Magnesium 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:

Potassium

(K)

3 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rada Recombinase in Complex with Amp-Pnp and High Concentration of K+, PDB code: 2fpm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rada Recombinase in Complex with Amp-Pnp and High Concentration of K+


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 Amp-Pnp and High Concentration of K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:16.9 occ:1.00 O1G A:ANP401 2.0 17.1 1.0 O1B A:ANP401 2.0 14.4 1.0 OG1 A:THR112 2.1 13.7 1.0 O A:HOH603 2.1 14.7 1.0 O A:HOH602 2.1 13.0 1.0 O A:HOH601 2.2 13.6 1.0 CB A:THR112 3.1 13.9 1.0 PG A:ANP401 3.2 20.4 1.0 PB A:ANP401 3.2 18.7 1.0 N3B A:ANP401 3.4 16.6 1.0 O A:HOH610 3.8 21.3 1.0 O A:HOH608 3.8 16.9 1.0 N A:THR112 3.9 16.6 1.0 CA A:THR112 4.0 15.0 1.0 O2A A:ANP401 4.0 21.1 1.0 OD1 A:ASP211 4.1 18.4 1.0 O3G A:ANP401 4.1 18.2 1.0 K A:K504 4.1 29.8 1.0 OE1 A:GLU151 4.1 30.1 1.0 O2B A:ANP401 4.2 16.3 1.0 CG2 A:THR112 4.2 12.7 1.0 O2G A:ANP401 4.2 18.3 1.0 O3A A:ANP401 4.3 20.5 1.0 OD2 A:ASP211 4.3 20.1 1.0 OG1 A:THR153 4.3 17.4 1.0 O1A A:ANP401 4.4 20.8 1.0 PA A:ANP401 4.5 20.1 1.0 CG A:ASP211 4.7 19.6 1.0 CE A:LYS111 4.8 13.7 1.0 CB A:LYS111 4.8 15.4 1.0 C A:LYS111 5.0 15.3 1.0 CB A:THR153 5.0 18.4 1.0

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


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 Amp-Pnp and High Concentration of K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:27.7 occ:1.00 O A:GLN98 2.0 18.5 1.0 O A:HOH606 2.1 21.4 1.0 O A:HOH605 2.1 18.9 1.0 O A:HOH607 2.1 20.7 1.0 OD1 A:ASP246 2.1 26.5 1.0 O A:HOH604 2.2 25.2 1.0 CG A:ASP246 3.1 26.2 1.0 C A:GLN98 3.1 18.9 1.0 OD2 A:ASP246 3.3 26.2 1.0 N A:SER99 4.0 19.0 1.0 CA A:SER99 4.0 18.5 1.0 CA A:GLN98 4.0 18.7 1.0 OG A:SER99 4.2 21.2 1.0 O A:HOH646 4.2 23.1 1.0 CB A:GLN98 4.3 18.1 1.0 O A:ASN242 4.3 19.6 1.0 ND2 A:ASN242 4.3 20.1 1.0 CB A:ASP246 4.5 26.9 1.0 CB A:SER99 4.8 18.8 1.0 N A:ASP246 4.8 24.4 1.0 CA A:ASP246 4.8 27.2 1.0 CB A:ALA245 5.0 20.5 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