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Zinc in PDB 2a68: Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifabutin

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

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

Protein crystallography data

The structure of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifabutin, PDB code: 2a68 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 (%) 22.5 / 25.7

Other elements in 2a68:

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

Magnesium (Mg) 562 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 Rifabutin (pdb code 2a68). 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 Rifabutin, PDB code: 2a68:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2a68

Go back to Zinc Binding Sites List in 2a68
Zinc binding site 1 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifabutin


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 Rifabutin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn7058

b:0.3
occ:1.00
 SG D:CYS60 2.4 98.9 1.0
SG D:CYS76 2.4 99.2 1.0
SG D:CYS58 2.4 98.2 1.0
SG D:CYS73 2.4 0.7 1.0
CB D:CYS60 3.6 97.0 1.0
CB D:CYS73 3.6 0.8 1.0
N D:CYS60 3.7 96.5 1.0
CB D:CYS76 3.8 99.0 1.0
O D:HOH2590 3.9 58.9 1.0
CB D:CYS58 3.9 95.2 1.0
CA D:CYS60 4.1 96.3 1.0
N D:GLY61 4.1 94.4 1.0
O D:HOH9808 4.2 43.4 1.0
N D:LYS62 4.3 95.5 1.0
O D:CYS76 4.4 97.3 1.0
CB D:LYS62 4.5 95.2 1.0
C D:CYS60 4.5 95.1 1.0
N D:ALA59 4.6 95.2 1.0
CA D:CYS76 4.6 98.7 1.0
N D:CYS76 4.7 99.4 1.0
C D:CYS76 4.8 97.2 1.0
C D:ALA59 4.8 97.0 1.0

Zinc binding site 2 out of 4 in 2a68

Go back to Zinc Binding Sites List in 2a68
Zinc binding site 2 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifabutin


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 Rifabutin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn7112

b:72.0
occ:1.00
 SG D:CYS1112 2.3 75.2 1.0
SG D:CYS1204 2.3 69.1 1.0
SG D:CYS1201 2.4 73.0 1.0
SG D:CYS1194 2.4 71.4 1.0
CB D:CYS1112 3.1 77.2 1.0
CB D:CYS1204 3.2 66.3 1.0
NH1 D:ARG1189 3.5 35.7 1.0
CB D:CYS1194 3.6 67.1 1.0
CB D:CYS1201 3.7 67.5 1.0
O D:HOH9616 3.8 47.7 1.0
CA D:CYS1194 3.9 66.1 1.0
N D:CYS1201 4.2 62.9 1.0
CA D:CYS1204 4.3 64.6 1.0
N D:GLN1195 4.4 71.5 1.0
CA D:CYS1112 4.4 79.0 1.0
N D:CYS1204 4.4 65.7 1.0
CA D:CYS1201 4.5 63.6 1.0
N D:CYS1112 4.6 79.1 1.0
O D:CYS1112 4.6 80.8 1.0
C D:CYS1194 4.8 68.0 1.0
CZ D:ARG1189 4.8 35.0 1.0
C D:CYS1112 4.9 80.0 1.0
O D:HOH9787 4.9 45.6 1.0
N D:CYS1194 5.0 61.8 1.0

Zinc binding site 3 out of 4 in 2a68

Go back to Zinc Binding Sites List in 2a68
Zinc binding site 3 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifabutin


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 Rifabutin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn7059

b:83.0
occ:1.00
 SG N:CYS76 2.4 82.1 1.0
SG N:CYS73 2.4 82.8 1.0
SG N:CYS60 2.4 84.0 1.0
SG N:CYS58 2.4 81.0 1.0
CB N:CYS73 3.4 85.3 1.0
O N:HOH9667 3.5 47.4 1.0
O N:HOH2262 3.6 82.2 1.0
O N:HOH9734 3.6 40.9 1.0
CB N:CYS76 3.7 81.9 1.0
CB N:CYS60 3.7 82.9 1.0
N N:CYS60 3.8 81.4 1.0
CB N:CYS58 3.9 78.4 1.0
O N:CYS76 4.1 80.5 1.0
CA N:CYS60 4.3 82.4 1.0
N N:GLY61 4.4 82.4 1.0
CA N:CYS76 4.5 80.9 1.0
C N:CYS76 4.5 79.3 1.0
N N:ALA59 4.5 77.9 1.0
CG N:LYS62 4.6 77.4 1.0
N N:CYS76 4.6 81.7 1.0
N N:LYS62 4.6 80.2 1.0
CB N:LYS62 4.7 79.2 1.0
C N:CYS60 4.8 82.8 1.0
CA N:CYS73 4.9 86.1 1.0
C N:ALA59 4.9 80.5 1.0

Zinc binding site 4 out of 4 in 2a68

Go back to Zinc Binding Sites List in 2a68
Zinc binding site 4 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Rifabutin


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 Rifabutin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn7113

b:79.8
occ:1.00
 SG N:CYS1112 2.3 80.0 1.0
SG N:CYS1194 2.3 79.7 1.0
SG N:CYS1201 2.3 79.0 1.0
SG N:CYS1204 2.3 76.8 1.0
CB N:CYS1112 3.2 80.0 1.0
CB N:CYS1204 3.2 73.1 1.0
CB N:CYS1194 3.4 75.9 1.0
CA N:CYS1194 3.7 74.3 1.0
CB N:CYS1201 3.8 75.7 1.0
NH1 N:ARG1189 3.8 47.2 1.0
N N:CYS1201 4.2 72.3 1.0
O N:HOH9600 4.2 44.6 1.0
N N:GLN1195 4.2 77.0 1.0
CA N:CYS1204 4.4 71.4 1.0
CA N:CYS1112 4.5 81.4 1.0
N N:CYS1204 4.5 72.0 1.0
CA N:CYS1201 4.6 73.3 1.0
C N:CYS1194 4.6 75.5 1.0
N N:CYS1112 4.7 80.2 1.0
O N:CYS1112 4.8 84.2 1.0
N N:CYS1194 4.8 72.0 1.0
CZ N:ARG1189 4.9 48.0 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 21:31:03 2024

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