Magnesium in PDB 4z4d: Human ARGONAUTE2 Bound to T1-G Target Rna

The structure of Human ARGONAUTE2 Bound to T1-G Target Rna, PDB code: 4z4d 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)	35.40 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.738, 117.016, 69.874, 90.00, 92.43, 90.00
R / Rfree (%)	16.3 / 18.9

The binding sites of Magnesium atom in the Human ARGONAUTE2 Bound to T1-G Target Rna (pdb code 4z4d). 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-G Target Rna, PDB code: 4z4d:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human ARGONAUTE2 Bound to T1-G 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-G Target Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:16.2 occ:1.00 O B:HOH227 1.9 20.2 1.0 O A:VAL598 2.1 14.6 1.0 O A:HOH1017 2.1 18.8 1.0 O A:HOH1286 2.1 19.9 1.0 OD1 A:ASP597 2.1 18.1 1.0 O A:HOH1118 2.2 15.5 1.0 CG A:ASP597 3.1 21.8 1.0 C A:VAL598 3.2 14.1 1.0 OD2 A:ASP597 3.5 26.9 1.0 N A:VAL598 3.7 13.9 1.0 O2 B:C10 4.0 23.6 1.0 CA A:VAL598 4.1 12.8 1.0 O A:HOH1096 4.1 23.2 1.0 N A:THR599 4.2 14.3 1.0 O A:HOH1434 4.3 39.3 1.0 OD1 A:ASP669 4.3 34.6 1.0 O A:ASP669 4.3 15.0 1.0 CA A:THR599 4.4 17.5 1.0 CE1 A:HIS807 4.4 30.3 1.0 CB A:ASP597 4.4 13.3 1.0 N3 B:C10 4.5 26.7 1.0 OG1 A:THR599 4.5 20.2 1.0 C2 B:C10 4.6 27.4 1.0 C A:ASP597 4.6 16.6 1.0 OE2 A:GLU637 4.6 20.0 1.0 CA A:ASP597 4.7 13.5 1.0 CA A:GLY670 4.7 16.5 1.0 CB A:VAL598 4.8 14.6 1.0 C A:ASP669 4.9 15.9 1.0 ND1 A:HIS807 5.0 32.4 1.0

Magnesium binding site 2 out of 3 in the Human ARGONAUTE2 Bound to T1-G 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-G Target Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:29.8 occ:1.00 O B:HOH219 2.0 28.6 1.0 O B:HOH218 2.0 29.9 1.0 O B:HOH220 2.1 30.8 1.0 OP2 B:A13 2.1 41.4 1.0 O B:HOH222 2.1 30.1 1.0 O B:HOH239 2.1 33.6 1.0 P B:A13 3.4 39.0 1.0 O5' B:A13 4.0 43.9 1.0 OP1 B:A13 4.1 41.8 1.0 N7 B:A14 4.2 47.8 1.0 OP1 B:C12 4.3 35.2 1.0 O6 B:G15 4.3 59.4 1.0 OP2 B:C12 4.3 38.1 1.0 N7 B:A13 4.3 40.9 1.0 C8 B:A13 4.4 38.8 1.0 O5' B:C12 4.4 32.6 1.0 N6 B:A14 4.4 48.4 1.0 P B:C12 4.5 34.6 1.0 O3' B:C12 4.5 36.1 1.0 C3' B:C12 4.9 33.5 1.0 C5' B:C12 4.9 36.5 1.0

Magnesium binding site 3 out of 3 in the Human ARGONAUTE2 Bound to T1-G 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-G Target Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:19.5 occ:1.00 O D:HOH209 2.1 21.5 1.0 O D:HOH235 2.1 22.5 1.0 O D:HOH229 2.1 21.9 1.0 O D:HOH219 2.1 22.6 1.0 O D:HOH227 2.1 21.6 1.0 O4 D:U4 2.1 19.1 1.0 C4 D:U4 3.1 23.4 1.0 C5 D:U4 3.7 19.4 1.0 O D:HOH214 4.0 27.6 1.0 O D:HOH211 4.1 25.4 1.0 O B:HOH235 4.1 36.2 1.0 O D:HOH218 4.2 25.1 1.0 N6 B:A6 4.2 15.6 1.0 O B:HOH230 4.2 21.6 1.0 O D:HOH224 4.3 30.7 1.0 N7 D:A3 4.3 22.2 1.0 O6 D:G5 4.3 18.3 1.0 N3 D:U4 4.3 21.9 1.0 O D:HOH237 4.4 38.7 1.0 O D:HOH236 4.4 37.3 1.0 N6 D:A3 4.5 20.2 1.0 O B:HOH224 5.0 35.5 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