Magnesium in PDB 8d6j: Human AGO2 Bound to MIR122(21NT) with Piwi Loop Swapped to ATAGO10 Sequence

The structure of Human AGO2 Bound to MIR122(21NT) with Piwi Loop Swapped to ATAGO10 Sequence, PDB code: 8d6j 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)	39.22 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.302, 107.512, 68.706, 90, 106.9, 90
R / Rfree (%)	23.2 / 28.4

The binding sites of Magnesium atom in the Human AGO2 Bound to MIR122(21NT) with Piwi Loop Swapped to ATAGO10 Sequence (pdb code 8d6j). 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) with Piwi Loop Swapped to ATAGO10 Sequence, PDB code: 8d6j:

Magnesium binding site 1 out of 1 in the Human AGO2 Bound to MIR122(21NT) with Piwi Loop Swapped to ATAGO10 Sequence


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) with Piwi Loop Swapped to ATAGO10 Sequence within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:50.1 occ:1.00 OD1 A:ASP597 2.1 43.5 1.0 O A:HOH1012 2.2 46.5 1.0 OD2 A:ASP669 2.4 41.9 1.0 CG A:ASP597 3.0 42.6 1.0 OD2 A:ASP597 3.2 43.5 1.0 O A:VAL598 3.4 51.8 1.0 H A:VAL598 3.4 58.6 1.0 CG A:ASP669 3.5 44.2 1.0 HB3 A:ASP669 3.6 48.3 1.0 CB A:ASP669 4.1 39.5 1.0 N A:VAL598 4.2 48.2 1.0 C A:VAL598 4.3 53.0 1.0 CB A:ASP597 4.4 43.9 1.0 HB2 A:ASP669 4.5 48.3 1.0 HA A:ASP597 4.5 54.1 1.0 OD1 A:ASP669 4.6 36.8 1.0 HB2 A:ASP597 4.7 53.5 1.0 HA A:THR599 4.8 70.6 1.0 CA A:ASP597 4.9 44.4 1.0 CA A:VAL598 4.9 48.7 1.0 OE2 A:GLU637 4.9 46.5 1.0 HB A:VAL598 5.0 63.8 1.0 O A:GLY670 5.0 39.8 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