Magnesium in PDB 2yu9: Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp

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

The structure of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp, PDB code: 2yu9 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)	19.98 / 3.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	170.610, 222.729, 196.160, 90.00, 101.87, 90.00
R / Rfree (%)	28.3 / 34.4

The structure of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp 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 Utp (pdb code 2yu9). 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 Utp, PDB code: 2yu9:
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 Utp


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 Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:0.7 occ:1.00 OD2 A:ASP485 2.1 0.8 1.0 OD2 A:ASP483 2.2 0.4 1.0 OD1 A:ASP485 2.3 0.8 1.0 CG A:ASP485 2.3 0.9 1.0 OD1 A:ASP481 2.4 1.0 1.0 CG A:ASP483 3.0 0.9 1.0 CG A:ASP481 3.1 0.7 1.0 OD1 A:ASP483 3.1 0.8 1.0 OD2 A:ASP481 3.2 0.9 1.0 O2A A:UTP2003 3.4 0.4 0.3 CB A:ASP485 3.5 0.8 1.0 O1A A:UTP2003 3.8 0.4 0.3 O2G A:UTP2003 3.8 0.1 0.7 C4' R:A10 4.0 0.4 1.0 PA A:UTP2003 4.0 0.4 0.3 C3' R:A10 4.0 0.9 1.0 N A:ASP481 4.2 0.3 1.0 NH2 A:ARG446 4.3 0.1 1.0 C5' A:UTP2003 4.3 0.4 0.3 CA A:ASP485 4.3 0.0 1.0 N A:ASP485 4.3 0.3 1.0 O2' R:A10 4.4 0.3 1.0 CB A:ASP481 4.4 0.2 1.0 N A:ASP483 4.5 0.6 1.0 CB A:ASP483 4.5 0.9 1.0 C5' R:A10 4.5 0.7 1.0 C A:ASP481 4.6 0.6 1.0 O A:ASP481 4.6 0.7 1.0 O5' A:UTP2003 4.7 0.4 0.3 CA A:ASP481 4.7 0.7 1.0 C2' R:A10 4.8 0.5 1.0 CA A:ASP483 4.9 0.4 1.0 O2A A:UTP2003 5.0 0.1 0.7 O4' A:UTP2003 5.0 0.4 0.3 N A:PHE482 5.0 0.1 1.0

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


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 Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:59.7 occ:1.00 O1G A:UTP2003 1.6 0.4 0.3 C6 A:UTP2003 2.6 0.9 0.7 PG A:UTP2003 2.6 0.4 0.3 C5 A:UTP2003 3.1 0.4 0.7 OD2 A:ASP481 3.1 0.9 1.0 O3B A:UTP2003 3.1 0.4 0.3 O3G A:UTP2003 3.3 0.4 0.3 O5' A:UTP2003 3.5 0.8 0.7 O4' A:UTP2003 3.6 0.1 0.7 N1 A:UTP2003 3.7 0.6 0.7 O2A A:UTP2003 3.9 0.4 0.3 C5' A:UTP2003 3.9 0.2 0.7 CG A:ASP481 4.0 0.7 1.0 CB A:ASP481 4.0 0.2 1.0 O2G A:UTP2003 4.1 0.4 0.3 O3A A:UTP2003 4.1 0.6 0.7 C1' A:UTP2003 4.1 0.5 0.7 O2A A:UTP2003 4.2 0.1 0.7 PA A:UTP2003 4.3 0.1 0.7 C4' A:UTP2003 4.3 0.6 0.7 OE1 B:GLU836 4.3 0.3 1.0 O5' A:UTP2003 4.3 0.4 0.3 C4 A:UTP2003 4.4 0.3 0.7 PB A:UTP2003 4.5 0.4 0.3 O2G A:UTP2003 4.5 0.1 0.7 O1B A:UTP2003 4.6 0.4 0.3 NH2 B:ARG1020 4.7 0.3 1.0 C5' A:UTP2003 4.7 0.4 0.3 PA A:UTP2003 4.7 0.4 0.3 C2 A:UTP2003 4.9 0.3 0.7 N A:ASP481 5.0 0.3 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