Magnesium in PDB 2nvt: Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Gmpcpp

All present enzymatic activity of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Gmpcpp:
2.7.7.6;

The structure of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Gmpcpp, PDB code: 2nvt 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 / 3.36
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	170.872, 222.824, 195.802, 90.00, 102.39, 90.00
R / Rfree (%)	23 / 28.3

The structure of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Gmpcpp also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Magnesium atom in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Gmpcpp (pdb code 2nvt). 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 Elongation Complex in 150 Mm Mg+2 with Gmpcpp, PDB code: 2nvt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Gmpcpp


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 Elongation Complex in 150 Mm Mg+2 with Gmpcpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:79.6 occ:1.00 OD2 A:ASP481 2.4 0.8 1.0 CG A:ASP481 3.2 0.8 1.0 O1G T:G2P3000 3.5 0.7 1.0 CB A:ASP481 3.7 0.8 1.0 OE1 B:GLU836 4.0 0.4 1.0 OD1 A:ASP481 4.2 0.2 1.0 O2G T:G2P3000 4.4 0.2 1.0 PG T:G2P3000 4.5 0.3 1.0 O A:ALA480 4.7 0.5 1.0 NH2 B:ARG1020 4.7 0.1 1.0 O3G T:G2P3000 4.9 0.8 1.0 CA A:ASP481 4.9 0.6 1.0 MG A:MG2003 5.0 50.9 1.0 OD2 B:ASP837 5.0 0.2 1.0

Magnesium binding site 2 out of 2 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Gmpcpp


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 Elongation Complex in 150 Mm Mg+2 with Gmpcpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2003 b:50.9 occ:1.00 OD1 A:ASP481 1.9 0.2 1.0 OD2 A:ASP483 2.3 0.5 1.0 O3' R:C10 2.3 71.6 1.0 OD1 A:ASP485 2.6 0.2 1.0 OD1 A:ASP483 2.8 0.5 1.0 CG A:ASP483 2.9 0.4 1.0 CG A:ASP481 2.9 0.8 1.0 OD2 A:ASP481 3.2 0.8 1.0 O2A T:G2P3000 3.5 0.5 1.0 CG A:ASP485 3.5 0.7 1.0 O2' R:C10 3.6 73.9 1.0 C3' R:C10 3.6 73.1 1.0 OD2 A:ASP485 3.6 0.3 1.0 C4' R:C10 4.3 73.2 1.0 C2' R:C10 4.3 77.5 1.0 CB A:ASP481 4.3 0.8 1.0 N A:ASP481 4.4 0.2 1.0 CB A:ASP483 4.4 0.5 1.0 NH2 A:ARG446 4.5 0.8 1.0 O A:ASP481 4.6 0.6 1.0 C A:ASP481 4.6 0.3 1.0 CA A:ASP481 4.7 0.6 1.0 N A:ASP483 4.7 0.5 1.0 C5' R:C10 4.9 68.2 1.0 PA T:G2P3000 4.9 0.3 1.0 CB A:ASP485 5.0 0.2 1.0 MG A:MG2002 5.0 79.6 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