Magnesium in PDB 7yfq: Cryo-Em Structure of the Efpiwi (N959K)-Pirna-Target Ternary Complex

The binding sites of Magnesium atom in the Cryo-Em Structure of the Efpiwi (N959K)-Pirna-Target Ternary Complex (pdb code 7yfq). 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 Efpiwi (N959K)-Pirna-Target Ternary Complex, PDB code: 7yfq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of the Efpiwi (N959K)-Pirna-Target Ternary Complex


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 Efpiwi (N959K)-Pirna-Target Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:9.3 occ:1.00 OP1 B:U1 2.1 7.2 1.0 O A:LEU987 2.5 20.8 1.0 NZ A:LYS739 2.6 19.7 1.0 OP2 B:U1 2.7 0.0 1.0 NE2 A:GLN735 2.8 25.9 1.0 CE A:LYS739 2.9 19.7 1.0 P B:U1 2.9 4.2 1.0 C A:LEU987 3.2 20.8 1.0 OXT A:LEU987 3.2 20.8 1.0 OE1 A:GLN712 3.5 17.7 1.0 OP3 B:U1 3.9 8.0 1.0 NE2 A:GLN712 4.0 17.7 1.0 CD A:GLN735 4.0 25.9 1.0 CD A:GLN712 4.0 17.7 1.0 O5' B:U1 4.1 3.0 1.0 CD A:LYS739 4.3 19.7 1.0 C5' B:U1 4.5 1.5 1.0 OP1 B:A3 4.5 6.9 1.0 O A:SER711 4.6 18.7 1.0 CG A:GLN735 4.6 25.9 1.0 CA A:LEU987 4.7 20.8 1.0 O A:PHE986 4.7 20.4 1.0 OE1 A:GLN735 4.9 25.9 1.0 C A:PHE986 4.9 20.4 1.0 N A:LEU987 4.9 20.8 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of the Efpiwi (N959K)-Pirna-Target Ternary Complex


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 Efpiwi (N959K)-Pirna-Target Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:22.7 occ:1.00 OD2 A:ASP760 2.0 18.4 1.0 ND1 A:HIS962 2.1 15.3 1.0 CG A:ASP760 2.4 18.4 1.0 OD1 A:ASP760 2.5 18.4 1.0 CE1 A:HIS962 2.7 15.3 1.0 CG A:HIS962 3.3 15.3 1.0 CB A:ASP760 3.8 18.4 1.0 CB A:HIS962 3.9 15.3 1.0 NE2 A:HIS962 3.9 15.3 1.0 O A:VAL761 3.9 25.3 1.0 CD2 A:HIS962 4.2 15.3 1.0 CA A:HIS962 4.6 15.3 1.0 N A:VAL761 4.7 25.3 1.0 CA A:GLY831 4.7 32.6 1.0 C A:VAL761 4.8 25.3 1.0 CA A:ASP760 4.8 18.4 1.0 OD1 A:ASP830 4.8 20.7 1.0 CG A:ASP830 4.9 20.7 1.0 C A:ASP760 4.9 18.4 1.0 N A:GLY831 5.0 32.6 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.