Magnesium in PDB 3s15: Rna Polymerase II Initiation Complex with A 7-Nt Rna

All present enzymatic activity of Rna Polymerase II Initiation Complex with A 7-Nt Rna:
2.7.7.6;

The structure of Rna Polymerase II Initiation Complex with A 7-Nt Rna, PDB code: 3s15 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)	44.11 / 3.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	167.928, 220.891, 194.623, 90.00, 100.16, 90.00
R / Rfree (%)	17.4 / 22.8

The structure of Rna Polymerase II Initiation Complex with A 7-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 7-Nt Rna (pdb code 3s15). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Rna Polymerase II Initiation Complex with A 7-Nt Rna, PDB code: 3s15:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Rna Polymerase II Initiation Complex with A 7-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 7-Nt Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:68.5 occ:1.00 O3' R:G10 1.9 91.8 1.0 OD1 A:ASP485 2.0 67.8 1.0 OD1 A:ASP481 2.1 76.8 1.0 OD2 A:ASP483 2.6 68.2 1.0 CG A:ASP485 2.7 68.7 1.0 OD2 A:ASP485 2.9 74.3 1.0 C3' R:G10 3.1 91.8 1.0 CG A:ASP481 3.3 75.2 1.0 CG A:ASP483 3.4 64.4 1.0 O2' R:G10 3.5 91.6 1.0 OD1 A:ASP483 3.6 65.3 1.0 C4' R:G10 3.7 91.8 1.0 C2' R:G10 3.8 92.0 1.0 OD2 A:ASP481 3.9 84.5 1.0 NH2 A:ARG446 4.0 82.6 1.0 CB A:ASP485 4.2 59.4 1.0 CB A:ASP481 4.4 56.6 1.0 O A:ASP481 4.5 58.2 1.0 N A:ASP481 4.5 53.7 1.0 C5' R:G10 4.5 92.0 1.0 CA A:ASP481 4.6 54.0 1.0 C A:ASP481 4.7 58.2 1.0 CB A:ASP483 4.7 53.1 1.0 N A:ASP485 4.7 57.8 1.0 O4' R:G10 4.8 92.0 1.0 CA A:ASP485 4.9 57.1 1.0 N A:ASP483 4.9 52.4 1.0 C1' R:G10 5.0 92.7 1.0

Magnesium binding site 2 out of 3 in the Rna Polymerase II Initiation Complex with A 7-Nt Rna


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 7-Nt Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:41.7 occ:0.66 NH2 B:ARG766 3.3 0.9 1.0 NE B:ARG1020 4.0 94.7 1.0 CD B:ARG1020 4.1 78.9 1.0 CZ B:ARG766 4.4 0.5 1.0 NH1 B:ARG766 4.6 77.8 1.0 CZ B:ARG1020 4.6 0.5 1.0 OG B:SER1019 4.6 83.3 1.0

Magnesium binding site 3 out of 3 in the Rna Polymerase II Initiation Complex with A 7-Nt Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rna Polymerase II Initiation Complex with A 7-Nt Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:3.0 occ:0.34 O B:LYS987 2.9 63.1 1.0 N B:LYS987 2.9 61.3 1.0 NH1 B:ARG1020 3.0 0.6 1.0 O B:GLY985 3.2 69.3 1.0 CA B:GLN986 3.3 65.5 1.0 OE1 B:GLN986 3.5 99.6 1.0 C B:GLN986 3.5 65.8 1.0 CG B:LYS987 3.5 68.1 1.0 C B:LYS987 3.7 63.4 1.0 CA B:LYS987 3.8 60.0 1.0 OD1 B:ASP837 3.8 90.1 1.0 C B:GLY985 3.9 69.4 1.0 N B:GLN986 4.0 66.5 1.0 CB B:LYS987 4.2 60.5 1.0 CG B:ASP837 4.2 86.8 1.0 CZ B:ARG1020 4.3 0.5 1.0 NH1 B:ARG766 4.4 77.8 1.0 CB B:GLN986 4.4 67.3 1.0 CD B:GLN986 4.5 0.8 1.0 CD B:LYS987 4.5 80.1 1.0 OD2 B:ASP837 4.6 94.3 1.0 O B:GLN986 4.6 63.5 1.0 CE B:LYS987 4.7 96.9 1.0 NH2 B:ARG1020 4.8 0.9 1.0 CG B:GLN986 4.8 77.4 1.0 N B:GLY988 5.0 58.1 1.0 OD1 A:ASP483 5.0 65.3 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