Magnesium in PDB 7eu0: The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex

All present enzymatic activity of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex:
2.7.7.48; 2.7.7.6;

The structure of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Magnesium atom in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex (pdb code 7eu0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex, PDB code: 7eu0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:21.9 occ:1.00 OD1 A:ASP447 2.1 20.9 1.0 CB A:ASP449 2.1 21.2 1.0 OD2 A:ASP451 2.2 20.9 1.0 OD2 A:ASP449 2.2 21.2 1.0 OP1 O:C11 2.3 76.2 1.0 CG A:ASP449 2.6 21.2 1.0 CG A:ASP447 2.8 20.9 1.0 OD2 A:ASP447 2.9 20.9 1.0 CG A:ASP451 3.0 20.9 1.0 OD1 A:ASP451 3.2 20.9 1.0 CA A:ASP449 3.6 21.2 1.0 P O:C11 3.8 76.2 1.0 OD1 A:ASP449 3.8 21.2 1.0 N A:ASP449 4.2 21.2 1.0 CB A:ASP447 4.2 20.9 1.0 O A:ASP447 4.2 20.9 1.0 C A:ASP449 4.3 21.2 1.0 O A:ASP449 4.3 21.2 1.0 CB A:ASP451 4.4 20.9 1.0 O3' O:A10 4.4 67.0 1.0 C A:ASP447 4.5 20.9 1.0 O5' O:C11 4.6 76.2 1.0 N A:ASP447 4.6 20.9 1.0 CA A:ASP447 4.7 20.9 1.0 OP2 O:C11 4.8 76.2 1.0 C5' O:A10 4.8 67.0 1.0 C A:PHE448 5.0 13.1 1.0

Magnesium binding site 2 out of 2 in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg2001 b:44.5 occ:1.00 OD1 M:ASP830 2.1 53.0 1.0 OD1 M:ASP832 2.1 56.9 1.0 OD2 M:ASP834 2.1 58.8 1.0 O3' R:A20 2.2 90.0 1.0 CG M:ASP834 2.9 58.8 1.0 C3' R:A20 3.0 90.0 1.0 CG M:ASP832 3.1 56.9 1.0 CG M:ASP830 3.1 53.0 1.0 C4' R:A20 3.3 90.0 1.0 OD2 M:ASP832 3.5 56.9 1.0 CB M:ASP834 3.5 58.8 1.0 O M:ASP830 3.5 53.0 1.0 N M:ASP830 3.7 53.0 1.0 C M:ASP830 3.8 53.0 1.0 OD2 M:ASP830 3.8 53.0 1.0 OD1 M:ASP834 3.8 58.8 1.0 CA M:ASP830 4.1 53.0 1.0 N M:ASP832 4.1 56.9 1.0 CB M:ASP830 4.1 53.0 1.0 C5' R:A20 4.2 90.0 1.0 CE M:LYS783 4.3 58.6 1.0 C2' R:A20 4.4 90.0 1.0 O4' R:A20 4.4 90.0 1.0 N M:LEU831 4.4 54.5 1.0 NZ M:LYS783 4.4 58.6 1.0 CB M:ASP832 4.4 56.9 1.0 CA M:ASP832 4.7 56.9 1.0 C M:GLY829 4.7 50.9 1.0 CA M:ASP834 4.8 58.8 1.0 C1' R:A20 4.9 90.0 1.0 CA M:LEU831 4.9 54.5 1.0 O2' R:A20 4.9 90.0 1.0 C M:LEU831 4.9 54.5 1.0 N M:ASP834 4.9 58.8 1.0 CA M:GLY829 4.9 50.9 1.0 C M:ASP832 5.0 56.9 1.0

K.Huang, X.X.Wu, C.L.Fang, Y.Zhang. Pol IV and RDR2: A Two-Rna-Polymerase Machine That Produces Double-Stranded Rna. Science 2021.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ABJ9184