Magnesium in PDB 2nvz: Rna Polymerase II Elongation Complex with Utp, Updated 11/2006

All present enzymatic activity of Rna Polymerase II Elongation Complex with Utp, Updated 11/2006:
2.7.7.6;

The structure of Rna Polymerase II Elongation Complex with Utp, Updated 11/2006, PDB code: 2nvz 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 / 4.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.647, 222.338, 194.316, 90.00, 101.67, 90.00
R / Rfree (%)	27 / 33.2

The structure of Rna Polymerase II Elongation Complex with Utp, Updated 11/2006 also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Magnesium atom in the Rna Polymerase II Elongation Complex with Utp, Updated 11/2006 (pdb code 2nvz). 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 with Utp, Updated 11/2006, PDB code: 2nvz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rna Polymerase II Elongation Complex with Utp, Updated 11/2006


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 with Utp, Updated 11/2006 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:97.5 occ:1.00 OD1 A:ASP485 2.2 95.1 1.0 OD1 A:ASP483 2.2 100.0 1.0 O2A B:UTP3000 2.6 0.6 1.0 O1A B:UTP3000 2.6 0.5 1.0 CG A:ASP483 2.9 99.4 1.0 OD2 A:ASP483 2.9 100.0 1.0 CG A:ASP485 3.0 94.3 1.0 PA B:UTP3000 3.0 0.6 1.0 OD2 A:ASP485 3.1 94.0 1.0 C3' R:A10 3.4 87.6 1.0 MG A:MG2002 3.6 0.4 1.0 OD1 A:ASP481 3.8 0.4 1.0 C5' R:A10 3.9 90.6 1.0 C4' R:A10 3.9 88.7 1.0 O3A B:UTP3000 3.9 0.2 1.0 CB A:ASP481 4.1 0.3 1.0 CG A:ASP481 4.1 0.8 1.0 O3G B:UTP3000 4.3 0.6 1.0 CB A:ASP483 4.3 98.8 1.0 O5' B:UTP3000 4.4 0.1 1.0 CB A:ASP485 4.4 94.4 1.0 C4' B:UTP3000 4.5 0.4 1.0 N A:ASP481 4.6 0.2 1.0 O5' R:A10 4.6 93.1 1.0 C2' R:A10 4.7 87.3 1.0 C5' B:UTP3000 4.7 0.5 1.0 O A:ASP481 4.8 0.5 1.0 N A:ASP485 4.8 95.1 1.0 CA A:ASP481 4.8 0.1 1.0 O4' B:UTP3000 4.8 0.7 1.0 CA A:ASP485 4.9 94.4 1.0 O2' R:A10 4.9 87.1 1.0 C A:ASP481 5.0 0.7 1.0 OD2 A:ASP481 5.0 0.9 1.0 N A:ASP483 5.0 98.9 1.0

Magnesium binding site 2 out of 2 in the Rna Polymerase II Elongation Complex with Utp, Updated 11/2006


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 with Utp, Updated 11/2006 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:0.4 occ:1.00 O3G B:UTP3000 2.0 0.6 1.0 OD1 B:ASP837 2.2 0.0 1.0 OD1 A:ASP483 2.2 100.0 1.0 OD1 A:ASP481 2.2 0.4 1.0 CG A:ASP481 3.1 0.8 1.0 O3A B:UTP3000 3.2 0.2 1.0 CB A:ASP481 3.2 0.3 1.0 NH1 B:ARG1020 3.3 0.6 1.0 CG A:ASP483 3.3 99.4 1.0 CG B:ASP837 3.3 0.7 1.0 MG A:MG2001 3.6 97.5 1.0 PG B:UTP3000 3.6 0.0 1.0 O1A B:UTP3000 3.6 0.5 1.0 CB A:ASP483 3.8 98.8 1.0 PA B:UTP3000 3.8 0.6 1.0 CB B:ASP837 3.9 0.2 1.0 O2B B:UTP3000 3.9 0.5 1.0 NH2 B:ARG1020 4.1 0.5 1.0 PB B:UTP3000 4.1 0.7 1.0 CZ B:ARG1020 4.1 0.1 1.0 O2A B:UTP3000 4.2 0.6 1.0 O3B B:UTP3000 4.3 0.3 1.0 OD2 A:ASP481 4.3 0.9 1.0 OD2 B:ASP837 4.4 0.1 1.0 O2G B:UTP3000 4.4 0.1 1.0 OD2 A:ASP483 4.4 100.0 1.0 O1G B:UTP3000 4.4 0.3 1.0 CA A:ASP481 4.7 0.1 1.0 N A:ASP483 4.9 98.9 1.0 OD1 A:ASP485 4.9 95.1 1.0 CA A:ASP483 5.0 98.5 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