Sodium 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:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Rada Recombinase D302K Mutant in Complex with Amp-Pnp, PDB code: 3ntu:

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na505 b:33.9 occ:1.00 O A:GLU164 2.3 26.7 1.0 OE2 A:GLU164 2.5 46.5 1.0 C A:GLU164 3.3 32.4 1.0 CD A:GLU164 3.5 46.1 1.0 O A:HOH654 3.6 41.9 1.0 CG A:GLU164 3.8 40.8 1.0 CA A:GLU164 4.1 32.1 1.0 N A:HIS165 4.2 28.0 1.0 CA A:HIS165 4.2 27.8 1.0 N A:GLY167 4.4 33.1 1.0 CA A:GLY167 4.4 35.3 1.0 CB A:GLU164 4.6 34.1 1.0 C A:HIS165 4.6 32.8 1.0 OE1 A:GLU164 4.6 48.4 1.0 O A:HIS165 4.8 32.4 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