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Zinc in PDB 2a69: Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin

Enzymatic activity of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin

All present enzymatic activity of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin, PDB code: 2a69 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 / 2.50
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 / 26.7

Other elements in 2a69:

The structure of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin also contains other interesting chemical elements:

Magnesium (Mg) 487 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin (pdb code 2a69). 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 in Complex with Antibiotic Rifapentin, PDB code: 2a69:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2a69

Go back to Zinc Binding Sites List in 2a69
Zinc binding site 1 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin


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 in Complex with Antibiotic Rifapentin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn7058

b:0.7
occ:1.00
 SG D:CYS60 2.3 0.2 1.0
SG D:CYS58 2.4 0.4 1.0
SG D:CYS76 2.4 0.8 1.0
SG D:CYS73 2.5 0.8 1.0
CB D:CYS60 3.5 99.7 1.0
CB D:CYS73 3.6 0.3 1.0
N D:CYS60 3.7 99.5 1.0
O D:HOH2134 3.7 62.3 1.0
CB D:CYS76 3.8 0.6 1.0
CB D:CYS58 3.9 99.5 1.0
N D:GLY61 4.0 96.4 1.0
CA D:CYS60 4.0 98.7 1.0
N D:LYS62 4.2 96.0 1.0
O D:CYS76 4.3 0.4 1.0
CB D:LYS62 4.4 95.5 1.0
C D:CYS60 4.5 97.5 1.0
N D:ALA59 4.6 99.1 1.0
CA D:CYS76 4.6 0.4 1.0
N D:CYS76 4.7 0.5 1.0
C D:CYS76 4.8 0.8 1.0
C D:ALA59 4.8 99.7 1.0
CA D:LYS62 5.0 96.8 1.0

Zinc binding site 2 out of 4 in 2a69

Go back to Zinc Binding Sites List in 2a69
Zinc binding site 2 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin


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 in Complex with Antibiotic Rifapentin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn7112

b:80.3
occ:1.00
 SG D:CYS1112 2.3 81.6 1.0
SG D:CYS1204 2.3 79.1 1.0
SG D:CYS1194 2.4 79.3 1.0
SG D:CYS1201 2.4 82.1 1.0
CB D:CYS1112 3.1 82.2 1.0
CB D:CYS1204 3.1 74.2 1.0
NH1 D:ARG1189 3.5 36.9 1.0
CB D:CYS1194 3.5 74.8 1.0
CB D:CYS1201 3.7 77.4 1.0
CA D:CYS1194 3.9 73.8 1.0
N D:CYS1201 4.2 74.1 1.0
CA D:CYS1112 4.3 83.7 1.0
N D:GLN1195 4.3 78.7 1.0
CA D:CYS1204 4.4 71.3 1.0
N D:CYS1204 4.5 70.5 1.0
CA D:CYS1201 4.5 74.1 1.0
N D:CYS1112 4.5 84.9 1.0
O D:CYS1112 4.6 83.5 1.0
C D:CYS1194 4.7 75.7 1.0
CZ D:ARG1189 4.8 37.6 1.0
O D:HOH9625 4.9 44.0 1.0
C D:CYS1112 4.9 83.0 1.0
N D:CYS1194 4.9 68.6 1.0

Zinc binding site 3 out of 4 in 2a69

Go back to Zinc Binding Sites List in 2a69
Zinc binding site 3 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin


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 in Complex with Antibiotic Rifapentin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn7059

b:93.2
occ:1.00
 SG N:CYS73 2.4 94.3 1.0
SG N:CYS58 2.4 90.1 1.0
SG N:CYS76 2.4 92.3 1.0
SG N:CYS60 2.4 93.2 1.0
CB N:CYS73 3.5 97.3 1.0
CB N:CYS60 3.6 92.2 1.0
CB N:CYS76 3.7 93.3 1.0
N N:CYS60 3.8 91.0 1.0
CB N:CYS58 3.9 87.1 1.0
O N:CYS76 3.9 92.6 1.0
O N:HOH9539 4.0 33.5 1.0
CA N:CYS60 4.3 91.5 1.0
N N:GLY61 4.3 91.5 1.0
CA N:CYS76 4.4 93.2 1.0
C N:CYS76 4.5 91.8 1.0
N N:ALA59 4.5 86.5 1.0
N N:CYS76 4.5 94.6 1.0
N N:LYS62 4.6 90.5 1.0
CB N:LYS62 4.6 89.7 1.0
C N:CYS60 4.8 91.7 1.0
C N:ALA59 4.9 89.8 1.0
CA N:CYS73 4.9 99.7 1.0

Zinc binding site 4 out of 4 in 2a69

Go back to Zinc Binding Sites List in 2a69
Zinc binding site 4 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifapentin


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 in Complex with Antibiotic Rifapentin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn7113

b:84.3
occ:1.00
 SG N:CYS1112 2.3 85.4 1.0
SG N:CYS1204 2.3 81.1 1.0
SG N:CYS1201 2.3 84.0 1.0
SG N:CYS1194 2.4 83.4 1.0
CB N:CYS1112 3.1 85.8 1.0
CB N:CYS1204 3.2 78.1 1.0
CB N:CYS1194 3.5 80.7 1.0
O N:HOH9589 3.7 35.2 1.0
CB N:CYS1201 3.8 81.8 1.0
CA N:CYS1194 3.8 80.4 1.0
NH1 N:ARG1189 4.1 59.2 1.0
N N:CYS1201 4.2 78.3 1.0
N N:GLN1195 4.3 86.0 1.0
CA N:CYS1112 4.4 87.7 1.0
CA N:CYS1204 4.4 76.6 1.0
O N:HOH9807 4.4 45.6 1.0
N N:CYS1204 4.5 77.3 1.0
CA N:CYS1201 4.6 79.8 1.0
N N:CYS1112 4.6 86.5 1.0
C N:CYS1194 4.7 82.4 1.0
O N:CYS1112 4.7 90.7 1.0
OE1 N:GLN1195 4.8 91.0 1.0
O N:HOH9816 4.8 62.4 1.0
NH2 N:ARG1189 4.8 57.2 1.0
N N:CYS1194 4.9 77.4 1.0
C N:CYS1112 4.9 89.4 1.0
CZ N:ARG1189 5.0 58.0 1.0

Reference:

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
Page generated: Wed Oct 16 21:31:38 2024

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