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Zinc in PDB 2cw0: Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme at 3.3 Angstroms Resolution

Enzymatic activity of Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme at 3.3 Angstroms Resolution

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme at 3.3 Angstroms Resolution:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme at 3.3 Angstroms Resolution, PDB code: 2cw0 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 Jr., 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 / 3.30
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 236.150, 236.150, 249.880, 90.00, 90.00, 120.00
R / Rfree (%) 28.2 / 32

Other elements in 2cw0:

The structure of Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme at 3.3 Angstroms Resolution also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme at 3.3 Angstroms Resolution (pdb code 2cw0). 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 Thermus Thermophilus Rna Polymerase Holoenzyme at 3.3 Angstroms Resolution, PDB code: 2cw0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2cw0

Go back to Zinc Binding Sites List in 2cw0
Zinc binding site 1 out of 4 in the Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme at 3.3 Angstroms Resolution


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 Thermus Thermophilus Rna Polymerase Holoenzyme at 3.3 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1525

b:0.1
occ:1.00
 SG D:CYS60 2.3 0.8 1.0
SG D:CYS73 2.5 0.2 1.0
SG D:CYS76 2.6 0.7 1.0
SG D:CYS58 2.7 0.3 1.0
CB D:CYS60 2.9 0.3 1.0
CB D:CYS76 3.4 0.8 1.0
CB D:CYS73 3.5 0.8 1.0
CA D:CYS60 4.1 0.6 1.0
N D:CYS60 4.1 0.1 1.0
CA D:CYS76 4.3 0.1 1.0
CB D:CYS58 4.4 0.3 1.0
CB D:LYS62 4.4 0.6 1.0
N D:CYS76 4.5 0.9 1.0
O D:CYS76 4.5 0.6 1.0
C D:CYS76 4.6 0.7 1.0
N D:GLY61 4.6 0.4 1.0
N D:LYS62 4.6 0.5 1.0
CG D:LYS62 4.7 0.6 1.0
C D:CYS60 4.8 0.3 1.0
CA D:CYS73 4.9 0.5 1.0

Zinc binding site 2 out of 4 in 2cw0

Go back to Zinc Binding Sites List in 2cw0
Zinc binding site 2 out of 4 in the Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme at 3.3 Angstroms Resolution


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 Thermus Thermophilus Rna Polymerase Holoenzyme at 3.3 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1526

b:78.9
occ:1.00
 SG D:CYS1194 2.4 90.4 1.0
SG D:CYS1204 2.4 86.7 1.0
SG D:CYS1201 2.8 86.2 1.0
CB D:CYS1204 2.9 80.8 1.0
CB D:CYS1194 3.0 85.0 1.0
CA D:CYS1194 3.2 83.4 1.0
SG D:CYS1112 3.2 91.2 1.0
N D:GLN1195 3.8 89.3 1.0
CG2 D:THR1114 3.8 80.2 1.0
O D:THR1193 3.8 76.1 1.0
C D:CYS1194 4.0 85.5 1.0
N D:CYS1194 4.2 79.0 1.0
CA D:CYS1204 4.3 77.7 1.0
C D:THR1193 4.4 75.5 1.0
CB D:CYS1201 4.5 79.3 1.0
O D:THR1114 4.8 79.6 1.0
N D:CYS1204 4.8 76.2 1.0
N D:CYS1201 4.8 75.0 1.0
NH1 D:ARG1189 4.9 53.8 1.0

Zinc binding site 3 out of 4 in 2cw0

Go back to Zinc Binding Sites List in 2cw0
Zinc binding site 3 out of 4 in the Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme at 3.3 Angstroms Resolution


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 Thermus Thermophilus Rna Polymerase Holoenzyme at 3.3 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1525

b:0.4
occ:1.00
 SG N:CYS60 2.4 0.4 1.0
SG N:CYS73 2.5 0.8 1.0
SG N:CYS58 2.7 0.1 1.0
CB N:CYS73 3.1 0.6 1.0
CB N:CYS76 3.6 0.1 1.0
CB N:CYS58 4.0 0.6 1.0
CB N:CYS60 4.1 0.5 1.0
O N:CYS76 4.2 0.0 1.0
CB N:LYS62 4.3 0.3 1.0
N N:CYS76 4.3 0.7 1.0
CG N:LYS62 4.3 0.5 1.0
CA N:CYS76 4.4 0.5 1.0
N N:LYS62 4.6 0.1 1.0
SG N:CYS76 4.6 0.6 1.0
CA N:CYS73 4.6 0.5 1.0
C N:CYS76 4.7 0.6 1.0
N N:CYS60 4.7 0.6 1.0
CB N:VAL78 4.7 97.2 1.0
N N:GLY61 4.8 0.5 1.0
CG2 N:VAL78 4.9 97.3 1.0
CA N:CYS60 5.0 0.4 1.0

Zinc binding site 4 out of 4 in 2cw0

Go back to Zinc Binding Sites List in 2cw0
Zinc binding site 4 out of 4 in the Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme at 3.3 Angstroms Resolution


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 Thermus Thermophilus Rna Polymerase Holoenzyme at 3.3 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1526

b:72.2
occ:1.00
 SG N:CYS1201 2.4 82.8 1.0
SG N:CYS1194 2.5 81.9 1.0
SG N:CYS1112 2.7 82.8 1.0
CB N:CYS1112 2.8 82.5 1.0
SG N:CYS1204 3.0 82.4 1.0
CB N:CYS1204 3.0 81.5 1.0
CB N:CYS1194 3.6 79.5 1.0
CB N:CYS1201 3.6 77.5 1.0
CA N:CYS1194 3.9 78.6 1.0
N N:CYS1201 4.0 74.7 1.0
N N:GLN1195 4.1 82.5 1.0
CA N:CYS1112 4.3 83.0 1.0
CA N:CYS1204 4.4 80.6 1.0
CA N:CYS1201 4.4 74.7 1.0
NH1 N:ARG1189 4.5 46.7 1.0
C N:CYS1194 4.5 80.2 1.0
OG1 N:THR1196 4.6 84.7 1.0
NH2 N:ARG1189 4.6 44.9 1.0
N N:CYS1204 4.6 79.8 1.0
N N:THR1196 4.7 86.5 1.0
N N:CYS1112 4.9 82.6 1.0
CB N:THR1196 4.9 85.8 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 Jr., 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 Oct 16 22:33:48 2024

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