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Magnesium in PDB 9g24: Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site Bound to Nucleotide Analog Ampcpp at E-Site

Enzymatic activity of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site Bound to Nucleotide Analog Ampcpp at E-Site

All present enzymatic activity of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site Bound to Nucleotide Analog Ampcpp at E-Site:
2.7.7.6;

Other elements in 9g24:

The structure of Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site Bound to Nucleotide Analog Ampcpp at E-Site also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site Bound to Nucleotide Analog Ampcpp at E-Site (pdb code 9g24). 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 Bound to Nucleotide Analog Ampcpp at E-Site, PDB code: 9g24:

Magnesium binding site 1 out of 1 in 9g24

Go back to Magnesium Binding Sites List in 9g24
Magnesium binding site 1 out of 1 in the Yeast Rna Polymerase I Elongation Complex Stalled By An Apurinic Site Bound to Nucleotide Analog Ampcpp at E-Site


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 Bound to Nucleotide Analog Ampcpp at E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1704

b:81.4
occ:1.00
NH2 A:ARG591 1.9 67.5 1.0
OD1 A:ASP627 2.2 77.6 1.0
O3' R:G12 2.4 100.4 1.0
OD2 A:ASP631 2.4 81.3 1.0
OD1 A:ASP631 2.5 81.3 1.0
OD2 A:ASP629 2.6 80.8 1.0
OD1 A:ASP629 2.7 80.8 1.0
CB A:ASP627 2.8 77.6 1.0
CG A:ASP627 2.8 77.6 1.0
CG A:ASP631 2.8 81.3 1.0
CG A:ASP629 3.0 80.8 1.0
CZ A:ARG591 3.1 67.5 1.0
N A:ASP627 3.4 77.6 1.0
NE A:ARG591 3.7 67.5 1.0
CA A:ASP627 3.7 77.6 1.0
C3' R:G12 3.8 100.4 1.0
C A:ALA626 3.8 67.8 1.0
OD2 A:ASP627 3.9 77.6 1.0
NH1 A:ARG591 4.1 67.5 1.0
CA A:ALA626 4.2 67.8 1.0
O2' R:G12 4.3 100.4 1.0
CB A:ASP631 4.3 81.3 1.0
C2' R:G12 4.4 100.4 1.0
CB A:ASP629 4.4 80.8 1.0
O A:ALA626 4.4 67.8 1.0
O A:ASN625 4.5 62.1 1.0
C A:ASP627 4.7 77.6 1.0
C4' R:G12 4.8 100.4 1.0
N A:ASP629 5.0 80.8 1.0

Reference:

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
Page generated: Sat Aug 16 02:39:09 2025

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