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Zinc in PDB 1zyr: Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin

Enzymatic activity of Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin

All present enzymatic activity of Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin:
2.7.7.6;

Protein crystallography data

The structure of Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin, PDB code: 1zyr was solved by S.Tuske, S.G.Sarafianos, X.Wang, B.Hudson, E.Sineva, J.Mukhopadhyay, J.J.Birktoft, O.Leroy, S.Ismail, A.D.Clark, C.Dharia, A.Napoli, O.Laptenko, J.Lee, S.Borukhov, R.H.Ebright, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.00
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 237.000, 237.000, 250.000, 90.00, 90.00, 120.00
R / Rfree (%) 26.1 / 28.1

Other elements in 1zyr:

The structure of Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin (pdb code 1zyr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin, PDB code: 1zyr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1zyr

Go back to Zinc Binding Sites List in 1zyr
Zinc binding site 1 out of 4 in the Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn9001

b:56.4
occ:1.00
 SG D:CYS58 2.7 84.2 1.0
SG D:CYS60 2.9 98.7 1.0
CB D:CYS76 2.9 95.2 1.0
SG D:CYS76 3.0 91.7 1.0
SG D:CYS73 3.3 0.5 1.0
N D:CYS60 3.6 95.9 1.0
N D:CYS76 3.9 99.8 1.0
CB D:LYS62 3.9 95.8 1.0
CB D:CYS60 3.9 97.7 1.0
CA D:CYS76 3.9 97.0 1.0
CB D:ALA59 4.1 92.2 1.0
N D:ALA59 4.2 91.9 1.0
CA D:CYS60 4.3 97.2 1.0
CB D:CYS73 4.3 0.3 1.0
CB D:CYS58 4.4 90.2 1.0
N D:LYS62 4.5 95.8 1.0
CA D:ALA59 4.5 93.0 1.0
N D:GLY77 4.5 96.2 1.0
C D:ALA59 4.5 93.9 1.0
C D:CYS76 4.7 96.9 1.0
C D:CYS60 4.7 96.9 1.0
N D:GLY61 4.8 96.8 1.0
CG D:LYS62 4.9 95.6 1.0
CA D:LYS62 4.9 95.0 1.0
C D:ARG75 4.9 0.1 1.0
CB D:ARG75 5.0 0.5 1.0

Zinc binding site 2 out of 4 in 1zyr

Go back to Zinc Binding Sites List in 1zyr
Zinc binding site 2 out of 4 in the Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn9002

b:47.7
occ:1.00
 CB D:CYS1194 2.6 65.1 1.0
OG1 D:THR1196 2.7 80.6 1.0
SG D:CYS1201 3.2 58.3 1.0
CA D:CYS1194 3.2 64.8 1.0
N D:GLN1195 3.3 68.2 1.0
CB D:CYS1204 3.3 55.3 1.0
SG D:CYS1112 3.3 79.7 1.0
SG D:CYS1204 3.4 53.8 1.0
N D:THR1196 3.4 75.9 1.0
C D:CYS1194 3.4 65.7 1.0
SG D:CYS1194 3.6 66.8 1.0
CG2 D:THR1196 3.6 81.0 1.0
CB D:THR1196 3.6 79.1 1.0
CB D:CYS1112 3.7 78.3 1.0
CB D:CYS1201 3.9 58.4 1.0
N D:CYS1201 4.0 58.3 1.0
CA D:THR1196 4.1 78.0 1.0
CA D:GLN1195 4.2 71.8 1.0
C D:GLN1195 4.3 73.3 1.0
O D:CYS1194 4.3 63.8 1.0
CB D:GLN1195 4.6 72.6 1.0
CA D:CYS1201 4.6 57.8 1.0
N D:CYS1194 4.6 62.4 1.0
C D:VAL1200 4.8 59.5 1.0
CA D:CYS1204 4.8 56.7 1.0
CA D:VAL1200 4.9 60.3 1.0

