Magnesium in PDB 6cbd: Crystal Structure of Human ARGONAUTE2 Bound to Three Tryptophans

The structure of Crystal Structure of Human ARGONAUTE2 Bound to Three Tryptophans, PDB code: 6cbd was solved by J.Sheu-Gruttadauria, I.J.Macrae, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.50 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.829, 116.995, 70.252, 90.00, 92.64, 90.00
R / Rfree (%)	17.6 / 21.5

The binding sites of Magnesium atom in the Crystal Structure of Human ARGONAUTE2 Bound to Three Tryptophans (pdb code 6cbd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human ARGONAUTE2 Bound to Three Tryptophans, PDB code: 6cbd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Human ARGONAUTE2 Bound to Three Tryptophans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human ARGONAUTE2 Bound to Three Tryptophans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg906 b:28.1 occ:1.00 O B:HOH215 2.0 27.0 1.0 O A:HOH1131 2.0 25.9 1.0 O A:VAL598 2.1 24.6 1.0 OD1 A:ASP597 2.1 30.0 1.0 O A:HOH1001 2.1 23.6 1.0 O A:HOH1034 2.2 26.9 1.0 CG A:ASP597 3.1 31.7 1.0 C A:VAL598 3.2 25.2 1.0 OD2 A:ASP597 3.4 26.4 1.0 N A:VAL598 3.7 27.9 1.0 OD1 A:ASP669 3.8 40.5 1.0 O A:HOH1110 3.9 34.6 1.0 O2 B:C10 4.0 31.5 1.0 CA A:VAL598 4.1 22.4 1.0 N A:THR599 4.2 24.1 1.0 CA A:THR599 4.3 25.1 1.0 CB A:ASP597 4.4 25.3 1.0 O A:ASP669 4.4 25.1 1.0 N3 B:C10 4.5 42.7 1.0 C2 B:C10 4.5 40.2 1.0 OE2 A:GLU637 4.6 28.4 1.0 C A:ASP597 4.6 25.6 1.0 NE2 A:HIS807 4.6 31.8 1.0 CA A:ASP597 4.7 22.7 1.0 CB A:VAL598 4.7 22.8 1.0 CA A:GLY670 4.7 29.1 1.0 CD2 A:HIS807 4.9 35.9 1.0 C A:ASP669 4.9 25.1 1.0 OE1 A:GLU637 5.0 31.9 1.0 CG A:ASP669 5.0 31.1 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human ARGONAUTE2 Bound to Three Tryptophans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human ARGONAUTE2 Bound to Three Tryptophans within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:60.2 occ:1.00 OP2 B:A13 2.2 53.0 1.0 O B:HOH204 2.3 54.6 1.0 O B:HOH218 2.4 52.6 1.0 OP1 B:C12 3.3 48.6 1.0 P B:A13 3.7 62.4 1.0 P B:C12 3.8 47.5 1.0 OP2 B:C12 3.8 46.5 1.0 O5' B:C12 3.9 52.5 1.0 C5' B:C12 4.4 46.4 1.0 O5' B:A13 4.5 57.6 1.0 O3' B:C12 4.5 58.1 1.0 OP1 B:A13 4.5 66.5 1.0 N7 B:A13 4.6 51.5 1.0 N6 B:A14 4.7 55.2 1.0 C3' B:C12 4.8 53.0 1.0 C8 B:A13 4.8 50.6 1.0 O6 B:G15 5.0 71.2 1.0 N7 B:A14 5.0 57.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human ARGONAUTE2 Bound to Three Tryptophans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human ARGONAUTE2 Bound to Three Tryptophans within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:38.9 occ:1.00 O C:HOH214 2.1 35.0 1.0 O C:HOH206 2.1 28.4 1.0 O C:HOH219 2.1 38.7 1.0 O C:HOH205 2.2 31.4 1.0 O4 C:U4 2.3 29.6 1.0 O C:HOH215 2.3 38.1 1.0 C4 C:U4 3.3 33.0 1.0 O C:HOH204 3.8 41.7 1.0 C5 C:U4 3.8 32.8 1.0 O C:HOH209 4.0 34.5 1.0 O B:HOH224 4.1 29.4 1.0 N7 C:A3 4.2 33.0 1.0 O C:HOH208 4.3 41.6 1.0 N6 B:A6 4.4 27.3 1.0 O B:HOH216 4.4 34.4 1.0 N6 C:A3 4.4 30.0 1.0 N3 C:U4 4.5 31.8 1.0 O6 C:G5 4.5 30.7 1.0 C5 C:A3 5.0 34.9 1.0

J.Sheu-Gruttadauria, I.J.Macrae. Phase Transitions in the Assembly and Function of Human Mirisc. Cell V. 173 946 2018.
ISSN: ISSN 1097-4172
PubMed: 29576456
DOI: 10.1016/J.CELL.2018.02.051