Magnesium in PDB 5da9: Atp-Gamma-S Bound RAD50 From Chaetomium Thermophilum in Complex with the RAD50-Binding Domain of MRE11

The structure of Atp-Gamma-S Bound RAD50 From Chaetomium Thermophilum in Complex with the RAD50-Binding Domain of MRE11, PDB code: 5da9 was solved by F.U.Seifert, K.Lammens, G.Stoehr, B.Kessler, K.-P.Hopfner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.90 / 3.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	116.511, 125.086, 168.304, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.8

The binding sites of Magnesium atom in the Atp-Gamma-S Bound RAD50 From Chaetomium Thermophilum in Complex with the RAD50-Binding Domain of MRE11 (pdb code 5da9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Atp-Gamma-S Bound RAD50 From Chaetomium Thermophilum in Complex with the RAD50-Binding Domain of MRE11, PDB code: 5da9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Atp-Gamma-S Bound RAD50 From Chaetomium Thermophilum in Complex with the RAD50-Binding Domain of MRE11


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Atp-Gamma-S Bound RAD50 From Chaetomium Thermophilum in Complex with the RAD50-Binding Domain of MRE11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1401 b:50.5 occ:1.00 O1B A:AGS1402 1.9 75.8 1.0 O3G A:AGS1402 2.0 0.1 1.0 O A:HOH1502 2.0 76.5 1.0 OG1 A:THR41 2.1 94.2 1.0 OE1 A:GLN159 2.1 68.1 1.0 O A:HOH1501 2.5 83.1 1.0 CB A:THR41 3.0 46.1 1.0 CD A:GLN159 3.0 67.9 1.0 PB A:AGS1402 3.2 59.3 1.0 PG A:AGS1402 3.4 46.7 1.0 NE2 A:GLN159 3.4 69.1 1.0 OD1 A:ASP1237 3.6 0.5 1.0 O3A A:AGS1402 3.7 96.9 1.0 O3B A:AGS1402 3.7 52.9 1.0 CG2 A:THR41 3.9 45.5 1.0 CA A:THR41 4.1 47.0 1.0 N A:THR41 4.1 56.8 1.0 OD2 A:ASP1237 4.1 97.1 1.0 CG A:ASP1237 4.3 97.3 1.0 O2G A:AGS1402 4.4 63.4 1.0 CB B:ALA1209 4.4 53.9 1.0 CG A:GLN159 4.4 66.4 1.0 O2B A:AGS1402 4.4 34.8 1.0 S1G A:AGS1402 4.5 74.3 1.0 O2A A:AGS1402 4.6 55.6 1.0 PA A:AGS1402 4.6 55.9 1.0 N B:ALA1209 4.6 74.6 1.0 CB A:GLN159 4.7 65.2 1.0 OG B:SER1208 4.7 55.4 1.0 O1A A:AGS1402 4.8 55.0 1.0

Magnesium binding site 2 out of 2 in the Atp-Gamma-S Bound RAD50 From Chaetomium Thermophilum in Complex with the RAD50-Binding Domain of MRE11


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Atp-Gamma-S Bound RAD50 From Chaetomium Thermophilum in Complex with the RAD50-Binding Domain of MRE11 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1401 b:73.2 occ:1.00 O3G B:AGS1402 2.0 60.5 1.0 OG1 B:THR41 2.0 66.2 1.0 OE1 B:GLN159 2.0 62.8 1.0 O B:HOH1503 2.1 86.7 1.0 O B:HOH1502 2.2 72.0 1.0 O1B B:AGS1402 2.4 59.6 1.0 CD B:GLN159 3.1 56.9 1.0 CB B:THR41 3.1 64.1 1.0 PG B:AGS1402 3.5 57.7 1.0 NE2 B:GLN159 3.6 58.7 1.0 OD1 B:ASP1237 3.7 64.9 1.0 PB B:AGS1402 3.8 59.2 1.0 OD2 B:ASP1237 3.8 69.0 1.0 CG2 B:THR41 4.0 58.2 1.0 CB A:ALA1209 4.0 65.7 1.0 O3B B:AGS1402 4.0 90.4 1.0 O1A B:AGS1402 4.1 65.4 1.0 CG B:ASP1237 4.2 74.3 1.0 CA B:THR41 4.2 59.3 1.0 N B:THR41 4.3 57.8 1.0 CG B:GLN159 4.4 57.2 1.0 N A:ALA1209 4.4 60.6 1.0 O2G B:AGS1402 4.4 50.2 1.0 S1G B:AGS1402 4.5 67.3 1.0 CB B:GLN159 4.6 58.0 1.0 O2B B:AGS1402 4.7 76.3 1.0 O3A B:AGS1402 4.8 66.4 1.0 OG A:SER1208 4.8 86.3 1.0 PA B:AGS1402 4.8 86.2 1.0 CA A:ALA1209 4.9 58.1 1.0 O2A B:AGS1402 4.9 79.8 1.0

F.U.Seifert, K.Lammens, G.Stoehr, B.Kessler, K.P.Hopfner. Structural Mechanism of Atp-Dependent Dna Binding and Dna End Bridging By Eukaryotic RAD50. Embo J. V. 35 759 2016.
ISSN: ESSN 1460-2075
PubMed: 26896444
DOI: 10.15252/EMBJ.201592934