Magnesium in PDB 5dny: Structure of the Atprs-MRE11/RAD50-Dna Complex

The structure of Structure of the Atprs-MRE11/RAD50-Dna Complex, PDB code: 5dny was solved by Y.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.87 / 3.11
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.303, 130.111, 166.656, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 27.3

The binding sites of Magnesium atom in the Structure of the Atprs-MRE11/RAD50-Dna Complex (pdb code 5dny). 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 the Atprs-MRE11/RAD50-Dna Complex, PDB code: 5dny:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Atprs-MRE11/RAD50-Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Atprs-MRE11/RAD50-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:92.2 occ:0.83 OD2 A:ASP8 1.9 0.2 1.0 NE2 A:HIS188 2.2 89.0 1.0 NE2 A:HIS10 2.4 68.3 1.0 OD2 A:ASP49 2.6 0.7 1.0 MG A:MG402 2.6 75.1 1.0 CE1 A:HIS10 3.0 87.7 1.0 O A:HOH501 3.1 68.4 1.0 CG A:ASP8 3.1 0.9 1.0 CE1 A:HIS188 3.2 99.3 1.0 CD2 A:HIS188 3.2 85.5 1.0 CG A:ASP49 3.5 0.6 1.0 CD2 A:HIS10 3.6 68.0 1.0 ND1 A:HIS186 3.8 0.1 1.0 O A:HIS186 3.9 0.1 1.0 OD1 A:ASP8 3.9 92.8 1.0 CB A:ASP49 4.0 86.3 1.0 CA A:HIS186 4.0 94.1 1.0 CB A:ASP8 4.1 77.9 1.0 C A:HIS186 4.2 89.0 1.0 ND1 A:HIS10 4.3 87.5 1.0 ND1 A:HIS188 4.3 0.2 1.0 CG A:HIS188 4.3 0.1 1.0 CE1 A:HIS186 4.5 0.9 1.0 CG A:HIS10 4.5 67.4 1.0 OD1 A:ASP49 4.6 0.1 1.0 CD2 A:HIS85 4.7 0.0 1.0 CE1 A:HIS158 4.8 81.6 1.0 CG A:HIS186 4.8 0.2 1.0 N A:HIS186 4.8 75.0 1.0 CA A:ASP8 4.8 64.1 1.0 ND2 A:ASN84 4.9 0.5 1.0 NE2 A:HIS158 4.9 54.2 1.0 NE2 A:HIS85 4.9 0.3 1.0 CB A:HIS186 5.0 0.3 1.0

Magnesium binding site 2 out of 4 in the Structure of the Atprs-MRE11/RAD50-Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Atprs-MRE11/RAD50-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:75.1 occ:1.00 OD2 A:ASP49 1.9 0.7 1.0 ND1 A:HIS186 2.0 0.1 1.0 ND2 A:ASN84 2.4 0.5 1.0 MG A:MG401 2.6 92.2 0.8 CE1 A:HIS186 2.6 0.9 1.0 CG A:HIS186 2.8 0.2 1.0 NE2 A:HIS158 3.1 54.2 1.0 CG A:ASP49 3.1 0.6 1.0 O A:HOH501 3.3 68.4 1.0 CA A:HIS186 3.4 94.1 1.0 NE2 A:HIS186 3.5 0.2 1.0 CB A:HIS186 3.5 0.3 1.0 CG A:ASN84 3.5 98.3 1.0 CD2 A:HIS186 3.6 0.4 1.0 CE1 A:HIS158 3.6 81.6 1.0 OD1 A:ASP49 3.7 0.1 1.0 O A:HIS186 3.7 0.1 1.0 OD2 A:ASP8 3.8 0.2 1.0 OD1 A:ASN84 3.9 0.8 1.0 C A:HIS186 4.0 89.0 1.0 CD2 A:HIS85 4.1 0.0 1.0 CD2 A:HIS158 4.3 60.5 1.0 CB A:ASP49 4.3 86.3 1.0 NE2 A:HIS10 4.4 68.3 1.0 N A:HIS186 4.5 75.0 1.0 NE2 A:HIS85 4.5 0.3 1.0 NE2 A:HIS188 4.5 89.0 1.0 CE1 A:HIS10 4.6 87.7 1.0 CG A:ASP8 4.8 0.9 1.0 CB A:ASN84 4.8 80.9 1.0 ND1 A:HIS158 4.9 82.0 1.0 OD1 A:ASP8 5.0 92.8 1.0

