Magnesium in PDB 4w9m: Amppnp Bound RAD50 in Complex with Dsdna

The structure of Amppnp Bound RAD50 in Complex with Dsdna, PDB code: 4w9m was solved by A.Rojowska, K.Lammens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.69 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	49.713, 96.386, 105.926, 90.01, 89.22, 81.67
R / Rfree (%)	21.5 / 27

The binding sites of Magnesium atom in the Amppnp Bound RAD50 in Complex with Dsdna (pdb code 4w9m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Amppnp Bound RAD50 in Complex with Dsdna, PDB code: 4w9m:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Amppnp Bound RAD50 in Complex with Dsdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Amppnp Bound RAD50 in Complex with Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg902 b:15.6 occ:1.00 O1B C:ANP901 2.0 17.5 1.0 OG C:SER37 2.0 18.0 1.0 O1G C:ANP901 2.0 17.9 1.0 O C:HOH1011 2.1 18.6 1.0 OE1 C:GLN142 2.2 19.0 1.0 O C:HOH1009 2.5 16.8 1.0 CB C:SER37 2.8 18.6 1.0 CD C:GLN142 3.1 17.6 1.0 PB C:ANP901 3.2 16.7 1.0 PG C:ANP901 3.3 14.2 1.0 NE2 C:GLN142 3.6 18.6 1.0 N C:SER37 3.7 16.8 1.0 N3B C:ANP901 3.7 15.9 1.0 CA C:SER37 3.8 19.6 1.0 OD2 C:ASP797 3.9 20.2 1.0 O2A C:ANP901 3.9 16.6 1.0 O2G C:ANP901 4.0 17.2 1.0 O3A C:ANP901 4.1 14.5 1.0 O2B C:ANP901 4.3 18.8 1.0 CG C:GLN142 4.4 19.7 1.0 O C:HOH1021 4.5 16.7 1.0 O3G C:ANP901 4.5 16.3 1.0 PA C:ANP901 4.5 15.9 1.0 OD1 C:ASP797 4.5 30.8 1.0 CB C:GLN142 4.5 20.7 1.0 CG C:ASP797 4.6 24.2 1.0 N E:GLY769 4.7 17.6 1.0 CB E:SER768 4.7 17.6 1.0 NZ C:LYS36 4.7 16.6 1.0 C C:LYS36 4.8 17.9 1.0 O1A C:ANP901 4.9 18.1 1.0 CB C:LYS36 4.9 17.7 1.0

Magnesium binding site 2 out of 4 in the Amppnp Bound RAD50 in Complex with Dsdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Amppnp Bound RAD50 in Complex with Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg902 b:14.6 occ:1.00 O1B E:ANP901 1.9 16.0 1.0 OE1 E:GLN142 2.1 26.1 1.0 O E:HOH1048 2.4 18.5 1.0 OG E:SER37 2.4 17.1 1.0 O1G E:ANP901 2.5 20.5 1.0 CB E:SER37 3.1 17.0 1.0 CD E:GLN142 3.3 21.8 1.0 PB E:ANP901 3.3 16.0 1.0 PG E:ANP901 3.5 11.6 1.0 O3G E:ANP901 3.7 16.1 1.0 N3B E:ANP901 3.8 19.4 1.0 N E:SER37 3.9 17.1 1.0 OD2 E:ASP797 3.9 27.4 1.0 NE2 E:GLN142 3.9 23.5 1.0 OD1 E:ASP797 3.9 36.8 1.0 CA E:SER37 4.0 17.3 1.0 O1A E:ANP901 4.1 15.4 1.0 O2B E:ANP901 4.2 15.2 1.0 CG E:ASP797 4.3 33.9 1.0 O3A E:ANP901 4.3 17.2 1.0 OE2 E:GLU798 4.3 32.5 1.0 CG E:GLN142 4.5 20.4 1.0 CB E:GLN142 4.5 21.1 1.0 N C:GLY769 4.7 21.6 1.0 PA E:ANP901 4.7 16.9 1.0 O2G E:ANP901 4.8 18.9 1.0 CB E:LYS36 4.9 16.8 1.0 NZ E:LYS36 4.9 17.8 1.0 CG E:GLU798 4.9 27.5 1.0 C E:LYS36 5.0 19.2 1.0

