Manganese in PDB 2nvy: Rna Polymerase II Form II in 150 Mm Mn+2

All present enzymatic activity of Rna Polymerase II Form II in 150 Mm Mn+2:
2.7.7.6;

The structure of Rna Polymerase II Form II in 150 Mm Mn+2, PDB code: 2nvy was solved by D.Wang, D.A.Bushnell, K.D.Westover, C.D.Kaplan, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 3.40
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	118.036, 218.914, 369.549, 90.00, 90.00, 90.00
R / Rfree (%)	24.9 / 32.3

The structure of Rna Polymerase II Form II in 150 Mm Mn+2 also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Manganese atom in the Rna Polymerase II Form II in 150 Mm Mn+2 (pdb code 2nvy). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Rna Polymerase II Form II in 150 Mm Mn+2, PDB code: 2nvy:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Rna Polymerase II Form II in 150 Mm Mn+2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Rna Polymerase II Form II in 150 Mm Mn+2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn3009 b:49.9 occ:1.00 OD1 A:ASP481 2.0 50.6 1.0 OD2 A:ASP485 2.3 53.7 1.0 OD2 A:ASP483 2.3 54.1 1.0 OD2 A:ASP481 2.5 54.5 1.0 CG A:ASP481 2.6 53.0 1.0 CG A:ASP485 3.2 51.9 1.0 CG A:ASP483 3.2 53.0 1.0 OD1 A:ASP485 3.3 52.0 1.0 OD1 A:ASP483 3.5 54.0 1.0 CB A:ASP481 4.1 52.7 1.0 N A:ASP481 4.5 52.6 1.0 NH2 A:ARG446 4.5 68.9 1.0 CB A:ASP485 4.6 51.5 1.0 CB A:ASP483 4.6 51.7 1.0 N A:ASP483 4.6 51.3 1.0 N A:ASP485 4.7 51.5 1.0 O A:ASP481 4.7 52.9 1.0 CA A:ASP481 4.7 52.5 1.0 C A:ASP481 4.7 52.5 1.0 CA A:ASP483 4.9 51.5 1.0 C A:ASP483 4.9 51.2 1.0 CA A:ASP485 5.0 51.6 1.0

Manganese binding site 2 out of 2 in the Rna Polymerase II Form II in 150 Mm Mn+2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Rna Polymerase II Form II in 150 Mm Mn+2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn3010 b:50.0 occ:1.00 OD2 A:ASP481 2.9 54.5 1.0 CB A:ASP481 3.3 52.7 1.0 CG A:ASP481 3.5 53.0 1.0 OE1 B:GLU836 3.6 67.1 1.0 OD2 B:ASP837 4.2 64.0 1.0 NH1 B:ARG1020 4.7 79.4 1.0 NH2 B:ARG1020 4.7 79.1 1.0 CA A:ASP481 4.7 52.5 1.0 OD1 A:ASP481 4.8 50.6 1.0 CD B:GLU836 4.9 65.2 1.0 CE A:LYS752 5.0 78.4 1.0

D.Wang, D.A.Bushnell, K.D.Westover, C.D.Kaplan, R.D.Kornberg. Structural Basis of Transcription: Role of the Trigger Loop in Substrate Specificity and Catalysis Cell(Cambridge,Mass.) V. 127 941 2006.
ISSN: ISSN 0092-8674
PubMed: 17129781
DOI: 10.1016/J.CELL.2006.11.023