Magnesium in PDB 6blo: Pol II Elongation Complex with An Abasic Lesion at I+1 Position

Enzymatic activity of Pol II Elongation Complex with An Abasic Lesion at I+1 Position

All present enzymatic activity of Pol II Elongation Complex with An Abasic Lesion at I+1 Position:
2.7.7.6;

Protein crystallography data

The structure of Pol II Elongation Complex with An Abasic Lesion at I+1 Position, PDB code: 6blo was solved by W.Wang, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.48 / 3.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.550, 222.280, 193.770, 90.00, 100.62, 90.00
R / Rfree (%) 20.3 / 22.7

Other elements in 6blo:

The structure of Pol II Elongation Complex with An Abasic Lesion at I+1 Position also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position (pdb code 6blo). 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 Pol II Elongation Complex with An Abasic Lesion at I+1 Position, PDB code: 6blo:

Magnesium binding site 1 out of 1 in 6blo

Go back to Magnesium Binding Sites List in 6blo
Magnesium binding site 1 out of 1 in the Pol II Elongation Complex with An Abasic Lesion at I+1 Position


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pol II Elongation Complex with An Abasic Lesion at I+1 Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1803

b:24.9
occ:1.00
O3' R:G8 1.9 58.7 1.0
OD1 A:ASP485 2.2 56.6 1.0
OD1 A:ASP483 2.3 38.9 1.0
OD1 A:ASP481 2.4 63.2 1.0
C3' R:G8 2.9 58.4 1.0
CG A:ASP485 3.0 56.4 1.0
CG A:ASP483 3.0 43.3 1.0
OD2 A:ASP483 3.1 45.1 1.0
OD2 A:ASP485 3.1 54.4 1.0
C4' R:G8 3.2 60.4 1.0
CG A:ASP481 3.3 71.1 1.0
O2' R:G8 3.4 61.6 1.0
OD2 A:ASP481 3.6 75.6 1.0
C2' R:G8 3.8 58.8 1.0
C5' R:G8 3.8 63.1 1.0
CB A:ASP485 4.4 55.3 1.0
O4' R:G8 4.4 58.5 1.0
CB A:ASP483 4.5 40.8 1.0
CB A:ASP481 4.6 65.5 1.0
N A:ASP481 4.7 61.1 1.0
O5' R:G8 4.7 59.4 1.0
NH2 A:ARG446 4.7 42.4 1.0
C1' R:G8 4.8 58.7 1.0
N A:ASP483 4.8 43.9 1.0
N A:ASP485 4.9 50.2 1.0
O A:ASP483 4.9 35.5 1.0
C A:ASP483 5.0 30.0 1.0
CA A:ASP485 5.0 50.4 1.0
CA A:ASP483 5.0 39.0 1.0

Reference:

W.Wang, C.Walmacq, J.Chong, M.Kashlev, D.Wang. Structural Basis of Transcriptional Stalling and Bypass of Abasic Dna Lesion By Rna Polymerase II. Proc. Natl. Acad. Sci. V. 115 E2538 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29487211
DOI: 10.1073/PNAS.1722050115
Page generated: Mon Dec 14 22:24:12 2020

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