Magnesium in PDB 2nvq: Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp

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

The structure of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp, PDB code: 2nvq 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)	48.45 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	170.646, 222.760, 195.281, 90.00, 101.31, 90.00
R / Rfree (%)	22.9 / 28.3

The structure of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp 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 2'Dutp (pdb code 2nvq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp, PDB code: 2nvq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp


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 2'Dutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:46.3 occ:1.00 OD2 A:ASP485 2.1 51.1 1.0 OD1 A:ASP485 2.2 54.5 1.0 CG A:ASP485 2.2 49.9 1.0 OD2 A:ASP483 2.3 53.2 1.0 OD1 A:ASP481 2.5 59.2 1.0 C3' R:A10 2.9 39.3 1.0 C4' R:A10 3.2 36.9 1.0 CG A:ASP483 3.2 54.7 1.0 C5' R:A10 3.5 31.2 1.0 OD1 A:ASP483 3.5 59.1 1.0 CB A:ASP485 3.6 48.1 1.0 C5' T:DUT29 3.6 74.7 0.3 O2A T:DUT29 3.7 77.4 0.3 CG A:ASP481 3.8 57.4 1.0 O1G T:DUT29 3.8 98.7 0.7 O2' R:A10 3.9 44.1 1.0 C2' R:A10 4.0 39.5 1.0 O5' T:DUT29 4.0 76.8 0.3 N A:ASP485 4.1 47.8 1.0 CA A:ASP485 4.2 47.3 1.0 NH2 A:ARG446 4.2 57.2 1.0 PA T:DUT29 4.3 77.5 0.3 O3G T:DUT29 4.4 98.8 0.7 C4' T:DUT29 4.5 73.1 0.3 N A:ASP481 4.5 51.8 1.0 O1A T:DUT29 4.6 77.4 0.3 OD2 A:ASP481 4.6 63.8 1.0 O4' R:A10 4.6 36.4 1.0 CB A:ASP483 4.7 50.4 1.0 O5' R:A10 4.7 24.9 1.0 CB A:ASP481 4.7 53.3 1.0 PG T:DUT29 4.8 97.9 0.7 C A:ASP483 4.8 48.4 1.0 N A:ASP483 4.9 49.4 1.0 CA A:ASP481 4.9 52.4 1.0 C A:GLY484 4.9 47.5 1.0 O A:ASP483 5.0 47.7 1.0 N A:GLY484 5.0 49.1 1.0

Magnesium binding site 2 out of 3 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp


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 2'Dutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:43.6 occ:0.66 O2B T:DUT29 2.3 94.2 0.7 O4' T:DUT29 2.8 77.7 0.7 C4' T:DUT29 3.2 80.4 0.7 PB T:DUT29 3.4 95.2 0.7 OD2 A:ASP481 3.5 63.8 1.0 C1' T:DUT29 3.5 77.6 0.7 O1G T:DUT29 3.7 80.3 0.3 O1B T:DUT29 3.9 94.4 0.7 O3' T:DUT29 4.0 76.4 0.7 O3A T:DUT29 4.1 91.1 0.7 C3' T:DUT29 4.2 78.9 0.7 C5' T:DUT29 4.4 87.0 0.7 N1 T:DUT29 4.4 77.5 0.7 O5' T:DUT29 4.6 95.5 0.7 C2' T:DUT29 4.6 78.6 0.7 NH2 B:ARG1020 4.7 68.2 1.0 OE1 B:GLU836 4.7 69.9 1.0 CG A:ASP481 4.7 57.4 1.0 O3B T:DUT29 4.8 96.7 0.7 O2 T:DUT29 4.8 77.0 0.7 PG T:DUT29 4.8 79.7 0.3 O1G T:DUT29 4.9 98.7 0.7 C2 T:DUT29 5.0 77.2 0.7

Magnesium binding site 3 out of 3 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:33.1 occ:0.34 O3G T:DUT29 2.1 78.6 0.3 O1G T:DUT29 2.4 80.3 0.3 OD2 B:ASP837 2.6 67.1 1.0 PG T:DUT29 2.7 79.7 0.3 OD1 A:ASP483 2.8 59.1 1.0 O3B T:DUT29 3.5 79.4 0.3 NH2 B:ARG1020 3.5 68.2 1.0 CG B:ASP837 3.6 65.8 1.0 O3B T:DUT29 3.8 96.7 0.7 CZ B:ARG1020 3.9 64.6 1.0 O1B T:DUT29 4.0 94.4 0.7 OD2 A:ASP481 4.0 63.8 1.0 O2B T:DUT29 4.0 94.2 0.7 CG A:ASP483 4.0 54.7 1.0 PB T:DUT29 4.1 95.2 0.7 O2G T:DUT29 4.3 79.6 0.3 OD1 B:ASP837 4.3 70.3 1.0 CG A:ASP481 4.4 57.4 1.0 NH1 B:ARG1020 4.4 63.0 1.0 OD1 A:ASP481 4.4 59.2 1.0 O1B T:DUT29 4.4 78.6 0.3 CB B:ASP837 4.5 60.7 1.0 NE B:ARG1020 4.5 62.7 1.0 O1G T:DUT29 4.5 98.7 0.7 CB A:ASP483 4.6 50.4 1.0 PG T:DUT29 4.6 97.9 0.7 O2A T:DUT29 4.6 77.4 0.3 O3G T:DUT29 4.7 98.8 0.7 PB T:DUT29 4.7 78.8 0.3

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