Magnesium in PDB 4z4h: Human ARGONAUTE2 A481T Mutant Bound to T1-A Target Rna

The structure of Human ARGONAUTE2 A481T Mutant Bound to T1-A Target Rna, PDB code: 4z4h 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)	44.81 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.695, 116.602, 70.099, 90.00, 92.29, 90.00
R / Rfree (%)	17.2 / 21.1

The binding sites of Magnesium atom in the Human ARGONAUTE2 A481T Mutant Bound to T1-A Target Rna (pdb code 4z4h). 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 A481T Mutant Bound to T1-A Target Rna, PDB code: 4z4h:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human ARGONAUTE2 A481T Mutant Bound to T1-A 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 A481T Mutant Bound to T1-A Target Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:29.2 occ:1.00 O A:HOH1055 2.0 38.6 1.0 O A:HOH1100 2.0 33.5 1.0 O A:VAL598 2.1 28.7 1.0 O A:HOH1037 2.3 38.4 1.0 O A:HOH1001 2.3 28.2 1.0 OD1 A:ASP597 2.7 38.0 1.0 C A:VAL598 3.3 22.4 1.0 CG A:ASP597 3.5 38.5 1.0 O2 B:C10 3.7 52.6 1.0 OD2 A:ASP597 3.7 40.8 1.0 O A:HOH1107 3.8 51.0 1.0 N A:VAL598 4.0 25.5 1.0 OD1 A:ASP669 4.0 52.3 1.0 N A:THR599 4.1 24.1 1.0 CA A:VAL598 4.2 20.3 1.0 CA A:THR599 4.2 24.3 1.0 C2 B:C10 4.3 60.6 1.0 N3 B:C10 4.4 63.0 1.0 CE1 A:HIS807 4.6 42.8 1.0 OE2 A:GLU637 4.7 41.8 1.0 O A:ASP669 4.7 27.2 1.0 OG1 A:THR599 4.7 41.3 1.0 CB A:VAL598 4.8 19.5 1.0 OE1 A:GLU637 4.8 35.8 1.0 CA A:GLY670 4.9 26.4 1.0 CB A:ASP597 4.9 27.6 1.0 C A:ASP597 5.0 26.3 1.0

Magnesium binding site 2 out of 3 in the Human ARGONAUTE2 A481T Mutant Bound to T1-A 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 A481T Mutant Bound to T1-A Target Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:73.9 occ:1.00 O B:HOH210 2.1 51.6 1.0 O B:HOH208 2.1 69.8 1.0 O B:HOH201 2.2 38.1 1.0 O B:HOH212 2.2 58.2 1.0 OP2 B:A13 2.2 74.5 1.0 O B:HOH203 2.3 67.2 1.0 P B:A13 3.6 77.6 1.0 OP1 B:C12 4.0 65.2 1.0 N6 B:A14 4.1 67.1 1.0 O5' B:A13 4.2 73.3 1.0 O6 B:G15 4.3 86.6 1.0 N7 B:A14 4.3 71.0 1.0 OP1 B:A13 4.3 81.5 1.0 O5' B:C12 4.5 62.4 1.0 N7 B:A13 4.5 64.6 1.0 P B:C12 4.5 59.0 1.0 OP2 B:C12 4.5 71.2 1.0 C8 B:A13 4.7 64.1 1.0 O3' B:C12 4.7 66.4 1.0

Magnesium binding site 3 out of 3 in the Human ARGONAUTE2 A481T Mutant Bound to T1-A 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 A481T Mutant Bound to T1-A Target Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:28.9 occ:1.00 O D:HOH202 2.0 17.2 1.0 O D:HOH207 2.1 21.4 1.0 O D:HOH201 2.2 23.1 1.0 O4 D:U4 2.2 26.3 1.0 O D:HOH209 2.2 42.9 1.0 O D:HOH213 2.4 30.2 1.0 C4 D:U4 3.4 39.7 1.0 O D:HOH206 3.9 30.2 1.0 C5 D:U4 4.0 27.4 1.0 N6 D:A3 4.2 24.8 1.0 N6 B:A6 4.2 23.8 1.0 N7 D:A3 4.3 29.9 1.0 O6 D:G5 4.3 31.6 1.0 O D:HOH205 4.4 64.4 1.0 N3 D:U4 4.5 31.8 1.0 O D:HOH204 4.8 39.7 1.0 N4 B:C5 4.9 22.2 1.0 C5 D:A3 5.0 31.5 1.0 C6 D:A3 5.0 33.4 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