Magnesium in PDB 7ked: Rna Polymerase II Elongation Complex with Unnatural Base DTPT3

All present enzymatic activity of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3:
2.7.7.6;

The structure of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, PDB code: 7ked was solved by J.Oh, W.Wang, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.60 / 3.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.89, 223.01, 194.7, 90, 101.6, 90
R / Rfree (%)	26.6 / 30.5

The structure of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3 also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Magnesium atom in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3 (pdb code 7ked). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, PDB code: 7ked:

Magnesium binding site 1 out of 1 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1803 b:51.0 occ:1.00 OD2 A:ASP483 2.0 54.2 1.0 O3' R:A10 2.2 64.6 1.0 OD1 A:ASP483 2.2 54.5 1.0 OD2 A:ASP485 2.4 48.0 1.0 CG A:ASP483 2.4 54.5 1.0 OD1 A:ASP481 2.5 57.6 1.0 OD1 A:ASP485 2.9 49.2 1.0 CG A:ASP485 3.0 48.3 1.0 CG A:ASP481 3.4 57.3 1.0 C3' R:A10 3.5 65.4 1.0 CB A:ASP481 3.7 53.9 1.0 CB A:ASP483 3.9 52.8 1.0 C2' R:A10 4.1 67.4 1.0 C4' R:A10 4.2 65.1 1.0 CB A:ASP485 4.4 47.2 1.0 N A:ASP481 4.5 51.0 1.0 O A:ASP483 4.6 52.0 1.0 OD2 A:ASP481 4.6 59.9 1.0 CA A:ASP481 4.6 52.0 1.0 CA A:ASP483 4.7 50.5 1.0 C A:ASP483 4.7 51.7 1.0 N A:ASP485 4.7 44.7 1.0 N A:ASP483 4.7 50.1 1.0 C5' R:A10 4.9 63.6 1.0 CA A:ASP485 5.0 44.8 1.0

J.Oh, W.Wang, D.Wang. Transcriptional Processing of Unnatural Base Pair By Eukaryotic Rna Polymerase II Nat.Chem.Biol. 2021.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-021-00817-3