Magnesium in PDB 3u60: Structure of T4 Bacteriophage Clamp Loader Bound to Open Clamp, Dna and Atp Analog

The structure of Structure of T4 Bacteriophage Clamp Loader Bound to Open Clamp, Dna and Atp Analog, PDB code: 3u60 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)	49.71 / 3.34
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	93.518, 118.443, 133.078, 90.00, 102.06, 90.00
R / Rfree (%)	24.4 / 28.2

The structure of Structure of T4 Bacteriophage Clamp Loader Bound to Open Clamp, 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 Open Clamp, Dna and Atp Analog (pdb code 3u60). 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 Open Clamp, Dna and Atp Analog, PDB code: 3u60:
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 Open Clamp, 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 Open Clamp, Dna and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg800 b:47.9 occ:1.00 F1 B:08T700 2.2 48.9 1.0 CG2 B:THR57 2.5 45.1 1.0 O1B B:08T700 2.8 47.9 1.0 OG1 B:THR57 2.9 46.3 1.0 OE2 B:GLU108 3.0 69.7 1.0 NH2 C:ARG151 3.0 36.4 1.0 CB B:THR57 3.2 45.5 1.0 OE1 C:GLU126 3.4 41.7 1.0 BE B:08T700 3.4 48.9 1.0 OD2 B:ASP107 3.5 49.9 1.0 F2 B:08T700 3.6 48.9 1.0 O2A B:08T700 3.7 47.9 1.0 OE2 C:GLU126 3.8 40.8 1.0 OD1 B:ASP107 3.9 50.0 1.0 CD B:GLU108 4.0 70.1 1.0 CD C:GLU126 4.0 41.5 1.0 PB B:08T700 4.1 47.9 1.0 O3B B:08T700 4.1 48.9 1.0 CG B:ASP107 4.1 50.1 1.0 CZ C:ARG151 4.2 35.5 1.0 CG B:GLU108 4.3 70.3 1.0 NH2 B:ARG205 4.3 43.7 1.0 NH1 C:ARG151 4.6 35.4 1.0 CA B:THR57 4.6 46.1 1.0 F3 B:08T700 4.6 48.9 1.0 N B:THR57 4.7 46.1 1.0 PA B:08T700 4.9 47.9 1.0 O3A B:08T700 5.0 48.9 1.0

Magnesium binding site 2 out of 4 in the Structure of T4 Bacteriophage Clamp Loader Bound to Open Clamp, 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 Open Clamp, Dna and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg800 b:47.9 occ:1.00 F1 C:08T700 2.3 48.9 1.0 CG2 C:THR57 2.5 38.4 1.0 O1B C:08T700 2.6 47.9 1.0 OE2 C:GLU108 2.8 55.7 1.0 NH2 D:ARG151 3.0 31.0 1.0 OG1 C:THR57 3.1 40.5 1.0 CB C:THR57 3.3 39.0 1.0 BE C:08T700 3.3 48.9 1.0 OE1 D:GLU126 3.4 33.7 1.0 F2 C:08T700 3.5 48.9 1.0 OD2 C:ASP107 3.6 57.1 1.0 OE2 D:GLU126 3.7 34.0 1.0 CD C:GLU108 3.8 55.9 1.0 PB C:08T700 3.8 47.9 1.0 O3B C:08T700 3.8 48.9 1.0 O2A C:08T700 3.9 47.9 1.0 OD1 C:ASP107 3.9 56.1 1.0 CD D:GLU126 4.0 33.5 1.0 NH2 C:ARG205 4.0 31.8 1.0 CZ D:ARG151 4.1 30.0 1.0 CG C:GLU108 4.2 56.3 1.0 CG C:ASP107 4.2 56.7 1.0 NH1 D:ARG151 4.4 30.2 1.0 CA C:THR57 4.6 30.4 1.0 F3 C:08T700 4.7 48.9 1.0 N C:THR57 4.7 30.1 1.0 O3A C:08T700 4.8 47.9 1.0 OE1 C:GLU108 4.9 55.8 1.0 O2B C:08T700 4.9 47.9 1.0 CG2 C:THR137 4.9 28.9 1.0 PA C:08T700 4.9 47.9 1.0

Magnesium binding site 3 out of 4 in the Structure of T4 Bacteriophage Clamp Loader Bound to Open Clamp, 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 Open Clamp, Dna and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg800 b:47.9 occ:1.00 O1B D:08T700 2.4 47.9 1.0 F1 D:08T700 2.5 48.9 1.0 CG2 D:THR57 2.5 62.7 1.0 OE2 D:GLU108 2.7 83.6 1.0 OG1 D:THR57 3.1 65.3 1.0 NH2 E:ARG151 3.2 31.9 1.0 OE1 E:GLU126 3.2 39.9 1.0 CB D:THR57 3.4 63.2 1.0 F2 D:08T700 3.4 48.9 1.0 BE D:08T700 3.4 48.9 1.0 OD2 D:ASP107 3.6 47.4 1.0 PB D:08T700 3.7 48.9 1.0 CD D:GLU108 3.7 83.8 1.0 OD1 D:ASP107 3.9 45.9 1.0 O3B D:08T700 3.9 48.9 1.0 CD E:GLU126 4.0 40.5 1.0 OE2 E:GLU126 4.0 41.4 1.0 NH2 D:ARG205 4.0 37.8 1.0 CG D:GLU108 4.1 83.9 1.0 O2A D:08T700 4.1 48.1 1.0 CG D:ASP107 4.2 46.5 1.0 CZ E:ARG151 4.4 31.9 1.0 O2B D:08T700 4.5 48.9 1.0 CA D:THR57 4.7 42.1 1.0 N D:THR57 4.7 42.0 1.0 F3 D:08T700 4.8 48.9 1.0 OE1 D:GLU108 4.8 84.2 1.0 O3A D:08T700 4.8 47.9 1.0 NH1 E:ARG151 4.9 32.4 1.0 CG2 D:THR137 4.9 25.4 1.0

Magnesium binding site 4 out of 4 in the Structure of T4 Bacteriophage Clamp Loader Bound to Open Clamp, 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 Open Clamp, Dna and Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg801 b:47.9 occ:1.00 O2A E:ADP700 2.4 48.9 1.0 O3B E:ADP700 2.7 47.9 1.0 NH2 E:ARG205 2.8 92.2 1.0 CG2 E:THR57 2.9 45.4 1.0 OE2 E:GLU108 3.2 88.5 1.0 OG1 E:THR57 3.2 48.3 1.0 CB E:THR57 3.6 45.3 1.0 OD2 E:ASP107 3.6 87.3 1.0 O1B E:ADP700 3.6 48.6 1.0 PB E:ADP700 3.6 48.9 1.0 PA E:ADP700 3.8 48.9 1.0 CZ E:ARG205 4.0 92.8 1.0 CD E:GLU108 4.1 88.3 1.0 O3A E:ADP700 4.1 47.9 1.0 OD1 E:ASP107 4.2 85.1 1.0 CG E:GLU108 4.3 87.7 1.0 CG E:ASP107 4.3 85.5 1.0 O5' E:ADP700 4.7 47.9 1.0 NE E:ARG205 4.7 94.5 1.0 NH1 E:ARG205 4.8 91.9 1.0 O1A E:ADP700 4.8 47.9 1.0 CA E:THR57 4.9 48.7 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