Magnesium in PDB 3rzd: Rna Polymerase II Initiation Complex with A 5-Nt Rna

All present enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt Rna:
2.7.7.6;

The structure of Rna Polymerase II Initiation Complex with A 5-Nt Rna, PDB code: 3rzd was solved by X.Liu, D.A.Bushnell, D.A.Silva, X.Huang, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.14 / 3.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	157.538, 221.266, 192.175, 90.00, 97.44, 90.00
R / Rfree (%)	18.8 / 23

The structure of Rna Polymerase II Initiation Complex with A 5-Nt Rna also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Magnesium atom in the Rna Polymerase II Initiation Complex with A 5-Nt Rna (pdb code 3rzd). 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 Initiation Complex with A 5-Nt Rna, PDB code: 3rzd:

Magnesium binding site 1 out of 1 in the Rna Polymerase II Initiation Complex with A 5-Nt Rna


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 Initiation Complex with A 5-Nt Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:39.0 occ:1.00 O3' R:G10 1.9 0.8 1.0 OD1 A:ASP481 2.2 68.1 1.0 OD2 A:ASP483 2.5 67.9 1.0 OD1 A:ASP485 2.6 61.9 1.0 CG A:ASP481 3.0 66.5 1.0 OD2 A:ASP481 3.2 73.6 1.0 CG A:ASP483 3.2 62.6 1.0 C3' R:G10 3.3 0.9 1.0 OD1 A:ASP483 3.3 64.0 1.0 CG A:ASP485 3.5 60.9 1.0 OD2 A:ASP485 3.6 67.2 1.0 O2' R:G10 3.8 0.7 1.0 C4' R:G10 3.8 0.2 1.0 C2' R:G10 4.0 0.8 1.0 C5' R:G10 4.4 0.8 1.0 CB A:ASP481 4.4 52.2 1.0 NH2 A:ARG446 4.5 66.0 1.0 O A:ASP481 4.5 52.8 1.0 CB A:ASP483 4.6 49.8 1.0 CB A:ASP485 4.9 48.0 1.0 C A:ASP481 4.9 53.7 1.0 N A:ASP481 5.0 50.3 1.0 CA A:ASP481 5.0 50.2 1.0

X.Liu, D.A.Bushnell, D.A.Silva, X.Huang, R.D.Kornberg. Initiation Complex Structure and Promoter Proofreading. Science V. 333 633 2011.
ISSN: ISSN 0036-8075
PubMed: 21798951
DOI: 10.1126/SCIENCE.1206629