Magnesium in PDB 9g2b: Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 12-Subunit

All present enzymatic activity of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 12-Subunit:
2.7.7.6;

The structure of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 12-Subunit also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Magnesium atom in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 12-Subunit (pdb code 9g2b). 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 Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 12-Subunit, PDB code: 9g2b:

Magnesium binding site 1 out of 1 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 12-Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site, 12-Subunit within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg1701 b:30.0 occ:1.00 O3' R:G12 1.6 114.1 1.0 OD1 A:ASP629 2.0 125.2 1.0 OD2 A:ASP631 2.1 107.9 1.0 OD1 A:ASP631 2.1 118.9 1.0 OD2 A:ASP627 2.1 127.9 1.0 OD2 A:ASP629 2.2 125.4 1.0 CG A:ASP631 2.4 115.9 1.0 CG A:ASP629 2.4 122.2 1.0 C3' R:G12 2.9 116.7 1.0 CG A:ASP627 3.1 123.3 1.0 O2' R:G12 3.3 122.9 1.0 C4' R:G12 3.5 118.1 1.0 C2' R:G12 3.6 119.9 1.0 OD1 A:ASP627 3.7 123.3 1.0 CB A:ASP631 3.9 113.1 1.0 CB A:ASP629 3.9 119.3 1.0 CB A:ASP627 4.1 115.5 1.0 C5' R:G12 4.1 118.6 1.0 N A:ASP627 4.4 114.1 1.0 O A:ASP629 4.5 121.1 1.0 N A:ASP629 4.5 118.3 1.0 CA A:ASP631 4.6 104.9 1.0 CA A:ASP627 4.6 113.0 1.0 CA A:ASP629 4.7 118.1 1.0 N A:ASP631 4.7 105.2 1.0 O4' R:G12 4.7 124.4 1.0 C A:ASP627 4.8 111.6 1.0 O A:ASP627 4.8 113.0 1.0 C A:ASP629 4.8 116.8 1.0 NH2 A:ARG591 4.8 99.8 1.0 C1' R:G12 4.8 119.1 1.0 O5' R:G12 4.9 121.2 1.0

A.Santos-Aledo, A.Plaza-Pegueroles, M.Sanz-Murillo, F.M.Ruiz, P.Hou, J.Xu, D.Gil-Carton, D.Wang, C.Fernandez-Tornero. Cryo-Em Uncovers A Sequential Mechanism For Rna Polymerase I Pausing and Stalling at Abasic Dna Lesions. Nat Commun V. 16 5254 2025.
ISSN: ESSN 2041-1723
PubMed: 40480971
DOI: 10.1038/S41467-025-60536-4