Zinc 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:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme, PDB code: 2a6e:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn7058 b:0.9 occ:1.00 SG D:CYS60 2.4 0.2 1.0 SG D:CYS58 2.4 0.1 1.0 SG D:CYS76 2.4 0.1 1.0 SG D:CYS73 2.5 0.9 1.0 CB D:CYS73 3.6 0.1 1.0 CB D:CYS60 3.6 0.3 1.0 N D:CYS60 3.7 0.2 1.0 CB D:CYS76 3.7 0.5 1.0 CB D:CYS58 3.9 0.5 1.0 N D:GLY61 4.1 0.8 1.0 CA D:CYS60 4.1 0.6 1.0 N D:LYS62 4.3 0.3 1.0 O D:CYS76 4.3 0.3 1.0 CB D:LYS62 4.5 0.8 1.0 N D:ALA59 4.5 0.6 1.0 C D:CYS60 4.5 0.2 1.0 CA D:CYS76 4.6 0.6 1.0 N D:CYS76 4.7 0.4 1.0 C D:CYS76 4.8 0.9 1.0 C D:ALA59 4.8 0.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 D:Zn7112 b:75.4 occ:1.00 SG D:CYS1112 2.3 77.1 1.0 SG D:CYS1204 2.3 75.0 1.0 SG D:CYS1201 2.4 76.7 1.0 SG D:CYS1194 2.4 75.2 1.0 CB D:CYS1112 3.1 78.8 1.0 CB D:CYS1204 3.2 70.5 1.0 NH1 D:ARG1189 3.4 49.6 1.0 CB D:CYS1194 3.5 72.9 1.0 CB D:CYS1201 3.6 70.9 1.0 CA D:CYS1194 3.8 71.8 1.0 N D:CYS1201 4.1 68.1 1.0 N D:GLN1195 4.3 78.0 1.0 CA D:CYS1112 4.3 81.6 1.0 CA D:CYS1204 4.3 68.1 1.0 N D:CYS1204 4.3 67.7 1.0 CA D:CYS1201 4.4 67.1 1.0 N D:CYS1112 4.5 82.7 1.0 O D:CYS1112 4.6 83.7 1.0 C D:CYS1194 4.7 74.1 1.0 CZ D:ARG1189 4.7 51.0 1.0 C D:CYS1112 4.9 82.1 1.0 N D:CYS1194 4.9 68.3 1.0 OE1 D:GLN1195 5.0 90.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn7059 b:0.9 occ:1.00 SG N:CYS76 2.4 99.8 1.0 SG N:CYS60 2.4 0.5 1.0 SG N:CYS58 2.4 99.2 1.0 SG N:CYS73 2.4 1.0 1.0 CB N:CYS73 3.5 0.9 1.0 CB N:CYS60 3.7 97.9 1.0 CB N:CYS76 3.7 99.4 1.0 N N:CYS60 3.8 95.9 1.0 CB N:CYS58 3.9 96.9 1.0 O N:CYS76 4.0 99.3 1.0 O N:HOH9378 4.3 57.7 1.0 CA N:CYS60 4.3 97.1 1.0 N N:GLY61 4.3 96.8 1.0 CG N:LYS62 4.4 89.3 1.0 CA N:CYS76 4.4 99.5 1.0 N N:ALA59 4.5 95.2 1.0 C N:CYS76 4.5 98.5 1.0 N N:CYS76 4.6 0.3 1.0 O N:HOH9267 4.6 47.2 1.0 N N:LYS62 4.6 94.1 1.0 CB N:LYS62 4.7 91.3 1.0 C N:CYS60 4.8 97.0 1.0 C N:ALA59 4.9 94.8 1.0 O N:HOH9291 4.9 30.7 1.0 CB N:ALA59 5.0 92.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn7113 b:87.6 occ:1.00 SG N:CYS1112 2.3 87.7 1.0 SG N:CYS1204 2.4 85.0 1.0 SG N:CYS1194 2.4 84.5 1.0 SG N:CYS1201 2.4 84.3 1.0 CB N:CYS1112 3.1 85.1 1.0 CB N:CYS1204 3.2 81.8 1.0 CB N:CYS1194 3.4 83.3 1.0 CA N:CYS1194 3.6 83.8 1.0 CB N:CYS1201 3.7 81.9 1.0 NH1 N:ARG1189 3.9 66.2 1.0 N N:CYS1201 4.1 78.0 1.0 N N:GLN1195 4.1 87.7 1.0 CA N:CYS1204 4.4 81.0 1.0 CA N:CYS1112 4.4 86.5 1.0 N N:CYS1204 4.4 81.0 1.0 C N:CYS1194 4.5 85.3 1.0 CA N:CYS1201 4.5 78.6 1.0 N N:CYS1112 4.7 84.8 1.0 O N:CYS1112 4.7 90.0 1.0 N N:CYS1194 4.7 81.8 1.0 OE1 N:GLN1195 4.8 90.1 1.0 CZ N:ARG1189 4.9 65.1 1.0 C N:CYS1112 5.0 88.1 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