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Magnesium in PDB 6upx: Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 1

Enzymatic activity of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 1

All present enzymatic activity of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 1:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 1, PDB code: 6upx was solved by J.Oh, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.30 / 3.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.988, 223.314, 193.102, 90.00, 101.03, 90.00
R / Rfree (%) 22 / 26.6

Other elements in 6upx:

The structure of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 1 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 5-Guanidinohydantoin Lesion in State 1 (pdb code 6upx). 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 5-Guanidinohydantoin Lesion in State 1, PDB code: 6upx:

Magnesium binding site 1 out of 1 in 6upx

Go back to Magnesium Binding Sites List in 6upx
Magnesium binding site 1 out of 1 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 1


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 5-Guanidinohydantoin Lesion in State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1803

b:83.9
occ:1.00
 OD2 A:ASP483 2.1 1.0 1.0
O3' R:G9 2.1 1.0 1.0
OD1 A:ASP485 2.2 0.5 1.0
C4' R:G9 2.8 84.1 1.0
CG A:ASP483 2.9 0.1 1.0
C3' R:G9 2.9 94.2 1.0
CG A:ASP485 2.9 0.0 1.0
OD1 A:ASP483 3.0 0.2 1.0
OD2 A:ASP485 3.1 0.1 1.0
C5' R:G9 3.2 97.6 1.0
O2' R:G9 3.8 97.6 1.0
CB A:ASP481 3.9 86.3 1.0
C2' R:G9 4.0 91.3 1.0
O5' R:G9 4.1 0.8 1.0
O4' R:G9 4.2 74.1 1.0
CB A:ASP483 4.3 0.6 1.0
CB A:ASP485 4.3 98.2 1.0
N A:ASP485 4.5 63.8 1.0
O A:ASP481 4.5 0.7 1.0
NH2 A:ARG446 4.5 83.0 1.0
N A:ASP483 4.7 86.2 1.0
CA A:ASP485 4.7 74.1 1.0
C1' R:G9 4.8 93.9 1.0
C A:ASP481 4.8 95.4 1.0
C A:ASP483 4.8 67.5 1.0
CA A:ASP481 4.8 80.4 1.0
CA A:ASP483 4.8 81.8 1.0
N A:GLY484 4.9 44.4 1.0
NZ B:LYS987 4.9 0.2 1.0
CG A:ASP481 4.9 0.2 1.0
CE B:LYS987 5.0 98.0 1.0

Reference:

J.Oh, A.M.Fleming, J.Xu, J.Chong, C.J.Burrows, D.Wang. Rna Polymerase II Stalls on Oxidative Dna Damage Via A Torsion-Latch Mechanism Involving Lone Pair-Pi and Ch-Pi Interactions. Proc.Natl.Acad.Sci.Usa V. 117 9338 2020.
ISSN: ESSN 1091-6490
PubMed: 32284409
DOI: 10.1073/PNAS.1919904117
Page generated: Wed Aug 13 18:40:24 2025

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