Magnesium in PDB 5w51: Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp

All present enzymatic activity of Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp:
2.7.7.6;

The structure of Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp, PDB code: 5w51 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)	82.79 / 3.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	168.700, 224.000, 193.060, 90.00, 101.04, 90.00
R / Rfree (%)	22.7 / 25.4

The structure of Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched 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 N6-Methyladenine-Containing Template and A Matched Umpnpp (pdb code 5w51). 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 N6-Methyladenine-Containing Template and A Matched Umpnpp, PDB code: 5w51:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched 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 N6-Methyladenine-Containing Template and A Matched Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1803 b:11.8 occ:1.00 O3' R:G9 2.0 41.1 1.0 OD1 A:ASP481 2.1 49.4 1.0 OD1 A:ASP485 2.2 31.6 1.0 OD1 A:ASP483 2.3 43.6 1.0 O1A A:2KH1805 2.3 79.6 0.4 CG A:ASP481 3.0 49.5 1.0 CG A:ASP485 3.1 31.0 1.0 C3' R:G9 3.1 41.0 1.0 CG A:ASP483 3.1 44.0 1.0 OD2 A:ASP485 3.2 31.2 1.0 OD2 A:ASP483 3.2 44.6 1.0 OD2 A:ASP481 3.3 50.3 1.0 C4' R:G9 3.3 39.9 1.0 C5' R:G9 3.5 37.9 1.0 PA A:2KH1805 3.7 98.2 0.4 O5' A:2KH1805 3.9 0.8 0.6 O4' A:2KH1805 4.2 0.4 0.6 N3A A:2KH1805 4.2 0.6 0.4 O2' R:G9 4.2 44.0 1.0 C4' A:2KH1805 4.2 0.9 0.6 C2' R:G9 4.2 42.9 1.0 O4' A:2KH1805 4.3 0.5 0.4 CB A:ASP481 4.4 48.5 1.0 O2A A:2KH1805 4.5 92.6 0.4 CB A:ASP485 4.5 30.2 1.0 O5' R:G9 4.5 37.3 1.0 C5' A:2KH1805 4.6 0.9 0.6 N A:ASP481 4.6 47.8 1.0 CB A:ASP483 4.6 43.6 1.0 O4' R:G9 4.7 40.7 1.0 C4' A:2KH1805 4.7 0.6 0.4 N A:ASP483 4.8 42.1 1.0 O5' A:2KH1805 4.8 0.5 0.4 CA A:ASP481 4.9 47.6 1.0 N A:ASP485 4.9 30.1 1.0 C A:ASP481 4.9 47.0 1.0 NH2 A:ARG446 4.9 16.7 1.0 CA A:ASP485 5.0 30.1 1.0

Magnesium binding site 2 out of 2 in the Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched 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 N6-Methyladenine-Containing Template and A Matched Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1804 b:31.0 occ:1.00 O2B A:2KH1805 2.3 0.2 0.6 O2G A:2KH1805 2.8 0.9 0.6 OE1 B:GLU836 3.2 32.1 1.0 PB A:2KH1805 3.4 0.3 0.6 OD2 A:ASP481 3.5 50.3 1.0 O2B A:2KH1805 3.7 0.9 0.4 N3A A:2KH1805 3.8 0.4 0.6 O3B A:2KH1805 3.9 0.7 0.6 NH2 B:ARG1020 3.9 61.6 1.0 CB A:ASP481 3.9 48.5 1.0 PG A:2KH1805 4.0 0.7 0.6 OD2 B:ASP837 4.0 75.5 1.0 CG A:ASP481 4.1 49.5 1.0 CD B:GLU836 4.3 32.4 1.0 NZ A:LYS752 4.4 56.0 1.0 CE A:LYS752 4.4 55.9 1.0 O3G A:2KH1805 4.5 0.8 0.6 O1B A:2KH1805 4.7 0.2 0.6 NH1 B:ARG1020 4.7 62.0 1.0 OE2 B:GLU836 4.8 32.7 1.0 CZ B:ARG1020 4.8 61.8 1.0 PB A:2KH1805 5.0 0.2 0.4

W.Wang, L.Xu, L.Hu, J.Chong, C.He, D.Wang. Epigenetic Dna Modification N6-Methyladenine Causes Site-Specific Rna Polymerase II Transcriptional Pausing. J.Am.Chem.Soc. V. 139 14436 2017.
ISSN: ESSN 1520-5126
PubMed: 28933854
DOI: 10.1021/JACS.7B06381