Magnesium in PDB 3qku: MRE11 RAD50 Binding Domain in Complex with RAD50 and Amp-Pnp

The structure of MRE11 RAD50 Binding Domain in Complex with RAD50 and Amp-Pnp, PDB code: 3qku was solved by G.J.Williams, R.S.Williams, A.Arvai, G.Moncalian, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.30
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	177.398, 177.398, 130.423, 90.00, 90.00, 120.00
R / Rfree (%)	25.8 / 30.8

The binding sites of Magnesium atom in the MRE11 RAD50 Binding Domain in Complex with RAD50 and Amp-Pnp (pdb code 3qku). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the MRE11 RAD50 Binding Domain in Complex with RAD50 and Amp-Pnp, PDB code: 3qku:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the MRE11 RAD50 Binding Domain in Complex with RAD50 and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of MRE11 RAD50 Binding Domain in Complex with RAD50 and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:76.4 occ:1.00 O1B A:ANP1001 2.0 82.7 1.0 OG A:SER37 2.0 0.3 1.0 OE1 A:GLN140 2.0 93.3 1.0 O1G A:ANP1001 2.3 81.8 1.0 CD A:GLN140 3.0 93.2 1.0 O3G A:ANP1001 3.0 73.1 1.0 PG A:ANP1001 3.0 92.5 1.0 PB A:ANP1001 3.2 69.8 1.0 CB A:SER37 3.4 94.7 1.0 N3B A:ANP1001 3.4 79.1 1.0 NE2 A:GLN140 3.5 73.2 1.0 OD1 A:ASP822 3.5 85.8 1.0 N A:SER37 3.7 87.8 1.0 OD2 A:ASP822 3.8 89.3 1.0 CA A:SER37 3.9 82.5 1.0 O3A A:ANP1001 3.9 74.7 1.0 CG A:ASP822 4.1 0.9 1.0 CE A:LYS36 4.1 87.0 1.0 CB A:LYS36 4.2 79.6 1.0 OE2 A:GLU823 4.3 0.6 1.0 CG A:GLU823 4.3 0.5 1.0 CG A:GLN140 4.3 61.6 1.0 NZ A:LYS36 4.4 96.3 1.0 O2B A:ANP1001 4.5 75.7 1.0 O2G A:ANP1001 4.5 63.9 1.0 C A:LYS36 4.6 97.3 1.0 O1A A:ANP1001 4.7 57.6 1.0 PA A:ANP1001 4.8 93.4 1.0 CG1 A:VAL853 4.8 0.9 1.0 CD A:GLU823 4.8 0.0 1.0 CD A:LYS36 4.9 0.1 1.0 CB A:GLN140 4.9 90.0 1.0 CA A:LYS36 5.0 91.5 1.0

Magnesium binding site 2 out of 2 in the MRE11 RAD50 Binding Domain in Complex with RAD50 and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of MRE11 RAD50 Binding Domain in Complex with RAD50 and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:0.3 occ:1.00 OG B:SER37 2.3 0.4 1.0 OE1 B:GLN140 2.4 0.9 1.0 OE2 B:GLU823 2.5 0.3 1.0 O1B B:ANP1001 2.7 0.1 1.0 O1G B:ANP1001 2.8 0.1 1.0 O3G B:ANP1001 2.8 0.1 1.0 OD1 B:ASP822 2.9 0.7 1.0 CD B:GLN140 3.2 0.3 1.0 PG B:ANP1001 3.2 0.1 1.0 NE2 B:GLN140 3.6 0.3 1.0 CB B:SER37 3.6 0.7 1.0 PB B:ANP1001 3.7 0.9 1.0 CD B:GLU823 3.7 0.7 1.0 OD2 B:ASP822 3.7 0.5 1.0 N3B B:ANP1001 3.7 0.5 1.0 CG B:ASP822 3.7 0.1 1.0 N B:SER37 3.7 0.3 1.0 CB B:LYS36 4.0 0.7 1.0 CE B:LYS36 4.0 0.0 1.0 NZ B:LYS36 4.0 0.8 1.0 O3A B:ANP1001 4.0 0.6 1.0 CA B:SER37 4.1 0.7 1.0 CG1 B:VAL853 4.3 0.3 1.0 OE1 B:GLU823 4.4 0.9 1.0 CG B:GLN140 4.4 0.9 1.0 CD B:LYS36 4.4 0.0 1.0 C B:LYS36 4.6 0.8 1.0 O2G B:ANP1001 4.7 0.3 1.0 CG B:GLU823 4.8 0.1 1.0 CG B:LYS36 4.8 0.4 1.0 CA B:LYS36 4.8 0.4 1.0

G.J.Williams, R.S.Williams, J.S.Williams, G.Moncalian, A.S.Arvai, O.Limbo, G.Guenther, S.Sildas, M.Hammel, P.Russell, J.A.Tainer. Abc Atpase Signature Helices in RAD50 Link Nucleotide State to MRE11 Interface For Dna Repair. Nat.Struct.Mol.Biol. V. 18 423 2011.
ISSN: ISSN 1545-9993
PubMed: 21441914
DOI: 10.1038/NSMB.2038