Magnesium in PDB 3ntu: Rada Recombinase D302K Mutant in Complex with Amp-Pnp

The structure of Rada Recombinase D302K Mutant in Complex with Amp-Pnp, PDB code: 3ntu was solved by Y.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.90
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	84.970, 84.970, 104.320, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 21.4

The structure of Rada Recombinase D302K Mutant in Complex with Amp-Pnp also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Rada Recombinase D302K Mutant in Complex with Amp-Pnp (pdb code 3ntu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rada Recombinase D302K Mutant in Complex with Amp-Pnp, PDB code: 3ntu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rada Recombinase D302K Mutant in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rada Recombinase D302K Mutant in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:25.9 occ:1.00 O2G A:ANP401 2.0 29.9 1.0 O1B A:ANP401 2.0 21.2 1.0 O A:HOH603 2.1 29.5 1.0 O A:HOH601 2.1 24.4 1.0 O A:HOH602 2.1 24.8 1.0 OG1 A:THR112 2.2 24.5 1.0 PG A:ANP401 3.1 29.2 1.0 CB A:THR112 3.2 21.9 1.0 PB A:ANP401 3.2 25.7 1.0 N3B A:ANP401 3.4 25.6 1.0 O A:HOH609 3.8 27.3 1.0 N A:THR112 3.9 22.5 1.0 OD1 A:ASP211 4.0 28.1 1.0 O1G A:ANP401 4.0 26.0 1.0 O2A A:ANP401 4.1 25.4 1.0 CA A:THR112 4.1 23.4 1.0 O2B A:ANP401 4.1 22.8 1.0 O3G A:ANP401 4.2 31.0 1.0 CG2 A:THR112 4.3 24.5 1.0 O3A A:ANP401 4.3 25.6 1.0 OD2 A:ASP211 4.4 26.0 1.0 OE1 A:GLU151 4.4 36.6 1.0 OG1 A:THR153 4.4 31.0 1.0 PA A:ANP401 4.6 27.2 1.0 CE A:LYS111 4.6 28.4 1.0 CG A:ASP211 4.7 26.5 1.0 O1A A:ANP401 4.7 27.1 1.0 CB A:LYS111 4.7 21.4 1.0 C A:LYS111 4.9 25.4 1.0 O A:HOH623 5.0 33.4 1.0

Magnesium binding site 2 out of 2 in the Rada Recombinase D302K Mutant in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rada Recombinase D302K Mutant in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:27.3 occ:1.00 O A:HOH607 1.9 27.3 1.0 O A:GLN98 2.0 24.8 1.0 O A:HOH604 2.1 25.2 1.0 O A:HOH606 2.1 26.8 1.0 OD1 A:ASP246 2.1 28.2 1.0 O A:HOH605 2.2 28.8 1.0 CG A:ASP246 3.1 37.4 1.0 C A:GLN98 3.1 25.1 1.0 OD2 A:ASP246 3.4 34.5 1.0 CA A:SER99 3.9 24.0 1.0 N A:SER99 4.0 23.8 1.0 CA A:GLN98 4.1 24.2 1.0 O A:HOH689 4.1 40.1 1.0 OG A:SER99 4.2 31.1 1.0 CB A:GLN98 4.2 21.4 1.0 O A:HOH630 4.3 35.9 1.0 O A:ASN242 4.3 25.2 1.0 OD1 A:ASN242 4.3 28.2 1.0 O A:HOH651 4.4 49.5 1.0 CB A:ASP246 4.5 31.3 1.0 CB A:SER99 4.7 27.0 1.0 N A:ASP246 4.7 26.5 1.0 CA A:ASP246 4.8 30.1 1.0 CB A:ALA245 4.9 24.3 1.0

R.Amunugama, Y.He, S.Willcox, R.A.Forties, K.S.Shim, R.Bundschuh, Y.Luo, J.Griffith, R.Fishel. RAD51 Protein Atp Cap Regulates Nucleoprotein Filament Stability. J.Biol.Chem. V. 287 8724 2012.
ISSN: ISSN 0021-9258
PubMed: 22275364
DOI: 10.1074/JBC.M111.239426