Magnesium in PDB 8uks: Rna Polymerase II Elongation Complex with Fapy-Dg Lesion Soaking with Ctp Before Chemistry

All present enzymatic activity of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion Soaking with Ctp Before Chemistry:
2.7.7.6;

The structure of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion Soaking with Ctp Before Chemistry, PDB code: 8uks was solved by P.Hou, J.Oh, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.76 / 3.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	157.118, 221.626, 189.961, 90, 97.4, 90
R / Rfree (%)	26.7 / 30.2

The structure of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion Soaking with Ctp Before Chemistry also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Magnesium atom in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion Soaking with Ctp Before Chemistry (pdb code 8uks). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion Soaking with Ctp Before Chemistry, PDB code: 8uks:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion Soaking with Ctp Before Chemistry


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 Fapy-Dg Lesion Soaking with Ctp Before Chemistry within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1801 b:141.1 occ:1.00 O1A B:CTP1301 2.0 121.0 1.0 O1G B:CTP1301 2.0 131.3 1.0 O2G B:CTP1301 2.2 98.5 1.0 OD1 A:ASP483 2.5 108.6 1.0 PG B:CTP1301 2.6 99.9 1.0 OD2 A:ASP481 2.9 98.1 1.0 NH1 B:ARG1020 3.2 126.7 1.0 PA B:CTP1301 3.3 137.2 1.0 CG A:ASP483 3.6 109.2 1.0 O3G B:CTP1301 3.7 122.1 1.0 O1B B:CTP1301 3.7 128.6 1.0 O3B B:CTP1301 3.8 123.1 1.0 CE B:LYS987 3.8 89.1 1.0 O3A B:CTP1301 3.8 114.4 1.0 O2A B:CTP1301 3.9 112.5 1.0 OD2 A:ASP483 3.9 94.9 1.0 OD2 B:ASP837 4.0 145.6 1.0 PB B:CTP1301 4.0 124.8 1.0 CZ B:ARG1020 4.1 122.7 1.0 CG A:ASP481 4.1 122.2 1.0 CG B:LYS987 4.3 67.7 1.0 CD B:LYS987 4.4 70.2 1.0 NH2 B:ARG1020 4.4 131.5 1.0 O5' B:CTP1301 4.5 129.5 1.0 CG B:ASP837 4.6 151.1 1.0 NZ B:LYS987 4.7 71.9 1.0 OD1 A:ASP481 4.7 127.8 1.0 NH1 B:ARG766 4.8 111.4 1.0 CB A:ASP483 4.9 80.2 1.0

Magnesium binding site 2 out of 2 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion Soaking with Ctp Before Chemistry


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion Soaking with Ctp Before Chemistry within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1804 b:137.6 occ:1.00 O A:ASP483 1.9 105.4 1.0 OD1 A:ASP485 2.0 101.7 1.0 N A:ASP485 2.1 85.0 1.0 C A:GLY484 2.4 62.7 1.0 CA A:ASP485 2.7 80.8 1.0 CG A:ASP485 2.8 105.5 1.0 C A:ASP483 2.9 77.6 1.0 O A:GLY484 3.0 60.1 1.0 C4' R:G9 3.0 98.9 1.0 CA A:GLY484 3.1 55.4 1.0 OD2 A:ASP483 3.2 94.9 1.0 CB A:ASP485 3.2 78.8 1.0 N A:GLY484 3.3 54.6 1.0 C5' R:G9 3.5 103.5 1.0 O5' R:G9 3.6 94.8 1.0 O4' R:G9 3.8 96.9 1.0 OD2 A:ASP485 3.9 108.3 1.0 O2' R:G9 4.0 109.2 1.0 C3' R:G9 4.0 112.0 1.0 O A:ASP481 4.0 97.9 1.0 NZ B:LYS987 4.1 71.9 1.0 C A:ASP485 4.2 60.2 1.0 CA A:ASP483 4.2 69.2 1.0 CG A:ASP483 4.3 109.2 1.0 C2' R:G9 4.5 107.4 1.0 C1' R:G9 4.6 107.2 1.0 CB A:ASP483 4.7 80.2 1.0 N A:ASP483 4.7 92.1 1.0 O A:ASP485 4.8 55.3 1.0 N A:GLU486 5.0 68.1 1.0

S.Gao, P.Hou, J.Oh, D.Wang, M.M.Greenberg. Molecular Mechanism of Rna Polymerase II Transcriptional Mutagenesis By the Epimerizable Dna Lesion, Fapy·Dg. J.Am.Chem.Soc. V. 146 6274 2024.
ISSN: ESSN 1520-5126
PubMed: 38393762
DOI: 10.1021/JACS.3C14476