Potassium 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:

Magnesium

(Mg)

2 atoms

The binding sites of Potassium 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 Potassium atom.
In total 3 binding sites of Potassium where determined in the Rada Recombinase in Complex with Amppnp at pH 6.0, PDB code: 2b21:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Rada Recombinase in Complex with Amppnp at pH 6.0


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K503 b:35.8 occ:1.00 OD2 A:ASP302 2.8 25.1 1.0 O A:ALA282 2.8 26.1 1.0 O A:HOH608 2.9 22.8 1.0 O A:THR283 3.2 22.7 1.0 CA A:THR283 3.5 23.5 1.0 C A:THR283 3.6 22.6 1.0 CG A:ASP302 3.6 25.3 1.0 C A:ALA282 3.9 25.1 1.0 OD1 A:ASP302 3.9 24.4 1.0 N A:THR283 4.2 24.3 1.0 NE A:ARG285 4.5 26.5 1.0 N A:PHE284 4.6 22.9 1.0 CB A:THR283 4.7 25.3 1.0 CA A:SER303 4.8 28.7 1.0 N A:SER303 4.9 27.3 1.0 CB A:ASP302 4.9 26.3 1.0 NH2 A:ARG285 4.9 28.4 1.0 C A:SER303 4.9 29.6 1.0 C A:ASP302 4.9 26.4 1.0 CD A:PRO304 5.0 31.3 1.0

Potassium binding site 2 out of 3 in the Rada Recombinase in Complex with Amppnp at pH 6.0


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K505 b:38.9 occ:1.00 O3' A:ANP401 2.7 29.5 1.0 O A:HOH616 2.7 19.4 1.0 O2' A:ANP401 2.8 31.4 1.0 C3' A:ANP401 3.4 28.7 1.0 C2' A:ANP401 3.7 30.1 1.0 NH2 A:ARG296 3.9 31.9 1.0 C4' A:ANP401 4.1 30.1 1.0 NZ A:LYS290 4.5 44.5 1.0 CE A:LYS290 4.8 47.7 1.0 C1' A:ANP401 4.8 29.5 1.0 C5' A:ANP401 4.9 27.8 1.0

Potassium binding site 3 out of 3 in the Rada Recombinase in Complex with Amppnp at pH 6.0


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Rada Recombinase in Complex with Amppnp at pH 6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:K506 b:43.9 occ:1.00 O A:LEU8 2.7 33.0 1.0 O A:HOH660 2.8 37.0 1.0 O A:THR6 2.9 34.9 1.0 O A:VAL11 3.1 43.1 1.0 N A:VAL11 3.6 45.8 1.0 C A:LEU8 3.6 35.3 1.0 C A:THR6 3.8 34.6 1.0 C A:VAL11 3.8 45.0 1.0 N A:GLY10 4.0 43.5 1.0 CA A:VAL11 4.1 44.5 1.0 CA A:PRO9 4.1 38.7 1.0 N A:PRO9 4.2 37.2 1.0 C A:PRO9 4.3 40.9 1.0 CB A:VAL11 4.4 43.1 1.0 C A:ASP7 4.4 36.5 1.0 CA A:THR6 4.4 36.0 1.0 O A:ASP7 4.5 36.4 1.0 N A:LEU8 4.5 35.5 1.0 CA A:LEU8 4.7 34.8 1.0 C A:GLY10 4.7 46.4 1.0 N A:ASP7 4.8 35.2 1.0 CA A:GLY10 4.8 45.6 1.0 N A:GLY12 4.9 46.3 1.0 CB A:THR6 5.0 37.6 1.0

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