Magnesium in PDB 2a6e: Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme

All present enzymatic activity of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme:
2.7.7.6;

The structure of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme, PDB code: 2a6e was solved by I.Artsimovitch, M.N.Vassylyeva, D.Svetlov, V.Svetlov, A.Perederina, N.Igarashi, N.Matsugaki, S.Wakatsuki, T.H.Tahirov, D.G.Vassylyev, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.80
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	239.500, 239.500, 253.100, 90.00, 90.00, 120.00
R / Rfree (%)	23.1 / 26.8

The structure of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme (pdb code 2a6e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme, PDB code: 2a6e:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg9001 b:67.7 occ:1.00 OD1 D:ASP739 2.2 61.5 1.0 OD1 D:ASP741 2.3 45.9 1.0 OD1 D:ASP743 2.3 40.5 1.0 CG D:ASP743 2.5 39.4 1.0 OD2 D:ASP743 2.7 40.5 1.0 CG D:ASP741 3.0 45.0 1.0 O D:ASP739 3.1 49.1 1.0 O D:HOH9165 3.2 31.5 1.0 OD2 D:ASP741 3.4 43.1 1.0 CG D:ASP739 3.4 59.1 1.0 CB D:ASP743 3.5 35.9 1.0 N D:ASP741 3.7 41.0 1.0 C D:ASP739 3.8 47.4 1.0 N D:ASP743 3.9 33.7 1.0 CA D:ASP743 4.1 33.6 1.0 N D:ASP739 4.1 48.7 1.0 CB D:ASP741 4.1 42.9 1.0 CB D:ASP739 4.2 54.3 1.0 CA D:ASP741 4.2 40.5 1.0 CA D:ASP739 4.3 49.4 1.0 C D:ASP741 4.3 40.0 1.0 OD2 D:ASP739 4.3 60.7 1.0 N D:GLY742 4.5 37.8 1.0 N D:PHE740 4.7 44.7 1.0 O D:ASP741 4.7 42.4 1.0 C D:GLY742 4.8 34.4 1.0 C D:PHE740 4.8 41.5 1.0 O D:HOH9985 4.9 67.2 1.0 CA D:PHE740 5.0 41.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg9002 b:64.1 occ:1.00 OD1 N:ASP741 2.2 52.9 1.0 OD2 N:ASP743 2.2 55.2 1.0 OD1 N:ASP743 2.3 54.8 1.0 OD1 N:ASP739 2.3 51.0 1.0 CG N:ASP743 2.3 54.4 1.0 O N:ASP739 3.3 49.5 1.0 CG N:ASP741 3.4 51.7 1.0 CG N:ASP739 3.5 49.7 1.0 CB N:ASP743 3.5 51.5 1.0 N N:ASP743 3.9 48.2 1.0 OD2 N:ASP741 4.0 51.4 1.0 CA N:ASP743 4.0 49.2 1.0 C N:ASP739 4.1 46.9 1.0 N N:ASP741 4.1 44.1 1.0 N N:ASP739 4.2 44.4 1.0 OD2 N:ASP739 4.2 50.9 1.0 CB N:ASP739 4.5 47.2 1.0 CA N:ASP739 4.5 46.5 1.0 CB N:ASP741 4.6 48.5 1.0 NH1 N:ARG704 4.6 35.5 1.0 C N:ASP741 4.6 46.8 1.0 O N:HOH9785 4.6 53.6 1.0 CA N:ASP741 4.6 45.9 1.0 N N:GLY742 4.7 46.7 1.0 C N:GLY742 4.8 46.8 1.0 O N:ASP741 4.9 47.5 1.0 N N:PHE740 5.0 45.5 1.0

I.Artsimovitch, M.N.Vassylyeva, D.Svetlov, V.Svetlov, A.Perederina, N.Igarashi, N.Matsugaki, S.Wakatsuki, T.H.Tahirov, D.G.Vassylyev. Allosteric Modulation of the Rna Polymerase Catalytic Reaction Is An Essential Component of Transcription Control By Rifamycins. Cell(Cambridge,Mass.) V. 122 351 2005.
ISSN: ISSN 0092-8674
PubMed: 16096056
DOI: 10.1016/J.CELL.2005.07.014