG205 4.5 38.5 1.0 F3 B:08T401 4.5 37.3 1.0 CA B:THR57 4.5 24.6 1.0 OE2 C:GLU126 4.6 38.3 1.0 OE1 B:GLU108 4.7 34.3 1.0 CD C:GLU126 4.7 34.6 1.0 OG1 B:THR137 4.8 46.9 1.0 O3A B:08T401 4.8 19.0 1.0 CZ C:ARG151 4.9 25.9 1.0 PA B:08T401 4.9 25.9 1.0 O1B B:08T401 4.9 21.8 1.0

Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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 C:Mg402 b:12.7 occ:1.00 O2B C:08T401 2.0 17.9 1.0 F1 C:08T401 2.1 15.3 1.0 OG1 C:THR57 2.1 26.3 1.0 OE2 C:GLU108 2.6 40.8 1.0 CB C:THR57 3.3 17.2 1.0 NH2 D:ARG151 3.4 20.6 1.0 BE C:08T401 3.5 18.0 1.0 PB C:08T401 3.5 16.2 1.0 O1A C:08T401 3.6 15.3 1.0 OD1 C:ASP107 3.7 20.6 1.0 CD C:GLU108 3.8 44.1 1.0 OD2 C:ASP107 3.8 30.5 1.0 OE1 D:GLU126 3.9 35.5 1.0 O3B C:08T401 3.9 10.2 1.0 F2 C:08T401 4.1 12.3 1.0 CG2 C:THR137 4.1 19.1 1.0 CG2 C:THR57 4.2 15.6 1.0 CG C:ASP107 4.2 19.1 1.0 N C:THR57 4.2 17.7 1.0 NH2 C:ARG205 4.3 18.6 1.0 CA C:THR57 4.3 13.9 1.0 O3A C:08T401 4.4 15.5 1.0 O1B C:08T401 4.5 18.9 1.0 PA C:08T401 4.5 22.0 1.0 F3 C:08T401 4.5 18.0 1.0 OE2 D:GLU126 4.5 22.4 1.0 CG C:GLU108 4.6 27.5 1.0 CD D:GLU126 4.6 21.6 1.0 CZ D:ARG151 4.7 12.4 1.0 OE1 C:GLU108 4.7 31.9 1.0 O2A C:08T401 4.9 24.7 1.0

Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg 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 D:Mg402 b:11.3 occ:1.00 F1 D:08T401 2.0 21.4 1.0 OE2 D:GLU108 2.2 53.2 1.0 O2B D:08T401 2.3 25.2 1.0 OG1 D:THR57 2.5 22.9 1.0 NH2 E:ARG151 3.0 25.2 1.0 O D:HOH508 3.3 23.4 1.0 CD D:GLU108 3.4 62.7 1.0 BE D:08T401 3.5 21.5 1.0 OD2 D:ASP107 3.5 39.5 1.0 OE1 E:GLU126 3.5 23.6 1.0 CB D:THR57 3.7 12.6 1.0 PB D:08T401 3.7 24.9 1.0 O1A D:08T401 3.8 19.2 1.0 OD1 D:ASP107 3.8 30.8 1.0 O3B D:08T401 4.0 16.5 1.0 CG D:ASP107 4.1 30.0 1.0 NH2 D:ARG205 4.1 27.7 1.0 F2 D:08T401 4.2 18.7 1.0 OE1 D:GLU108 4.3 54.5 1.0 CG D:GLU108 4.3 35.2 1.0 CZ E:ARG151 4.3 24.3 1.0 F3 D:08T401 4.4 18.3 1.0 CG2 D:THR57 4.4 16.6 1.0 CD E:GLU126 4.5 32.3 1.0 O3A D:08T401 4.6 15.2 1.0 N D:THR57 4.7 11.5 1.0 O1B D:08T401 4.7 30.8 1.0 PA D:08T401 4.8 14.7 1.0 CA D:THR57 4.8 14.6 1.0 OG1 D:THR137 5.0 33.3 1.0

Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg 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 E:Mg402 b:20.4 occ:1.00 OG1 E:THR57 2.5 42.5 1.0 O2B E:ADP401 2.6 42.0 1.0 O1A E:ADP401 2.6 43.4 1.0 O3B E:ADP401 3.4 46.0 1.0 PB E:ADP401 3.5 40.5 1.0 CB E:THR57 3.6 21.6 1.0 OD2 E:ASP107 3.7 44.8 1.0 OE2 E:GLU108 3.8 60.1 1.0 PA E:ADP401 3.8 34.7 1.0 OD1 E:ASP107 3.9 34.3 1.0 NZ E:LYS56 3.9 35.2 1.0 O3A E:ADP401 4.1 25.9 1.0 CG E:ASP107 4.2 36.7 1.0 CG2 E:THR57 4.3 25.0 1.0 CD E:GLU108 4.5 48.8 1.0 O2A E:ADP401 4.5 36.6 1.0 CG E:GLU108 4.6 40.4 1.0 N E:THR57 4.7 26.0 1.0 CA E:THR57 4.8 22.7 1.0 O1B E:ADP401 4.8 29.4 1.0

K.Marcus, Y.Huang, S.Subramanian, C.L.Gee, K.Gorday, S.Ghaffari-Kashani, X.R.Luo, L.Zheng, M.O'donnell, S.Subramaniam, J.Kuriyan. Autoinhibition of A Clamp-Loader Atpase Revealed By Deep Mutagenesis and Cryo-Em To Be Published.