Magnesium in PDB 5guh: Crystal Structure of Silkworm Piwi-Clade Argonaute Siwi Bound to Pirna

The structure of Crystal Structure of Silkworm Piwi-Clade Argonaute Siwi Bound to Pirna, PDB code: 5guh was solved by N.Matsumoto, H.Nishimasu, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.84 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.899, 114.619, 136.718, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 23.6

The binding sites of Magnesium atom in the Crystal Structure of Silkworm Piwi-Clade Argonaute Siwi Bound to Pirna (pdb code 5guh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Silkworm Piwi-Clade Argonaute Siwi Bound to Pirna, PDB code: 5guh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Silkworm Piwi-Clade Argonaute Siwi Bound to Pirna


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 Silkworm Piwi-Clade Argonaute Siwi Bound to Pirna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:30.2 occ:1.00 OP3 B:U1 2.0 67.0 1.0 O A:LEU899 2.0 56.7 1.0 OP1 B:U3 2.0 66.6 1.0 O A:HOH1027 2.1 38.4 1.0 OE1 A:GLN645 2.1 44.1 1.0 OXT A:LEU899 2.4 52.4 1.0 C A:LEU899 2.5 53.0 1.0 CD A:GLN645 3.2 43.2 1.0 P B:U1 3.2 57.8 1.0 OP2 B:U1 3.4 54.0 1.0 P B:U3 3.4 55.8 1.0 NE2 A:GLN645 3.7 43.4 1.0 NZ A:LYS875 3.8 46.0 1.0 NZ A:LYS649 4.0 42.0 1.0 CA A:LEU899 4.0 45.8 1.0 O3' B:A2 4.1 58.1 1.0 O5' B:U1 4.2 63.1 1.0 OP1 B:U1 4.2 58.2 1.0 C5' B:U1 4.3 58.8 1.0 OP2 B:U3 4.3 57.8 1.0 ND2 A:ASN859 4.4 35.3 1.0 O5' B:U3 4.4 59.6 1.0 CE A:LYS649 4.4 35.1 1.0 CG A:GLN645 4.5 41.1 1.0 NE2 A:GLN623 4.5 49.1 1.0 C5' B:U3 4.5 61.5 1.0 OE1 A:GLN623 4.5 46.4 1.0 CB A:LEU899 4.6 43.1 1.0 O A:HOH1066 4.7 54.7 1.0 N A:LEU899 4.9 38.1 1.0 CD A:GLN623 5.0 48.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Silkworm Piwi-Clade Argonaute Siwi Bound to Pirna


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 Silkworm Piwi-Clade Argonaute Siwi Bound to Pirna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:60.8 occ:1.00 N A:LYS780 3.2 43.8 1.0 OD1 A:ASP740 3.3 77.5 1.0 CA A:SER779 3.9 37.5 1.0 N A:ARG781 3.9 52.9 1.0 C A:SER779 4.0 41.3 1.0 CB A:LYS780 4.1 44.3 1.0 CA A:LYS780 4.1 44.7 1.0 O A:VAL778 4.3 38.6 1.0 N A:GLY741 4.3 57.8 1.0 CG A:ASP740 4.4 73.3 1.0 CD A:LYS780 4.5 58.4 1.0 C A:LYS780 4.5 50.6 1.0 CA A:GLY741 4.6 61.3 1.0 CB A:SER779 4.6 37.3 1.0 CG A:LYS780 4.7 48.4 1.0 CB A:ARG781 4.8 51.5 1.0 O A:HOH1077 4.8 71.4 1.0 OD2 A:ASP740 4.8 77.1 1.0 N A:SER779 4.8 37.3 1.0 CA A:ARG781 5.0 52.1 1.0 C A:VAL778 5.0 35.5 1.0

N.Matsumoto, H.Nishimasu, K.Sakakibara, K.M.Nishida, T.Hirano, R.Ishitani, H.Siomi, M.C.Siomi, O.Nureki. Crystal Structure of Silkworm Piwi-Clade Argonaute Siwi Bound to Pirna Cell V. 167 484 2016.
ISSN: ISSN 1097-4172
PubMed: 27693359
DOI: 10.1016/J.CELL.2016.09.002