Magnesium in PDB 3s1q: Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp

All present enzymatic activity of Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp:
2.7.7.6;

The structure of Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp, PDB code: 3s1q 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)	29.67 / 3.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.940, 220.530, 193.720, 90.00, 98.48, 90.00
R / Rfree (%)	17.6 / 22.9

The structure of Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp 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 3'-Deoxy Rna Soaked with Atp (pdb code 3s1q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp, PDB code: 3s1q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp


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 3'-Deoxy Rna Soaked with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:0.8 occ:1.00 OD1 A:ASP485 2.2 0.6 1.0 O2A A:ATP1736 2.3 0.5 1.0 OD2 A:ASP483 2.3 0.0 1.0 OD1 A:ASP481 2.8 0.1 1.0 OD1 A:ASP483 2.9 0.0 1.0 CG A:ASP483 2.9 0.9 1.0 C3' R:G10 2.9 0.8 1.0 CB A:ASP481 3.1 0.3 1.0 O2' R:G10 3.1 0.9 1.0 CG A:ASP485 3.2 0.9 1.0 CG A:ASP481 3.3 0.0 1.0 OD2 A:ASP485 3.5 0.4 1.0 C2' R:G10 3.5 0.0 1.0 C4' R:G10 3.6 0.6 1.0 PA A:ATP1736 3.8 0.6 1.0 MG A:MG2002 4.1 0.8 1.0 NH2 A:ARG446 4.1 0.0 1.0 CA A:ASP481 4.2 97.5 1.0 O1A A:ATP1736 4.2 0.2 1.0 O A:ASP481 4.3 99.7 1.0 OD2 A:ASP481 4.3 0.7 1.0 CB A:ASP483 4.3 96.3 1.0 N A:ASP481 4.4 97.8 1.0 C A:ASP481 4.4 99.9 1.0 O3A A:ATP1736 4.5 0.8 1.0 C5' R:G10 4.5 0.3 1.0 CB A:ASP485 4.6 93.2 1.0 C5' A:ATP1736 4.6 0.3 1.0 N A:ASP485 4.7 90.4 1.0 C4' A:ATP1736 4.7 1.0 1.0 N A:ASP483 4.7 95.3 1.0 C1' R:G10 4.7 0.6 1.0 O4' R:G10 4.7 0.7 1.0 O5' A:ATP1736 4.8 0.3 1.0 CA A:ASP483 4.9 94.3 1.0 CA A:ASP485 5.0 90.4 1.0 C A:ASP483 5.0 95.8 1.0 N A:GLY484 5.0 91.5 1.0

Magnesium binding site 2 out of 2 in the Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rna Polymerase II Initiation Complex with A 5-Nt 3'-Deoxy Rna Soaked with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:0.8 occ:1.00 OD1 A:ASP483 2.2 0.0 1.0 O3G A:ATP1736 2.4 1.0 1.0 OD2 A:ASP481 2.6 0.7 1.0 CB A:ASP481 2.7 0.3 1.0 CG A:ASP481 2.8 0.0 1.0 OD2 B:ASP837 3.3 0.9 1.0 CG A:ASP483 3.3 0.9 1.0 CG B:ASP837 3.5 0.9 1.0 OD1 A:ASP481 3.8 0.1 1.0 NH2 B:ARG1020 3.9 1.0 1.0 PG A:ATP1736 3.9 0.4 1.0 OD1 B:ASP837 4.0 0.9 1.0 CB A:ASP483 4.0 96.3 1.0 O3A A:ATP1736 4.0 0.8 1.0 CA A:ASP481 4.0 97.5 1.0 CB B:ASP837 4.0 0.4 1.0 O2B A:ATP1736 4.0 0.2 1.0 MG A:MG2001 4.1 0.8 1.0 O2A A:ATP1736 4.1 0.5 1.0 OD2 A:ASP483 4.3 0.0 1.0 O B:GLU836 4.4 0.9 1.0 PB A:ATP1736 4.6 0.5 1.0 PA A:ATP1736 4.6 0.6 1.0 O2G A:ATP1736 4.6 0.6 1.0 CZ B:ARG1020 4.7 0.5 1.0 O3B A:ATP1736 4.7 0.4 1.0 C A:ASP481 4.8 99.9 1.0 O1G A:ATP1736 4.8 0.4 1.0 O1A A:ATP1736 4.8 0.2 1.0 N A:ASP483 4.9 95.3 1.0 N A:PHE482 4.9 95.2 1.0 NH1 B:ARG1020 5.0 0.1 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