Zinc binding site 3 out of 4 in 1zyr

Go back to Zinc Binding Sites List in 1zyr
Zinc binding site 3 out of 4 in the Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn9003

b:55.7
occ:1.00
 CB N:CYS73 2.6 79.7 1.0
SG N:CYS60 2.7 78.9 1.0
SG N:CYS73 2.8 78.9 1.0
CB N:CYS60 2.9 78.7 1.0
SG N:CYS58 3.0 82.1 1.0
O N:CYS76 3.4 82.5 1.0
SG N:CYS76 3.6 80.2 1.0
N N:CYS60 3.9 78.1 1.0
CA N:CYS73 3.9 80.9 1.0
CA N:CYS60 4.0 76.9 1.0
N N:CYS76 4.0 85.6 1.0
C N:CYS73 4.2 80.7 1.0
CG2 N:VAL78 4.3 77.3 1.0
C N:CYS76 4.3 83.3 1.0
CB N:CYS76 4.3 84.2 1.0
CA N:CYS76 4.4 83.9 1.0
CB N:CYS58 4.5 80.2 1.0
N N:ARG75 4.5 84.9 1.0
O N:CYS73 4.6 79.9 1.0
CB N:VAL78 4.6 77.7 1.0
N N:GLU74 4.6 81.8 1.0
N N:GLY61 4.8 74.0 1.0
CB N:LYS62 4.8 74.7 1.0
N N:ALA59 4.9 78.7 1.0
N N:CYS73 4.9 82.7 1.0
C N:ARG75 4.9 85.7 1.0
C N:CYS60 5.0 75.3 1.0

Zinc binding site 4 out of 4 in 1zyr

Go back to Zinc Binding Sites List in 1zyr
Zinc binding site 4 out of 4 in the Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Streptolydigin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn9004

b:56.5
occ:1.00
 SG N:CYS1204 2.2 44.7 1.0
SG N:CYS1112 2.7 71.8 1.0
CB N:CYS1204 2.7 44.1 1.0
CB N:CYS1194 2.9 57.1 1.0
CA N:CYS1194 3.0 56.1 1.0
SG N:CYS1194 3.1 59.5 1.0
CB N:CYS1201 3.3 53.8 1.0
SG N:CYS1201 3.5 55.3 1.0
CB N:CYS1112 3.7 66.7 1.0
N N:GLN1195 3.8 62.8 1.0
N N:CYS1201 3.8 54.9 1.0
C N:CYS1194 3.9 59.0 1.0
N N:CYS1194 4.1 52.9 1.0
CA N:CYS1201 4.1 54.1 1.0
CA N:CYS1204 4.3 43.8 1.0
OG1 N:THR1196 4.4 70.2 1.0
O N:CYS1201 4.5 53.4 1.0
O N:SER1190 4.6 38.6 1.0
NE N:ARG1189 4.7 39.2 1.0
N N:THR1196 4.7 70.8 1.0
CD N:ARG1189 4.7 38.5 1.0
C N:CYS1201 4.8 52.8 1.0
C N:VAL1200 4.9 55.4 1.0
CG1 N:VAL1200 4.9 52.9 1.0
N N:CYS1204 4.9 45.4 1.0
C N:THR1193 4.9 50.9 1.0
CA N:VAL1200 5.0 54.3 1.0
O N:THR1193 5.0 50.1 1.0

Reference:

S.Tuske, S.G.Sarafianos, X.Wang, B.Hudson, E.Sineva, J.Mukhopadhyay, J.J.Birktoft, O.Leroy, S.Ismail, A.D.Clark, C.Dharia, A.Napoli, O.Laptenko, J.Lee, S.Borukhov, R.H.Ebright, E.Arnold. Inhibition of Bacterial Rna Polymerase By Streptolydigin: Stabilization of A Straight-Bridge-Helix Active-Center Conformation. Cell(Cambridge,Mass.) V. 122 541 2005.
ISSN: ISSN 0092-8674
PubMed: 16122422
DOI: 10.1016/J.CELL.2005.07.017
Page generated: Wed Aug 20 01:01:09 2025

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