Magnesium binding site 3 out of 4 in the Structure of the Atprs-MRE11/RAD50-Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Atprs-MRE11/RAD50-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:83.9 occ:1.00 OD2 C:ASP49 1.9 0.3 1.0 CD2 C:HIS186 2.1 0.8 1.0 ND2 C:ASN84 2.1 84.5 1.0 NE2 C:HIS158 2.6 96.5 1.0 CG C:HIS186 2.8 0.3 1.0 MG C:MG402 2.9 79.2 1.0 CG C:ASP49 2.9 94.1 1.0 NE2 C:HIS186 3.1 0.9 1.0 CA C:HIS186 3.1 0.1 1.0 CG C:ASN84 3.2 91.2 1.0 CB C:HIS186 3.2 0.5 1.0 CE1 C:HIS158 3.3 81.9 1.0 OD1 C:ASP49 3.4 82.4 1.0 CD2 C:HIS158 3.8 83.7 1.0 OD1 C:ASN84 3.8 97.8 1.0 O C:HIS186 3.8 0.5 1.0 O C:HOH501 3.9 69.8 1.0 ND1 C:HIS186 3.9 0.6 1.0 C C:HIS186 4.0 0.9 1.0 OD2 C:ASP8 4.0 86.9 1.0 CE1 C:HIS186 4.0 0.7 1.0 CB C:ASP49 4.1 88.8 1.0 N C:HIS186 4.2 98.1 1.0 CB C:ASN84 4.4 85.2 1.0 CD2 C:HIS85 4.4 71.8 1.0 ND1 C:HIS158 4.5 62.3 1.0 N C:ASN84 4.6 89.3 1.0 CG C:HIS158 4.8 63.6 1.0 NE2 C:HIS85 4.8 93.0 1.0 NE2 C:HIS10 4.8 80.5 1.0 CG C:ASP8 4.9 87.0 1.0 OD1 C:ASP8 4.9 94.5 1.0

Magnesium binding site 4 out of 4 in the Structure of the Atprs-MRE11/RAD50-Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Atprs-MRE11/RAD50-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:79.2 occ:1.00 NE2 C:HIS10 2.3 80.5 1.0 OD2 C:ASP49 2.4 0.3 1.0 OD2 C:ASP8 2.4 86.9 1.0 NE2 C:HIS188 2.5 84.2 1.0 CE1 C:HIS10 2.8 87.0 1.0 MG C:MG401 2.9 83.9 1.0 O C:HOH501 3.1 69.8 1.0 CE1 C:HIS188 3.3 92.5 1.0 CG C:ASP49 3.4 94.1 1.0 CD2 C:HIS188 3.5 71.9 1.0 CD2 C:HIS10 3.6 79.4 1.0 CG C:ASP8 3.6 87.0 1.0 CD2 C:HIS186 4.0 0.8 1.0 O C:HIS186 4.0 0.5 1.0 CB C:ASP49 4.1 88.8 1.0 ND1 C:HIS10 4.1 91.5 1.0 OD1 C:ASP49 4.3 82.4 1.0 CA C:HIS186 4.3 0.1 1.0 CD2 C:HIS85 4.3 71.8 1.0 OD1 C:ASP8 4.4 94.5 1.0 C C:HIS186 4.4 0.9 1.0 ND2 C:ASN84 4.5 84.5 1.0 NE2 C:HIS85 4.5 93.0 1.0 CG C:HIS10 4.5 65.3 1.0 ND1 C:HIS188 4.5 88.7 1.0 CG C:HIS188 4.6 79.5 1.0 CB C:ASP8 4.6 76.4 1.0 NE2 C:HIS186 4.9 0.9 1.0 CG C:HIS186 5.0 0.3 1.0

Y.Liu, S.Sung, Y.Kim, F.Li, G.Gwon, A.Jo, A.K.Kim, T.Kim, O.K.Song, S.E.Lee, Y.Cho. Atp-Dependent Dna Binding, Unwinding, and Resection By the MRE11/RAD50 Complex. Embo J. V. 35 743 2016.
ISSN: ESSN 1460-2075
PubMed: 26717941
DOI: 10.15252/EMBJ.201592462