Magnesium in PDB 2gdj: Delta-62 Rada Recombinase in Complex with Amp-Pnp and Magnesium

The structure of Delta-62 Rada Recombinase in Complex with Amp-Pnp and Magnesium, PDB code: 2gdj was solved by Y.Wu, X.Qian, Y.He, Y.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.50
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	67.750, 67.750, 90.080, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 26.8

The binding sites of Magnesium atom in the Delta-62 Rada Recombinase in Complex with Amp-Pnp and Magnesium (pdb code 2gdj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Delta-62 Rada Recombinase in Complex with Amp-Pnp and Magnesium, PDB code: 2gdj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Delta-62 Rada Recombinase in Complex with Amp-Pnp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Delta-62 Rada Recombinase in Complex with Amp-Pnp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:39.7 occ:1.00 O2G A:ANP401 2.0 39.5 1.0 O1B A:ANP401 2.2 37.0 1.0 OG1 A:THR112 2.3 29.3 1.0 PG A:ANP401 3.3 37.3 1.0 CB A:THR112 3.4 26.0 1.0 PB A:ANP401 3.4 36.5 1.0 N3B A:ANP401 3.6 37.9 1.0 O1G A:ANP401 4.1 36.6 1.0 O2A A:ANP401 4.2 35.0 1.0 CG2 A:THR153 4.2 37.6 1.0 OD2 A:ASP211 4.2 27.4 1.0 O2B A:ANP401 4.2 37.2 1.0 N A:THR112 4.3 26.9 1.0 OD1 A:ASP211 4.3 26.3 1.0 O3G A:ANP401 4.3 39.2 1.0 OG1 A:THR153 4.3 37.9 1.0 CA A:THR112 4.4 26.8 1.0 CG2 A:THR112 4.4 22.4 1.0 CB A:THR153 4.6 34.5 1.0 O3A A:ANP401 4.6 35.3 1.0 CG A:ASP211 4.7 26.9 1.0 OE1 A:GLU151 4.8 45.6 1.0 PA A:ANP401 4.8 35.5 1.0 CE A:LYS111 4.8 29.7 1.0 O1A A:ANP401 4.9 36.0 1.0 NE2 A:GLN257 5.0 66.1 1.0 CG A:GLU151 5.0 40.4 1.0 CB A:LYS111 5.0 26.9 1.0

Magnesium binding site 2 out of 2 in the Delta-62 Rada Recombinase in Complex with Amp-Pnp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Delta-62 Rada Recombinase in Complex with Amp-Pnp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:49.5 occ:1.00 O A:GLN98 2.4 27.4 1.0 OD1 A:ASP246 2.5 40.6 1.0 CG A:ASP246 3.3 41.1 1.0 OD2 A:ASP246 3.3 40.4 1.0 C A:GLN98 3.4 26.4 1.0 ND2 A:ASN242 3.6 41.1 1.0 O A:ASN242 3.9 42.2 1.0 CA A:SER99 4.1 28.4 1.0 N A:SER99 4.1 25.8 1.0 CA A:GLN98 4.4 27.5 1.0 CG A:ASN242 4.6 42.9 1.0 CB A:ASN242 4.6 41.2 1.0 C A:ASN242 4.7 41.8 1.0 CB A:ALA245 4.7 36.0 1.0 CB A:ASP246 4.7 40.0 1.0 CB A:GLN98 4.7 26.5 1.0 OG A:SER99 4.8 29.0 1.0 CA A:ASN242 4.8 41.5 1.0 N A:ASP246 4.9 37.9 1.0

V.E.Galkin, Y.Wu, X.-P.Zhang, X.Qian, Y.He, X.Yu, W.-D.Heyer, Y.Luo, E.H.Egelman. The RAD51/Rada N-Terminal Domain Activates Nucleoprotein Filament Atpase Activity. Structure V. 14 983 2006.
ISSN: ISSN 0969-2126
PubMed: 16765891
DOI: 10.1016/J.STR.2006.04.001