Magnesium in PDB 8d71: Human AGO2 Bound to MIR122(21NT)

The structure of Human AGO2 Bound to MIR122(21NT), PDB code: 8d71 was solved by Y.Xiao, I.Macrae, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.20 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.126, 107.735, 68.817, 90, 106.89, 90
R / Rfree (%)	22.3 / 28

The binding sites of Magnesium atom in the Human AGO2 Bound to MIR122(21NT) (pdb code 8d71). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Human AGO2 Bound to MIR122(21NT), PDB code: 8d71:

Magnesium binding site 1 out of 1 in the Human AGO2 Bound to MIR122(21NT)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human AGO2 Bound to MIR122(21NT) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:49.7 occ:1.00 OD1 A:ASP597 2.1 51.1 1.0 O A:HOH1043 2.3 42.6 1.0 O A:VAL598 3.1 50.4 1.0 CG A:ASP597 3.1 48.5 1.0 H A:VAL598 3.3 59.8 1.0 OD2 A:ASP597 3.4 50.5 1.0 HA3 A:GLY670 3.5 63.8 1.0 C A:VAL598 4.0 51.7 1.0 N A:VAL598 4.1 49.6 1.0 O A:ASP669 4.3 47.5 1.0 HA A:THR599 4.4 64.6 1.0 HA A:ASP597 4.4 56.0 1.0 CA A:GLY670 4.4 53.0 1.0 CB A:ASP597 4.5 45.7 1.0 HB3 A:ASP669 4.5 62.3 1.0 HG22 A:THR599 4.6 55.2 1.0 HD2 A:HIS807 4.6 66.6 1.0 CA A:VAL598 4.7 51.6 1.0 OD1 A:ASP669 4.7 52.3 1.0 C A:ASP669 4.7 46.2 1.0 HB2 A:ASP597 4.8 55.0 1.0 HA2 A:GLY670 4.8 63.8 1.0 CA A:ASP597 4.9 46.5 1.0 HB A:VAL598 4.9 60.5 1.0 N A:THR599 4.9 51.1 1.0 N A:GLY670 4.9 50.7 1.0 C A:ASP597 5.0 49.2 1.0 CG A:ASP669 5.0 47.0 1.0 O A:GLY670 5.0 51.7 1.0

Y.Xiao, T.M.Liu, I.J.Macrae. A Tiny Loop in the Argonaute Piwi Domain Tunes Small Rna Seed Strength. Embo Rep. 55806 2023.
ISSN: ESSN 1469-3178
PubMed: 37082939
DOI: 10.15252/EMBR.202255806