Magnesium in PDB 7ygn: Cryo-Em Structure of the Mili in Complex with Pirna

The binding sites of Magnesium atom in the Cryo-Em Structure of the Mili in Complex with Pirna (pdb code 7ygn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of the Mili in Complex with Pirna, PDB code: 7ygn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of the Mili in Complex with Pirna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the Mili in Complex with Pirna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:12.1 occ:1.00 OP1 B:U1 1.9 0.0 1.0 O A:LEU971 1.9 25.1 1.0 OP1 B:A3 2.1 0.0 1.0 NE2 A:GLN718 2.4 16.3 1.0 C A:LEU971 2.8 25.1 1.0 OXT A:LEU971 3.0 25.1 1.0 P B:U1 3.4 0.0 1.0 P B:A3 3.6 0.0 1.0 CD A:GLN718 3.6 16.3 1.0 OP3 B:U1 4.1 0.0 1.0 C5' B:U1 4.1 0.0 1.0 OE1 A:GLN718 4.1 16.3 1.0 O5' B:U1 4.2 0.0 1.0 O3' B:U2 4.2 0.0 1.0 CA A:LEU971 4.2 25.1 1.0 OP2 B:U1 4.3 0.0 1.0 C5' B:A3 4.4 0.0 1.0 O5' B:A3 4.4 0.0 1.0 OP2 B:A3 4.6 0.0 1.0 ND2 A:ASN931 4.6 16.7 1.0 CG A:GLN718 4.8 16.3 1.0 NZ A:LYS722 4.8 16.4 1.0 CB A:LEU971 4.8 25.1 1.0 CE A:LYS722 4.9 16.4 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of the Mili in Complex with Pirna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of the Mili in Complex with Pirna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:16.2 occ:1.00 OD2 A:ASP743 2.0 21.9 1.0 OD1 A:ASP743 2.4 21.9 1.0 CG A:ASP743 2.5 21.9 1.0 NZ A:LYS852 3.6 13.1 1.0 ND1 A:HIS946 3.6 19.9 1.0 OD2 A:ASP813 4.0 17.3 1.0 CB A:ASP743 4.1 21.9 1.0 CE1 A:HIS946 4.1 19.9 1.0 OD1 A:ASP813 4.1 17.3 1.0 CG A:ASP813 4.2 17.3 1.0 O A:VAL744 4.2 24.6 1.0 CG A:HIS946 4.2 19.9 1.0 CA A:GLY814 4.6 15.8 1.0 CB A:HIS946 4.6 19.9 1.0 N A:VAL744 4.7 24.6 1.0 N A:GLY814 4.8 15.8 1.0 CE A:LYS852 4.8 13.1 1.0 NE2 A:HIS946 4.8 19.9 1.0 CD2 A:HIS946 4.9 19.9 1.0 CA A:ASP743 4.9 21.9 1.0

Z.Q.Li, H.B.Liu, J.P.Wu, E.Z.Shen. Structure Basis of Mammalian Piwi-Pirna Silencing Machinery To Be Published.