Magnesium in PDB 5dac: Atp-Gamma-S Bound RAD50 From Chaetomium Thermophilum in Complex with Dna

The structure of Atp-Gamma-S Bound RAD50 From Chaetomium Thermophilum in Complex with Dna, PDB code: 5dac 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)	49.48 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.312, 97.078, 115.012, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 24.6

The structure of Atp-Gamma-S Bound RAD50 From Chaetomium Thermophilum in Complex with Dna also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Magnesium atom in the Atp-Gamma-S Bound RAD50 From Chaetomium Thermophilum in Complex with Dna (pdb code 5dac). 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 Dna, PDB code: 5dac:
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 Dna


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 Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1401 b:49.7 occ:1.00 OG1 A:THR41 1.9 34.9 1.0 O A:HOH1524 1.9 35.6 1.0 O A:HOH1517 2.0 48.9 1.0 OE1 A:GLN159 2.1 47.8 1.0 O2B A:AGS1402 2.2 42.5 1.0 O3G A:AGS1402 2.2 45.8 1.0 CB A:THR41 3.0 34.9 1.0 CD A:GLN159 3.2 41.0 1.0 PG A:AGS1402 3.5 42.4 1.0 PB A:AGS1402 3.5 46.7 1.0 NE2 A:GLN159 3.7 47.3 1.0 OD2 A:ASP1237 3.8 40.1 1.0 O3B A:AGS1402 3.8 42.5 1.0 CG2 A:THR41 3.9 33.0 1.0 OD1 A:ASP1237 4.0 39.9 1.0 CA A:THR41 4.1 35.1 1.0 N A:THR41 4.1 35.1 1.0 O2A A:AGS1402 4.1 43.3 1.0 O3A A:AGS1402 4.2 43.1 1.0 S1G A:AGS1402 4.3 45.1 1.0 CB B:ALA1209 4.3 39.2 1.0 N B:ALA1209 4.3 42.1 1.0 CG A:ASP1237 4.3 38.0 1.0 PA A:AGS1402 4.5 46.2 1.0 CG A:GLN159 4.5 41.2 1.0 O1A A:AGS1402 4.5 44.2 1.0 O1B A:AGS1402 4.6 43.3 1.0 CB A:GLN159 4.6 40.9 1.0 O2G A:AGS1402 4.7 41.7 1.0 CB B:SER1208 4.9 40.5 1.0 CA B:ALA1209 5.0 41.8 1.0

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


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 Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1401 b:43.0 occ:1.00 OE1 B:GLN159 2.0 45.3 1.0 OG1 B:THR41 2.0 35.0 1.0 O3G B:AGS1402 2.0 33.7 1.0 O B:HOH1504 2.0 36.0 1.0 O B:HOH1512 2.1 31.4 1.0 O1B B:AGS1402 2.5 35.9 1.0 CD B:GLN159 3.1 39.0 1.0 CB B:THR41 3.2 32.9 1.0 PG B:AGS1402 3.4 36.3 1.0 NE2 B:GLN159 3.6 45.5 1.0 PB B:AGS1402 3.8 34.5 1.0 CG2 B:THR41 3.8 31.6 1.0 N A:ALA1209 4.0 38.8 1.0 O3B B:AGS1402 4.0 45.8 1.0 OD2 B:ASP1237 4.1 38.9 1.0 CB A:ALA1209 4.1 38.7 1.0 O2A B:AGS1402 4.1 38.1 1.0 S1G B:AGS1402 4.2 36.1 1.0 OD1 B:ASP1237 4.2 39.0 1.0 CA B:THR41 4.4 34.6 1.0 CG B:GLN159 4.4 38.5 1.0 O3A B:AGS1402 4.5 36.3 1.0 N B:THR41 4.5 34.2 1.0 CG B:ASP1237 4.5 34.9 1.0 O2G B:AGS1402 4.6 33.1 1.0 CB B:GLN159 4.6 39.6 1.0 CB A:SER1208 4.7 32.5 1.0 CA A:ALA1209 4.7 40.0 1.0 PA B:AGS1402 4.7 38.6 1.0 CA A:SER1208 4.8 34.2 1.0 C A:SER1208 4.9 32.3 1.0 O1A B:AGS1402 4.9 38.9 1.0 O2B B:AGS1402 4.9 35.6 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