Magnesium in PDB 7eu1: The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme

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

The structure of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Holoenzyme 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 Holoenzyme (pdb code 7eu1). 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 Holoenzyme, PDB code: 7eu1:
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 Holoenzyme


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 Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:10.3 occ:1.00 OD1 A:ASP447 2.1 15.9 1.0 OD2 A:ASP451 2.1 10.3 1.0 OD1 A:ASP449 2.1 10.3 1.0 OD1 A:ASP451 2.3 10.3 1.0 CG A:ASP451 2.4 10.3 1.0 CG A:ASP449 3.0 10.3 1.0 CG A:ASP447 3.1 15.9 1.0 OD2 A:ASP449 3.3 10.3 1.0 OD2 A:ASP447 3.6 15.9 1.0 CB A:ASP451 3.9 10.3 1.0 NH2 A:ARG411 4.0 7.9 1.0 N A:ASP447 4.0 15.9 1.0 O A:ASP447 4.1 15.9 1.0 CB A:ASP447 4.4 15.9 1.0 C A:ASP447 4.4 15.9 1.0 CB A:ASP449 4.4 10.3 1.0 N A:ASP451 4.4 10.3 1.0 CA A:ASP447 4.5 15.9 1.0 N A:ASP449 4.5 10.3 1.0 CA A:ASP451 4.7 10.3 1.0 CA A:ASP449 4.8 10.3 1.0 C A:ASP449 4.8 10.3 1.0 N A:GLY450 4.9 9.4 1.0

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


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 Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg2001 b:62.5 occ:1.00 OD1 M:ASP830 2.1 61.2 1.0 OD1 M:ASP832 2.1 63.6 1.0 OD2 M:ASP834 2.1 59.4 1.0 CG M:ASP834 2.7 59.4 1.0 O M:ASP830 2.8 61.2 1.0 CG M:ASP830 3.1 61.2 1.0 CG M:ASP832 3.2 63.6 1.0 CB M:ASP834 3.4 59.4 1.0 OD1 M:ASP834 3.4 59.4 1.0 C M:ASP830 3.5 61.2 1.0 N M:ASP830 3.5 61.2 1.0 OD2 M:ASP832 3.8 63.6 1.0 CA M:ASP830 3.8 61.2 1.0 OD2 M:ASP830 3.9 61.2 1.0 N M:ASP832 3.9 63.6 1.0 O M:ASP832 3.9 63.6 1.0 CB M:ASP830 4.0 61.2 1.0 C M:ASP832 4.2 63.6 1.0 C M:GLY829 4.4 62.0 1.0 CB M:ASP832 4.4 63.6 1.0 CA M:ASP832 4.4 63.6 1.0 N M:LEU831 4.4 64.5 1.0 CA M:ASP834 4.7 59.4 1.0 CA M:GLY829 4.7 62.0 1.0 N M:ASP834 4.7 59.4 1.0 C M:LEU831 4.8 64.5 1.0 C M:GLY833 4.9 58.3 1.0 O M:GLY833 4.9 58.3 1.0 CA M:LEU831 5.0 64.5 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