Magnesium in PDB 4z4f: Human ARGONAUTE2 Bound to T1-Dap Target Rna

The structure of Human ARGONAUTE2 Bound to T1-Dap Target Rna, PDB code: 4z4f 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)	35.46 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.859, 116.591, 70.375, 90.00, 92.52, 90.00
R / Rfree (%)	18.4 / 23.3

The binding sites of Magnesium atom in the Human ARGONAUTE2 Bound to T1-Dap Target Rna (pdb code 4z4f). 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-Dap Target Rna, PDB code: 4z4f:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human ARGONAUTE2 Bound to T1-Dap 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-Dap Target Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:24.9 occ:1.00 O A:VAL598 2.1 33.7 1.0 O A:HOH1007 2.1 37.6 1.0 O A:HOH1006 2.1 45.6 1.0 O B:HOH204 2.2 28.1 1.0 O A:HOH1003 2.3 32.7 1.0 OD1 A:ASP597 2.4 35.9 1.0 C A:VAL598 3.3 28.1 1.0 CG A:ASP597 3.4 32.5 1.0 O2 B:C10 3.5 56.3 1.0 OD2 A:ASP597 3.7 39.3 1.0 OD2 A:ASP669 3.7 83.5 1.0 N A:VAL598 3.9 22.6 1.0 CA A:VAL598 4.2 22.9 1.0 C2 B:C10 4.2 66.9 1.0 N3 B:C10 4.2 74.2 1.0 N A:THR599 4.3 29.5 1.0 CA A:THR599 4.4 30.5 1.0 O A:ASP669 4.6 32.8 1.0 CE1 A:HIS807 4.6 58.5 1.0 OE2 A:GLU637 4.6 49.3 1.0 OG1 A:THR599 4.6 53.7 1.0 CB A:ASP597 4.7 25.8 1.0 CA A:GLY670 4.8 35.0 1.0 CB A:VAL598 4.8 23.2 1.0 C A:ASP597 4.8 29.4 1.0 OE1 A:GLU637 4.9 47.8 1.0 CG A:ASP669 4.9 70.9 1.0

Magnesium binding site 2 out of 3 in the Human ARGONAUTE2 Bound to T1-Dap 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-Dap Target Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:91.3 occ:1.00 O B:HOH201 2.1 45.6 1.0 O B:HOH202 2.3 80.9 1.0 OP2 B:A13 2.8 79.0 1.0 N6 B:A14 3.7 79.4 1.0 O6 B:G15 3.8 0.9 1.0 P B:A13 4.2 78.9 1.0 N7 B:A14 4.2 95.0 1.0 C6 B:G15 4.6 0.4 1.0 O5' B:A13 4.7 91.9 1.0 C6 B:A14 4.7 83.3 1.0 OP1 B:C12 4.7 70.0 1.0 N7 B:A13 4.8 77.7 1.0 C5 B:A14 4.9 91.0 1.0 OP1 B:A13 4.9 78.0 1.0 OP2 B:C12 4.9 81.2 1.0

Magnesium binding site 3 out of 3 in the Human ARGONAUTE2 Bound to T1-Dap 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-Dap Target Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:45.4 occ:1.00 O D:HOH202 2.0 25.2 1.0 O4 D:U4 2.1 45.9 1.0 O D:HOH203 2.4 53.3 1.0 O D:HOH201 2.4 61.9 1.0 O D:HOH205 2.7 25.0 1.0 O D:HOH204 3.0 29.1 1.0 C4 D:U4 3.2 42.3 1.0 C5 D:U4 3.7 43.5 1.0 N7 D:A3 4.1 42.7 1.0 N6 D:A3 4.4 35.2 1.0 N3 D:U4 4.4 38.2 1.0 O6 D:G5 4.5 36.5 1.0 N6 B:A6 4.6 42.7 1.0 C5 D:A3 4.9 38.4 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