Magnesium in PDB 2e2h: Rna Polymerase II Elongation Complex at 5 Mm MG2+ with Gtp

All present enzymatic activity of Rna Polymerase II Elongation Complex at 5 Mm MG2+ with Gtp:
2.7.7.6;

The structure of Rna Polymerase II Elongation Complex at 5 Mm MG2+ with Gtp, PDB code: 2e2h 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)	45.08 / 3.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	171.108, 222.005, 195.163, 90.00, 102.61, 90.00
R / Rfree (%)	29 / 36.8

The structure of Rna Polymerase II Elongation Complex at 5 Mm MG2+ with Gtp also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Magnesium atom in the Rna Polymerase II Elongation Complex at 5 Mm MG2+ with Gtp (pdb code 2e2h). 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 at 5 Mm MG2+ with Gtp, PDB code: 2e2h:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rna Polymerase II Elongation Complex at 5 Mm MG2+ with Gtp


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 at 5 Mm MG2+ with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:96.2 occ:1.00 O2A T:GTP3000 2.0 0.4 1.0 OD1 A:ASP483 2.2 97.2 1.0 OD1 A:ASP485 2.2 93.4 1.0 OD2 A:ASP483 2.3 97.1 1.0 O1A T:GTP3000 2.5 0.9 1.0 CG A:ASP483 2.6 95.9 1.0 PA T:GTP3000 2.7 0.8 1.0 OD1 A:ASP481 2.9 99.9 1.0 CB A:ASP481 3.3 97.6 1.0 CG A:ASP481 3.4 98.8 1.0 CG A:ASP485 3.4 90.7 1.0 MG A:MG2002 3.4 0.0 1.0 O3A T:GTP3000 3.6 0.8 1.0 OD2 A:ASP485 3.9 91.6 1.0 O3G T:GTP3000 3.9 0.9 1.0 C3' R:A10 4.1 88.9 1.0 CB A:ASP483 4.1 95.0 1.0 O5' T:GTP3000 4.1 0.9 1.0 C4' R:A10 4.5 89.0 1.0 OD2 A:ASP481 4.5 0.4 1.0 C5' R:A10 4.5 88.9 1.0 C5' T:GTP3000 4.5 0.1 1.0 CA A:ASP481 4.5 97.3 1.0 O2G T:GTP3000 4.6 1.0 1.0 N A:ASP481 4.7 97.0 1.0 CB A:ASP485 4.7 89.7 1.0 C4' T:GTP3000 4.7 0.8 1.0 PG T:GTP3000 4.8 0.5 1.0 N A:ASP483 4.8 95.3 1.0 O5' R:A10 4.8 88.4 1.0 CA A:ASP483 4.9 94.6 1.0 PB T:GTP3000 5.0 0.7 1.0

Magnesium binding site 2 out of 2 in the Rna Polymerase II Elongation Complex at 5 Mm MG2+ with Gtp


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 at 5 Mm MG2+ with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:0.0 occ:1.00 O3G T:GTP3000 2.0 0.9 1.0 OD1 A:ASP481 2.2 99.9 1.0 OD1 A:ASP483 2.2 97.2 1.0 OD1 B:ASP837 2.3 0.6 1.0 O3A T:GTP3000 3.1 0.8 1.0 CG A:ASP481 3.1 98.8 1.0 NH1 B:ARG1020 3.1 99.9 1.0 O2B T:GTP3000 3.1 0.3 1.0 CG B:ASP837 3.3 0.4 1.0 CG A:ASP483 3.3 95.9 1.0 MG A:MG2001 3.4 96.2 1.0 PG T:GTP3000 3.4 0.5 1.0 CB A:ASP481 3.5 97.6 1.0 O1A T:GTP3000 3.5 0.9 1.0 PB T:GTP3000 3.6 0.7 1.0 PA T:GTP3000 3.7 0.8 1.0 CB B:ASP837 3.8 0.4 1.0 O3B T:GTP3000 4.1 0.0 1.0 CZ B:ARG1020 4.1 99.2 1.0 O2A T:GTP3000 4.1 0.4 1.0 CB A:ASP483 4.1 95.0 1.0 OD2 A:ASP481 4.2 0.4 1.0 NH2 B:ARG1020 4.2 99.0 1.0 O2G T:GTP3000 4.2 1.0 1.0 OD2 A:ASP483 4.3 97.1 1.0 O1G T:GTP3000 4.3 0.3 1.0 OD2 B:ASP837 4.4 0.5 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