Magnesium in PDB 2b21: Rada Recombinase in Complex with Amppnp at pH 6.0

The structure of Rada Recombinase in Complex with Amppnp at pH 6.0, PDB code: 2b21 was solved by X.Qian, Y.He, Y.Wu, Y.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.40
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	83.071, 83.071, 107.168, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 25.6

The structure of Rada Recombinase in Complex with Amppnp at pH 6.0 also contains other interesting chemical elements:

Potassium

(K)

3 atoms

The binding sites of Magnesium atom in the Rada Recombinase in Complex with Amppnp at pH 6.0 (pdb code 2b21). 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 in Complex with Amppnp at pH 6.0, PDB code: 2b21:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rada Recombinase in Complex with Amppnp at pH 6.0


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rada Recombinase in Complex with Amppnp at pH 6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:19.0 occ:1.00 O2G A:ANP401 1.9 23.6 1.0 O1B A:ANP401 2.0 24.2 1.0 O A:HOH602 2.1 22.2 1.0 O A:HOH603 2.1 13.9 1.0 OG1 A:THR112 2.2 18.1 1.0 O A:HOH601 2.2 9.8 1.0 PG A:ANP401 3.1 26.8 1.0 PB A:ANP401 3.2 26.1 1.0 CB A:THR112 3.3 18.7 1.0 N3B A:ANP401 3.4 24.2 1.0 O A:HOH624 3.8 29.7 1.0 N A:THR112 4.0 20.1 1.0 O A:HOH621 4.0 27.4 1.0 O2A A:ANP401 4.0 27.3 1.0 O3G A:ANP401 4.0 26.7 1.0 O A:HOH610 4.1 23.8 1.0 O1G A:ANP401 4.1 24.4 1.0 O2B A:ANP401 4.1 24.2 1.0 CA A:THR112 4.3 19.1 1.0 OD1 A:ASP211 4.3 19.0 1.0 OD2 A:ASP211 4.3 17.4 1.0 O3A A:ANP401 4.4 28.0 1.0 CG2 A:THR112 4.4 19.1 1.0 OG1 A:THR153 4.4 17.9 1.0 O1A A:ANP401 4.5 25.9 1.0 PA A:ANP401 4.5 26.0 1.0 CE A:LYS111 4.5 13.3 1.0 CB A:LYS111 4.6 16.7 1.0 CG A:ASP211 4.8 18.5 1.0 O A:HOH649 5.0 34.9 1.0

Magnesium binding site 2 out of 2 in the Rada Recombinase in Complex with Amppnp at pH 6.0


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rada Recombinase in Complex with Amppnp at pH 6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:26.7 occ:1.00 OD1 A:ASP246 2.0 22.4 1.0 O A:GLN98 2.1 25.2 1.0 O A:HOH607 2.1 17.6 1.0 O A:HOH604 2.1 19.1 1.0 O A:HOH606 2.1 26.4 1.0 O A:HOH605 2.2 22.1 1.0 CG A:ASP246 2.9 25.3 1.0 OD2 A:ASP246 3.1 24.0 1.0 C A:GLN98 3.2 24.1 1.0 CA A:GLN98 4.1 23.7 1.0 N A:SER99 4.1 25.1 1.0 O A:HOH617 4.1 22.6 1.0 ND2 A:ASN242 4.2 29.1 1.0 OG A:SER99 4.2 21.4 1.0 CB A:GLN98 4.2 22.7 1.0 CA A:SER99 4.2 23.5 1.0 CB A:ASP246 4.3 23.7 1.0 O A:ASN242 4.4 28.1 1.0 CA A:ASP246 4.8 25.3 1.0 CB A:SER99 4.8 22.8 1.0 N A:ASP246 4.9 24.7 1.0

X.Qian, Y.He, Y.Wu, Y.Luo. Crystal Structure of Methanococcus Voltae Rada at An Acidic pH To Be Published.