Magnesium in PDB 5f3w: Structure of the Atprs-MRE11/RAD50-Dna Complex

The structure of Structure of the Atprs-MRE11/RAD50-Dna Complex, PDB code: 5f3w 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 (%)	22.2 / 26.9

The binding sites of Magnesium atom in the Structure of the Atprs-MRE11/RAD50-Dna Complex (pdb code 5f3w). 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: 5f3w:
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:95.7 occ:1.00 OD2 A:ASP8 1.9 0.0 1.0 NE2 A:HIS188 2.2 90.1 1.0 NE2 A:HIS10 2.3 66.5 1.0 OD2 A:ASP49 2.7 0.2 1.0 MG A:MG402 2.9 80.3 1.0 CE1 A:HIS10 3.0 85.5 1.0 CE1 A:HIS188 3.1 0.5 1.0 O A:HOH501 3.1 70.7 1.0 CD2 A:HIS188 3.2 86.3 1.0 CG A:ASP8 3.2 1.0 1.0 CD2 A:HIS10 3.5 71.4 1.0 CG A:ASP49 3.7 1.0 1.0 ND1 A:HIS186 3.9 1.0 1.0 OD1 A:ASP8 4.0 93.1 1.0 CB A:ASP49 4.1 86.4 1.0 O A:HIS186 4.1 0.1 1.0 CB A:ASP8 4.1 85.8 1.0 CA A:HIS186 4.2 0.4 1.0 ND1 A:HIS188 4.2 0.9 1.0 ND1 A:HIS10 4.2 89.2 1.0 CG A:HIS188 4.3 0.6 1.0 C A:HIS186 4.3 0.6 1.0 CG A:HIS10 4.5 67.0 1.0 CE1 A:HIS186 4.6 0.5 1.0 OD1 A:ASP49 4.7 99.7 1.0 CD2 A:HIS85 4.7 98.8 1.0 CA A:ASP8 4.8 68.2 1.0 CE1 A:HIS158 4.9 86.5 1.0 CG A:HIS186 4.9 0.1 1.0 N A:HIS186 4.9 84.3 1.0 NE2 A:HIS85 5.0 1.0 1.0 ND2 A:ASN84 5.0 0.0 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:80.3 occ:1.00 OD2 A:ASP49 1.9 0.2 1.0 ND1 A:HIS186 2.1 1.0 1.0 ND2 A:ASN84 2.3 0.0 1.0 CE1 A:HIS186 2.6 0.5 1.0 CG A:HIS186 2.8 0.1 1.0 MG A:MG401 2.9 95.7 1.0 NE2 A:HIS158 3.0 58.4 1.0 CG A:ASP49 3.1 1.0 1.0 O A:HOH501 3.4 70.7 1.0 NE2 A:HIS186 3.4 1.0 1.0 CA A:HIS186 3.4 0.4 1.0 CB A:HIS186 3.4 0.9 1.0 CG A:ASN84 3.4 0.5 1.0 CD2 A:HIS186 3.5 0.5 1.0 CE1 A:HIS158 3.6 86.5 1.0 OD1 A:ASP49 3.7 99.7 1.0 OD1 A:ASN84 3.8 0.8 1.0 O A:HIS186 3.9 0.1 1.0 OD2 A:ASP8 3.9 0.0 1.0 CD2 A:HIS85 4.1 98.8 1.0 C A:HIS186 4.1 0.6 1.0 CD2 A:HIS158 4.2 61.7 1.0 CB A:ASP49 4.3 86.4 1.0 N A:HIS186 4.5 84.3 1.0 NE2 A:HIS85 4.5 1.0 1.0 NE2 A:HIS10 4.5 66.5 1.0 NE2 A:HIS188 4.6 90.1 1.0 CB A:ASN84 4.7 83.1 1.0 CE1 A:HIS10 4.8 85.5 1.0 ND1 A:HIS158 4.8 84.2 1.0 CG A:ASP8 4.9 1.0 1.0 N A:ASN84 4.9 82.6 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:93.2 occ:1.00 OD2 C:ASP49 1.8 0.1 1.0 CD2 C:HIS186 2.1 0.7 1.0 ND2 C:ASN84 2.1 95.0 1.0 NE2 C:HIS158 2.8 0.2 1.0 MG C:MG402 2.8 85.8 1.0 CG C:HIS186 2.9 0.7 1.0 CG C:ASP49 2.9 0.1 1.0 NE2 C:HIS186 3.1 0.0 1.0 CG C:ASN84 3.2 0.6 1.0 CA C:HIS186 3.3 0.5 1.0 CB C:HIS186 3.4 0.4 1.0 OD1 C:ASP49 3.4 92.2 1.0 CE1 C:HIS158 3.5 88.9 1.0 O C:HOH501 3.7 73.5 1.0 OD1 C:ASN84 3.7 0.2 1.0 O C:HIS186 3.9 0.3 1.0 CD2 C:HIS158 3.9 87.0 1.0 ND1 C:HIS186 4.0 0.8 1.0 OD2 C:ASP8 4.0 96.4 1.0 CE1 C:HIS186 4.0 0.3 1.0 C C:HIS186 4.1 1.0 1.0 CB C:ASP49 4.1 96.7 1.0 CD2 C:HIS85 4.3 80.8 1.0 N C:HIS186 4.3 0.6 1.0 CB C:ASN84 4.4 97.2 1.0 NE2 C:HIS85 4.7 98.0 1.0 ND1 C:HIS158 4.7 65.4 1.0 N C:ASN84 4.7 92.9 1.0 NE2 C:HIS10 4.7 88.0 1.0 CE1 C:HIS10 4.9 88.9 1.0 CG C:HIS158 4.9 66.8 1.0 CG C:ASP8 4.9 87.9 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:85.8 occ:1.00 NE2 C:HIS10 2.3 88.0 1.0 OD2 C:ASP8 2.3 96.4 1.0 NE2 C:HIS188 2.4 85.0 1.0 OD2 C:ASP49 2.5 0.1 1.0 CE1 C:HIS10 2.8 88.9 1.0 MG C:MG401 2.8 93.2 1.0 O C:HOH501 3.2 73.5 1.0 CE1 C:HIS188 3.3 99.1 1.0 CD2 C:HIS188 3.4 75.5 1.0 CG C:ASP49 3.5 0.1 1.0 CG C:ASP8 3.6 87.9 1.0 CD2 C:HIS10 3.6 82.0 1.0 CD2 C:HIS186 4.0 0.7 1.0 CB C:ASP49 4.1 96.7 1.0 O C:HIS186 4.1 0.3 1.0 ND1 C:HIS10 4.1 87.4 1.0 CA C:HIS186 4.3 0.5 1.0 OD1 C:ASP8 4.3 90.5 1.0 OD1 C:ASP49 4.4 92.2 1.0 C C:HIS186 4.4 1.0 1.0 CD2 C:HIS85 4.5 80.8 1.0 ND1 C:HIS188 4.5 99.8 1.0 CG C:HIS10 4.5 67.4 1.0 CG C:HIS188 4.6 84.0 1.0 CB C:ASP8 4.6 83.8 1.0 ND2 C:ASN84 4.6 95.0 1.0 NE2 C:HIS85 4.6 98.0 1.0 NE2 C:HIS186 5.0 0.0 1.0 CG C:HIS186 5.0 0.7 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