Magnesium in PDB 1r9s: Rna Polymerase II Strand Separated Elongation Complex, Matched Nucleotide

All present enzymatic activity of Rna Polymerase II Strand Separated Elongation Complex, Matched Nucleotide:
2.7.7.6;

The structure of Rna Polymerase II Strand Separated Elongation Complex, Matched Nucleotide, PDB code: 1r9s was solved by K.D.Westover, D.A.Bushnell, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 4.25
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 (%)	34.9 / 39.8

The structure of Rna Polymerase II Strand Separated Elongation Complex, Matched Nucleotide also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Magnesium atom in the Rna Polymerase II Strand Separated Elongation Complex, Matched Nucleotide (pdb code 1r9s). 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 Strand Separated Elongation Complex, Matched Nucleotide, PDB code: 1r9s:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rna Polymerase II Strand Separated Elongation Complex, Matched Nucleotide


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 Strand Separated Elongation Complex, Matched Nucleotide within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg2001 b:36.7 occ:1.00 O3' R:A10 1.8 0.5 1.0 C5' R:UTP3000 2.2 78.7 1.0 O5' R:UTP3000 2.2 78.7 1.0 O2A R:UTP3000 2.3 78.7 1.0 PA R:UTP3000 2.4 78.7 1.0 O2' R:A10 2.9 0.3 1.0 C3' R:A10 2.9 0.5 1.0 O1A R:UTP3000 2.9 78.7 1.0 C2' R:A10 3.2 0.1 1.0 OD1 A:ASP483 3.3 0.6 1.0 C4' R:UTP3000 3.3 78.7 1.0 OD2 A:ASP481 3.4 0.7 1.0 OD1 A:ASP485 3.4 0.6 1.0 OD2 A:ASP483 3.5 0.6 1.0 CG A:ASP483 3.8 0.6 1.0 C4' R:A10 3.9 0.7 1.0 O3A R:UTP3000 3.9 78.7 1.0 O4' R:UTP3000 4.0 78.7 1.0 C3' R:UTP3000 4.1 78.7 1.0 MG A:MG2002 4.2 44.6 1.0 CG A:ASP481 4.2 0.7 1.0 OD1 A:ASP481 4.3 0.7 1.0 CG A:ASP485 4.3 0.6 1.0 OD2 A:ASP485 4.4 0.6 1.0 O3B R:UTP3000 4.4 78.7 1.0 O3' R:UTP3000 4.6 78.7 1.0 C1' R:A10 4.6 1.0 1.0 C5' R:A10 4.8 0.7 1.0 PB R:UTP3000 4.9 78.7 1.0 O4' R:A10 4.9 0.1 1.0 O1G R:UTP3000 5.0 78.7 1.0

Magnesium binding site 2 out of 2 in the Rna Polymerase II Strand Separated Elongation Complex, Matched Nucleotide


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 Strand Separated Elongation Complex, Matched Nucleotide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:44.6 occ:1.00 O1G R:UTP3000 2.1 78.7 1.0 OD1 A:ASP483 2.5 0.6 1.0 PG R:UTP3000 2.9 78.7 1.0 O3G R:UTP3000 3.0 78.7 1.0 O3B R:UTP3000 3.2 78.7 1.0 CG A:ASP483 3.4 0.6 1.0 OD2 B:ASP837 3.4 0.7 1.0 OD2 A:ASP481 3.4 0.7 1.0 NH1 B:ARG1020 3.5 0.6 1.0 O2A R:UTP3000 3.6 78.7 1.0 CG A:ASP481 3.8 0.7 1.0 OD1 A:ASP481 3.9 0.7 1.0 CB A:ASP483 4.0 0.6 1.0 MG R:MG2001 4.2 36.7 1.0 OD2 A:ASP483 4.2 0.6 1.0 O1B R:UTP3000 4.2 78.7 1.0 O5' R:UTP3000 4.3 78.7 1.0 CG B:ASP837 4.3 0.7 1.0 O2G R:UTP3000 4.3 78.7 1.0 PB R:UTP3000 4.4 78.7 1.0 PA R:UTP3000 4.5 78.7 1.0 CZ B:ARG1020 4.5 0.6 1.0 NH2 B:ARG1020 4.7 0.6 1.0 O3A R:UTP3000 4.8 78.7 1.0 CB A:ASP481 4.9 0.7 1.0 OD1 B:ASP837 4.9 0.7 1.0

K.D.Westover, D.A.Bushnell, R.D.Kornberg. Structural Basis of Transcription: Nucleotide Selection By Rotation in the Rna Polymerase II Active Center. Cell(Cambridge,Mass.) V. 119 481 2004.
ISSN: ISSN 0092-8674
PubMed: 15537538
DOI: 10.1016/J.CELL.2004.10.016