Potassium in PDB 2fpm: Rada Recombinase in Complex with Amp-Pnp and High Concentration of K+

The structure of Rada Recombinase in Complex with Amp-Pnp and High Concentration of K+, PDB code: 2fpm was solved by Y.Wu, X.Qian, Y.He, I.A.Moya, Y.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	83.699, 83.699, 105.440, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 23.9

The structure of Rada Recombinase in Complex with Amp-Pnp and High Concentration of K+ also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Potassium atom in the Rada Recombinase in Complex with Amp-Pnp and High Concentration of K+ (pdb code 2fpm). 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 Amp-Pnp and High Concentration of K+, PDB code: 2fpm:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Rada Recombinase in Complex with Amp-Pnp and High Concentration of K+


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 Amp-Pnp and High Concentration of K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:K503 b:18.0 occ:1.00 O2G A:ANP401 2.6 18.3 1.0 O A:HOH610 3.3 21.3 1.0 PG A:ANP401 4.0 20.4 1.0 CB A:PHE107 4.3 20.6 1.0 N3B A:ANP401 4.4 16.6 1.0 K A:K504 4.4 29.8 1.0 CD1 A:PHE107 4.7 23.3 1.0 O1G A:ANP401 4.8 17.1 1.0 O A:HOH609 4.8 31.7 1.0 O3G A:ANP401 4.9 18.2 1.0 N A:GLY108 4.9 17.5 1.0 CG A:PHE107 5.0 22.4 1.0

Potassium binding site 2 out of 3 in the Rada Recombinase in Complex with Amp-Pnp and High Concentration of K+


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 Amp-Pnp and High Concentration of K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:K504 b:29.8 occ:1.00 O A:HOH610 2.6 21.3 1.0 O A:HOH609 2.8 31.7 1.0 O1G A:ANP401 2.9 17.1 1.0 OE1 A:GLU151 3.1 30.1 1.0 O2G A:ANP401 3.1 18.3 1.0 O A:HOH603 3.1 14.7 1.0 CD A:GLU151 3.4 28.8 1.0 OE2 A:GLU151 3.5 34.6 1.0 PG A:ANP401 3.5 20.4 1.0 O A:HOH608 3.7 16.9 1.0 MG A:MG501 4.1 16.9 1.0 O A:HOH602 4.2 13.0 1.0 O3G A:ANP401 4.3 18.2 1.0 K A:K503 4.4 18.0 1.0 CB A:GLU151 4.5 21.4 1.0 CG A:GLU151 4.5 25.3 1.0 CG2 A:THR153 4.5 20.5 1.0 NE2 A:GLN257 4.7 24.0 1.0 N3B A:ANP401 4.9 16.6 1.0 O A:HOH601 5.0 13.6 1.0

Potassium binding site 3 out of 3 in the Rada Recombinase in Complex with Amp-Pnp and High Concentration of K+


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 Amp-Pnp and High Concentration of K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:K506 b:28.2 occ:1.00 O A:THR6 2.6 26.4 1.0 O A:HOH710 2.6 41.6 1.0 O A:LEU8 2.7 29.8 1.0 O A:VAL11 2.7 36.7 1.0 O A:HOH709 2.9 40.7 1.0 C A:THR6 3.5 26.8 1.0 C A:VAL11 3.6 37.6 1.0 C A:LEU8 3.6 31.4 1.0 N A:VAL11 3.7 39.3 1.0 N A:GLY10 4.1 39.1 1.0 CA A:VAL11 4.1 37.0 1.0 CA A:THR6 4.2 26.3 1.0 N A:LEU8 4.3 30.0 1.0 CA A:PRO9 4.3 35.7 1.0 N A:PRO9 4.4 33.5 1.0 C A:ASP7 4.4 30.1 1.0 C A:PRO9 4.4 37.3 1.0 CB A:VAL11 4.4 35.6 1.0 C A:GLY10 4.5 40.7 1.0 N A:ASP7 4.5 27.9 1.0 CA A:LEU8 4.6 30.4 1.0 CB A:THR6 4.6 26.5 1.0 O A:ASP7 4.7 29.7 1.0 N A:GLY12 4.7 37.5 1.0 CA A:ASP7 4.8 30.9 1.0 CA A:GLY10 4.8 40.2 1.0

X.Qian, Y.Wu, Y.He, I.A.Moya, Y.Luo. Crystal Structure of Methanoccocus Voltae Rada in Complex with Adp: Hydrolysis-Induced Conformational Change Biochemistry V. 44 13753 2005.
ISSN: ISSN 0006-2960
PubMed: 16229465
DOI: 10.1021/BI051222I