Magnesium in PDB 6bm2: 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;

The structure of Pol II Elongation Complex with An Abasic Lesion at I-1 Position, PDB code: 6bm2 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)	82.92 / 3.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.110, 222.270, 193.710, 90.00, 101.28, 90.00
R / Rfree (%)	21.9 / 24.4

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

The binding sites of Magnesium atom in the Pol II Elongation Complex with An Abasic Lesion at I-1 Position (pdb code 6bm2). 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: 6bm2:

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:10.0 occ:1.00 O3' R:A9 2.0 0.3 1.0 OD1 A:ASP485 2.3 29.9 1.0 OD1 A:ASP481 2.6 54.1 1.0 OD1 A:ASP483 2.6 25.8 1.0 C3' R:A9 3.0 0.3 1.0 C4' R:A9 3.0 0.2 1.0 CG A:ASP485 3.1 29.0 1.0 OD2 A:ASP483 3.2 27.3 1.0 OD2 A:ASP485 3.2 28.6 1.0 CG A:ASP483 3.3 26.5 1.0 CG A:ASP481 3.4 55.3 1.0 C5' R:A9 3.4 0.8 1.0 OD2 A:ASP481 3.7 56.0 1.0 O2' R:A9 3.8 0.6 1.0 C2' R:A9 4.0 0.3 1.0 O5' R:A9 4.2 0.5 1.0 O4' R:A9 4.4 0.2 1.0 CB A:ASP485 4.6 28.8 1.0 CB A:ASP481 4.7 54.3 1.0 CB A:ASP483 4.7 26.5 1.0 O A:ASP483 4.9 26.7 1.0 N A:ASP481 4.9 54.2 1.0 C1' R:A9 4.9 0.2 1.0 N A:ASP485 5.0 28.9 1.0 NH2 A:ARG446 5.0 32.4 1.0

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