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Magnesium in PDB 8ukt: Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added

Enzymatic activity of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added

All present enzymatic activity of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added, PDB code: 8ukt 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) 47.75 / 3.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 156.681, 221.393, 190.539, 90, 97.67, 90
R / Rfree (%) 25.1 / 29

Other elements in 8ukt:

The structure of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added (pdb code 8ukt). 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 Fapy-Dg Lesion with Amp Added, PDB code: 8ukt:

Magnesium binding site 1 out of 1 in 8ukt

Go back to Magnesium Binding Sites List in 8ukt
Magnesium binding site 1 out of 1 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added


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 with Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg2001

b:124.0
occ:1.00
 OD2 A:ASP483 2.1 118.9 1.0
O3' R:G9 2.1 134.1 1.0
OP1 R:A10 2.2 124.1 1.0
OD1 A:ASP485 2.2 105.4 1.0
OD1 A:ASP483 2.3 110.2 1.0
CG A:ASP483 2.5 107.9 1.0
P R:A10 2.6 180.6 1.0
OD2 A:ASP485 2.7 77.5 1.0
CG A:ASP485 2.7 85.9 1.0
C3' R:G9 3.0 113.3 1.0
C4' R:G9 3.1 106.8 1.0
O2' R:G9 3.3 113.2 1.0
O5' R:A10 3.4 188.2 1.0
C5' R:G9 3.7 104.8 1.0
C2' R:G9 3.8 110.8 1.0
OP2 R:A10 3.9 172.2 1.0
CB A:ASP483 4.0 90.2 1.0
CB A:ASP485 4.2 84.2 1.0
O4' R:G9 4.3 105.0 1.0
O A:ASP481 4.4 99.2 1.0
NH2 A:ARG446 4.6 78.0 1.0
C1' R:G9 4.7 107.3 1.0
CA A:ASP485 4.7 78.6 1.0
N A:ASP485 4.7 59.1 1.0
CB A:ASP481 4.8 108.5 1.0
C5' R:A10 4.8 145.4 1.0
CA A:ASP483 4.9 80.0 1.0
N A:ASP483 5.0 107.0 1.0

Reference:

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
Page generated: Fri Aug 15 16:58:58 2025

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