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Zinc in PDB 2a6h: Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Sterptolydigin

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

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

Protein crystallography data

The structure of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Sterptolydigin, PDB code: 2a6h was solved by D.Temiakov, N.Zenkin, M.N.Vassylyeva, A.Perederina, T.H.Tahirov, M.Savkina, S.Zorov, V.Nikiforov, N.Igarashi, N.Matsugaki, S.Wakatsuki, K.Severinov, D.G.Vassylyev, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.40
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 / 26.8

Other elements in 2a6h:

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

Magnesium (Mg) 2 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 Sterptolydigin (pdb code 2a6h). 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 Sterptolydigin, PDB code: 2a6h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2a6h

Go back to Zinc Binding Sites List in 2a6h
Zinc binding site 1 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Sterptolydigin


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 Sterptolydigin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn7458

b:64.2
occ:1.00
SG D:CYS60 2.3 66.4 1.0
SG D:CYS76 2.3 68.3 1.0
SG D:CYS58 2.4 62.9 1.0
SG D:CYS73 2.5 70.3 1.0
CB D:CYS60 3.2 69.1 1.0
N D:CYS60 3.6 67.0 1.0
CB D:CYS73 3.7 78.1 1.0
O D:HOH9481 3.8 32.4 1.0
O D:HOH9088 3.8 59.3 1.0
CB D:CYS76 3.8 73.4 1.0
CA D:CYS60 3.9 69.1 1.0
CB D:CYS58 3.9 60.8 1.0
N D:GLY61 4.0 71.9 1.0
N D:LYS62 4.2 79.3 1.0
CB D:LYS62 4.4 82.7 1.0
C D:CYS60 4.4 70.6 1.0
O D:CYS76 4.4 76.4 1.0
N D:CYS76 4.5 77.3 1.0
CA D:CYS76 4.6 76.2 1.0
O D:HOH9382 4.7 40.7 1.0
N D:ALA59 4.7 60.7 1.0
C D:CYS76 4.7 76.9 1.0
O D:HOH9870 4.8 58.2 1.0
C D:ALA59 4.9 65.5 1.0
O D:HOH9374 5.0 68.1 1.0
CA D:LYS62 5.0 82.6 1.0

Zinc binding site 2 out of 4 in 2a6h

Go back to Zinc Binding Sites List in 2a6h
Zinc binding site 2 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Sterptolydigin


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 Sterptolydigin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn7412

b:58.1
occ:1.00
SG D:CYS1112 2.3 63.3 1.0
SG D:CYS1204 2.3 59.7 1.0
SG D:CYS1201 2.3 62.2 1.0
SG D:CYS1194 2.3 56.6 1.0
CB D:CYS1112 3.0 70.5 1.0
CB D:CYS1204 3.2 60.7 1.0
CB D:CYS1194 3.6 59.5 1.0
NH1 D:ARG1189 3.6 40.6 1.0
CB D:CYS1201 3.7 56.5 1.0
CA D:CYS1194 3.9 61.5 1.0
N D:CYS1201 4.2 56.3 1.0
CA D:CYS1112 4.2 75.8 1.0
N D:GLN1195 4.2 68.7 1.0
OG1 D:THR1196 4.4 73.5 1.0
N D:CYS1112 4.4 77.7 1.0
CA D:CYS1204 4.4 62.1 1.0
O D:CYS1112 4.5 78.6 1.0
N D:CYS1204 4.5 62.5 1.0
CA D:CYS1201 4.5 55.3 1.0
C D:CYS1194 4.6 64.3 1.0
C D:CYS1112 4.7 77.7 1.0
CZ D:ARG1189 4.8 41.3 1.0
N D:CYS1194 5.0 59.3 1.0

Zinc binding site 3 out of 4 in 2a6h

Go back to Zinc Binding Sites List in 2a6h
Zinc binding site 3 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Sterptolydigin


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 Sterptolydigin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn7459

b:64.0
occ:1.00
SG N:CYS58 2.3 55.8 1.0
SG N:CYS60 2.3 64.8 1.0
SG N:CYS76 2.4 60.7 1.0
SG N:CYS73 2.4 61.0 1.0
O N:HOH9306 3.4 60.6 1.0
O N:HOH9191 3.4 59.5 1.0
CB N:CYS73 3.4 63.8 1.0
CB N:CYS76 3.6 65.1 1.0
CB N:CYS60 3.7 65.1 1.0
CB N:CYS58 3.7 58.2 1.0
N N:CYS60 3.8 64.8 1.0
O N:CYS76 3.9 68.7 1.0
CA N:CYS60 4.3 64.3 1.0
C N:CYS76 4.3 66.3 1.0
CA N:CYS76 4.3 66.0 1.0
N N:GLY61 4.3 61.6 1.0
N N:ALA59 4.3 61.4 1.0
N N:CYS76 4.4 67.0 1.0
CG N:LYS62 4.5 57.6 1.0
N N:LYS62 4.7 59.4 1.0
C N:CYS60 4.8 63.3 1.0
CB N:LYS62 4.8 59.5 1.0
C N:ALA59 4.9 63.6 1.0
O N:HOH2111 4.9 73.7 1.0
CA N:CYS58 4.9 59.3 1.0
CA N:CYS73 4.9 66.1 1.0
CB N:ALA59 4.9 60.6 1.0
CA N:ALA59 5.0 62.2 1.0

Zinc binding site 4 out of 4 in 2a6h

Go back to Zinc Binding Sites List in 2a6h
Zinc binding site 4 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Sterptolydigin


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 Sterptolydigin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn7413

b:65.6
occ:1.00
SG N:CYS1112 2.2 67.4 1.0
SG N:CYS1204 2.3 65.0 1.0
SG N:CYS1194 2.3 64.4 1.0
SG N:CYS1201 2.3 64.6 1.0
CB N:CYS1112 3.0 72.0 1.0
O N:HOH9751 3.1 70.2 1.0
NH1 N:ARG1189 3.1 63.3 1.0
CB N:CYS1204 3.2 67.4 1.0
CB N:CYS1194 3.4 67.0 1.0
CB N:CYS1201 3.7 66.5 1.0
CA N:CYS1194 3.7 69.2 1.0
N N:GLN1195 4.1 75.2 1.0
N N:CYS1201 4.2 63.9 1.0
CA N:CYS1112 4.2 75.8 1.0
OE1 N:GLN1195 4.3 86.7 1.0
CA N:CYS1204 4.4 70.0 1.0
CZ N:ARG1189 4.4 63.0 1.0
N N:CYS1204 4.5 71.2 1.0
N N:CYS1112 4.5 75.5 1.0
C N:CYS1194 4.5 72.7 1.0
CA N:CYS1201 4.5 65.3 1.0
O N:CYS1112 4.6 79.1 1.0
C N:CYS1112 4.8 77.8 1.0
N N:CYS1194 4.9 67.2 1.0
O N:HOH9768 5.0 37.1 1.0

Reference:

D.Temiakov, N.Zenkin, M.N.Vassylyeva, A.Perederina, T.H.Tahirov, E.Kashkina, M.Savkina, S.Zorov, V.Nikiforov, N.Igarashi, N.Matsugaki, S.Wakatsuki, K.Severinov, D.G.Vassylyev. Structural Basis of Transcription Inhibition By Antibiotic Streptolydigin. Mol.Cell V. 19 655 2005.
ISSN: ISSN 1097-2765
PubMed: 16167380
DOI: 10.1016/J.MOLCEL.2005.07.020
Page generated: Wed Dec 16 03:16:49 2020

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