Magnesium in PDB 6bm4: Pol II Elongation Complex with An Abasic Lesion at I-1 Position, Soaking Umpnpp

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

The structure of Pol II Elongation Complex with An Abasic Lesion at I-1 Position, Soaking Umpnpp, PDB code: 6bm4 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)	55.61 / 2.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	168.720, 220.430, 193.150, 90.00, 100.97, 90.00
R / Rfree (%)	23.4 / 26

The structure of Pol II Elongation Complex with An Abasic Lesion at I-1 Position, Soaking Umpnpp 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, Soaking Umpnpp (pdb code 6bm4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pol II Elongation Complex with An Abasic Lesion at I-1 Position, Soaking Umpnpp, PDB code: 6bm4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pol II Elongation Complex with An Abasic Lesion at I-1 Position, Soaking Umpnpp


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, Soaking Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1803 b:9.7 occ:1.00 OD1 A:ASP481 2.0 35.1 1.0 OD1 A:ASP485 2.2 25.7 1.0 O3' R:A9 2.3 0.6 1.0 OD1 A:ASP483 2.3 21.2 1.0 CG A:ASP481 2.8 38.1 1.0 CG A:ASP485 3.0 24.5 1.0 OD2 A:ASP485 3.0 24.3 1.0 OD2 A:ASP481 3.1 38.7 1.0 CG A:ASP483 3.2 20.9 1.0 C3' R:A9 3.3 0.7 1.0 C4' R:A9 3.3 0.2 1.0 OD2 A:ASP483 3.4 20.9 1.0 C5' R:A9 3.7 0.4 1.0 O2' R:A9 4.1 0.7 1.0 CB A:ASP481 4.2 38.0 1.0 C2' R:A9 4.3 0.5 1.0 N A:ASP481 4.4 37.8 1.0 CB A:ASP485 4.4 24.7 1.0 NH2 A:ARG446 4.5 33.0 1.0 CB A:ASP483 4.7 21.1 1.0 CA A:ASP481 4.7 36.2 1.0 O5' R:A9 4.7 1.0 1.0 O4' R:A9 4.7 0.8 1.0 N A:ASP483 4.7 21.0 1.0 C A:ASP481 4.8 35.7 1.0 N A:ASP485 4.9 24.1 1.0 O A:ASP481 4.9 34.3 1.0 CA A:ASP485 5.0 23.3 1.0

Magnesium binding site 2 out of 2 in the Pol II Elongation Complex with An Abasic Lesion at I-1 Position, Soaking Umpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pol II Elongation Complex with An Abasic Lesion at I-1 Position, Soaking Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1804 b:36.3 occ:1.00 O2' B:2KH1302 2.3 0.9 1.0 OD2 A:ASP481 3.0 38.7 1.0 O1B B:2KH1302 3.3 0.8 1.0 C2' B:2KH1302 3.6 0.1 1.0 CG A:ASP481 3.7 38.1 1.0 C1' B:2KH1302 3.8 0.8 1.0 O4' B:2KH1302 3.8 0.1 1.0 CB A:ASP481 3.9 38.0 1.0 C4' B:2KH1302 4.0 0.4 1.0 O3' B:2KH1302 4.2 0.7 1.0 OE1 B:GLU836 4.2 44.6 1.0 C3' B:2KH1302 4.2 0.3 1.0 OD2 B:ASP837 4.2 53.1 1.0 O3G B:2KH1302 4.4 0.6 1.0 NH2 B:ARG1020 4.6 38.0 1.0 OD1 A:ASP481 4.7 35.1 1.0 PB B:2KH1302 4.7 0.9 1.0 CA A:ASP481 5.0 36.2 1.0 NH1 B:ARG1020 5.0 39.4 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