Magnesium in PDB 4z4e: Human ARGONAUTE2 Bound to T1-U Target Rna

The structure of Human ARGONAUTE2 Bound to T1-U Target Rna, PDB code: 4z4e was solved by N.T.Schirle, I.J.Macrae, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.27 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.645, 116.841, 69.744, 90.00, 92.43, 90.00
R / Rfree (%)	15.8 / 18.5

The binding sites of Magnesium atom in the Human ARGONAUTE2 Bound to T1-U Target Rna (pdb code 4z4e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human ARGONAUTE2 Bound to T1-U Target Rna, PDB code: 4z4e:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human ARGONAUTE2 Bound to T1-U Target Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human ARGONAUTE2 Bound to T1-U Target Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:15.0 occ:1.00 O A:HOH1243 2.0 16.4 1.0 O A:HOH1047 2.1 15.3 1.0 O B:HOH229 2.1 19.4 1.0 OD1 A:ASP597 2.1 17.2 1.0 O A:VAL598 2.1 14.1 1.0 O A:HOH1080 2.1 14.2 1.0 CG A:ASP597 3.1 22.9 1.0 C A:VAL598 3.2 14.4 1.0 OD2 A:ASP597 3.4 22.0 1.0 N A:VAL598 3.7 10.0 1.0 O2 B:C10 4.0 24.2 1.0 CA A:VAL598 4.1 10.3 1.0 O A:HOH1131 4.1 21.0 1.0 N A:THR599 4.2 14.1 1.0 O A:ASP669 4.3 14.2 1.0 CE1 A:HIS807 4.3 33.7 1.0 O B:HOH251 4.3 41.8 1.0 OD1 A:ASP669 4.3 29.4 1.0 CA A:THR599 4.4 13.1 1.0 CB A:ASP597 4.4 13.5 1.0 N3 B:C10 4.4 26.4 1.0 C2 B:C10 4.6 24.4 1.0 C A:ASP597 4.6 15.3 1.0 OG1 A:THR599 4.6 21.0 1.0 OE2 A:GLU637 4.6 17.3 1.0 CA A:ASP597 4.7 13.4 1.0 CA A:GLY670 4.7 15.2 1.0 CB A:VAL598 4.7 11.9 1.0 C A:ASP669 4.9 12.9 1.0 ND1 A:HIS807 4.9 30.6 1.0 O A:HOH1018 5.0 42.1 1.0

Magnesium binding site 2 out of 3 in the Human ARGONAUTE2 Bound to T1-U Target Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human ARGONAUTE2 Bound to T1-U Target Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:33.5 occ:1.00 OP2 B:A13 2.0 38.9 1.0 O B:HOH207 2.1 31.1 1.0 O B:HOH222 2.1 28.1 1.0 O B:HOH216 2.1 36.8 1.0 O B:HOH230 2.1 34.3 1.0 O B:HOH239 2.1 39.0 1.0 P B:A13 3.4 38.3 1.0 O5' B:A13 4.0 38.0 1.0 OP1 B:A13 4.1 39.5 1.0 OP1 B:C12 4.2 33.7 1.0 O B:HOH250 4.2 52.9 1.0 N7 B:A14 4.3 43.5 1.0 O6 B:G15 4.3 57.6 1.0 OP2 B:C12 4.4 33.3 1.0 N7 B:A13 4.4 35.5 1.0 N6 B:A14 4.4 43.3 1.0 O5' B:C12 4.5 31.2 1.0 C8 B:A13 4.5 35.1 1.0 P B:C12 4.5 32.2 1.0 O3' B:C12 4.5 34.3 1.0 C3' B:C12 4.9 34.2 1.0 C5' B:C12 4.9 34.2 1.0

Magnesium binding site 3 out of 3 in the Human ARGONAUTE2 Bound to T1-U Target Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human ARGONAUTE2 Bound to T1-U Target Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:22.8 occ:1.00 O D:HOH207 2.0 19.6 1.0 O D:HOH228 2.1 23.4 1.0 O D:HOH233 2.1 21.7 1.0 O D:HOH211 2.1 19.5 1.0 O D:HOH226 2.1 21.7 1.0 O4 D:U4 2.1 21.6 1.0 C4 D:U4 3.1 18.6 1.0 C5 D:U4 3.7 19.5 1.0 O D:HOH212 4.0 29.4 1.0 O D:HOH216 4.1 23.0 1.0 O D:HOH209 4.1 24.4 1.0 O B:HOH225 4.2 20.2 1.0 N6 B:A6 4.2 16.7 1.0 O B:HOH240 4.2 33.3 1.0 N7 D:A3 4.3 21.9 1.0 O6 D:G5 4.3 19.1 1.0 N3 D:U4 4.3 20.5 1.0 O D:HOH235 4.3 40.6 1.0 O D:HOH225 4.3 31.3 1.0 O D:HOH234 4.4 31.6 1.0 N6 D:A3 4.4 18.5 1.0 N4 B:C5 4.9 15.2 1.0

N.T.Schirle, J.Sheu-Gruttadauria, S.D.Chandradoss, C.Joo, I.J.Macrae. Water-Mediated Recognition of T1-Adenosine Anchors ARGONAUTE2 to Microrna Targets. Elife V. 4 2015.
ISSN: ESSN 2050-084X
PubMed: 26359634
DOI: 10.7554/ELIFE.07646