Magnesium binding site 3 out of 4 in the Amppnp Bound RAD50 in Complex with Dsdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Amppnp Bound RAD50 in Complex with Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg902 b:16.3 occ:1.00 O1G I:ANP901 2.0 16.8 1.0 O2B I:ANP901 2.2 19.1 1.0 OG I:SER37 2.3 16.3 1.0 O I:HOH1005 2.5 16.1 1.0 OE1 I:GLN142 2.5 23.1 1.0 PG I:ANP901 3.3 15.7 1.0 CD I:GLN142 3.3 19.8 1.0 CB I:SER37 3.4 18.2 1.0 PB I:ANP901 3.5 15.8 1.0 NE2 I:GLN142 3.8 20.5 1.0 N I:SER37 3.8 17.4 1.0 N3B I:ANP901 3.8 15.4 1.0 O I:HOH1037 3.8 25.5 1.0 OD2 I:ASP797 3.9 24.6 1.0 OD1 I:ASP797 3.9 32.7 1.0 CA I:SER37 4.1 19.6 1.0 O2G I:ANP901 4.1 16.5 1.0 CG I:ASP797 4.2 27.2 1.0 O1B I:ANP901 4.3 16.2 1.0 O3G I:ANP901 4.4 18.1 1.0 NZ I:LYS36 4.4 17.1 1.0 CG I:GLN142 4.4 22.3 1.0 CB I:GLN142 4.5 20.4 1.0 O3A I:ANP901 4.7 15.6 1.0 C I:LYS36 4.7 19.4 1.0 CB I:LYS36 4.7 19.8 1.0 O2A I:ANP901 4.7 18.5 1.0 CG2 I:ILE828 4.8 18.8 1.0 CE I:LYS36 4.9 19.6 1.0 O I:HOH1057 4.9 23.7 1.0 CB I:GLU798 5.0 31.0 0.3 N K:GLY769 5.0 17.0 1.0

Magnesium binding site 4 out of 4 in the Amppnp Bound RAD50 in Complex with Dsdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Amppnp Bound RAD50 in Complex with Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg902 b:13.3 occ:1.00 O K:HOH1022 1.9 16.7 1.0 O1G K:ANP901 2.0 17.9 1.0 OE1 K:GLN142 2.1 18.2 1.0 O1B K:ANP901 2.1 11.6 1.0 OG K:SER37 2.2 15.6 1.0 CB K:SER37 3.0 15.4 1.0 O K:HOH1055 3.0 16.3 1.0 CD K:GLN142 3.2 17.9 1.0 PG K:ANP901 3.2 15.1 1.0 PB K:ANP901 3.3 11.6 1.0 O3G K:ANP901 3.7 15.8 1.0 N3B K:ANP901 3.7 18.9 1.0 O1A K:ANP901 3.7 15.4 1.0 NE2 K:GLN142 3.8 18.0 1.0 O3A K:ANP901 4.0 16.3 1.0 OD2 K:ASP797 4.0 19.4 1.0 N K:SER37 4.0 16.1 1.0 CA K:SER37 4.1 16.1 1.0 OD1 K:ASP797 4.1 23.9 1.0 N I:GLY769 4.2 19.9 1.0 OE2 K:GLU798 4.3 29.9 1.0 PA K:ANP901 4.4 15.2 1.0 CG K:GLN142 4.4 15.9 1.0 CG K:ASP797 4.5 22.0 1.0 O2G K:ANP901 4.5 18.7 1.0 O2B K:ANP901 4.5 14.8 1.0 CB K:GLN142 4.6 15.7 1.0 CB I:SER768 4.7 19.3 1.0 CA I:GLY769 4.8 20.7 1.0 O I:HOH1049 4.9 24.8 1.0 CG K:GLU798 4.9 24.6 1.0

A.Rojowska, K.Lammens, F.U.Seifert, C.Direnberger, H.Feldmann, K.P.Hopfner. Structure of the RAD50 Dna Double-Strand Break Repair Protein in Complex with Dna. Embo J. V. 33 2847 2014.
ISSN: ESSN 1460-2075
PubMed: 25349191
DOI: 10.15252/EMBJ.201488889