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Zinc in PDB 6kqd: Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt

Enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt

All present enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt, PDB code: 6kqd was solved by Y.Zhang, L.Li, R.H.Ebright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.35 / 3.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 185.501, 104.044, 297.441, 90.00, 98.50, 90.00
R / Rfree (%) 20.7 / 25

Other elements in 6kqd:

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt (pdb code 6kqd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt, PDB code: 6kqd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6kqd

Go back to Zinc Binding Sites List in 6kqd
Zinc binding site 1 out of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:49.4
occ:1.00
 SG D:CYS1204 2.2 48.2 1.0
SG D:CYS1201 2.2 52.5 1.0
SG D:CYS1112 2.2 48.4 1.0
SG D:CYS1194 2.5 48.9 1.0
CB D:CYS1204 3.1 46.9 1.0
CB D:CYS1194 3.3 47.8 1.0
CB D:CYS1201 3.5 52.0 1.0
CB D:CYS1112 3.6 48.5 1.0
CA D:CYS1194 3.6 44.9 1.0
NH2 D:ARG1189 4.0 42.4 1.0
OG1 D:THR1196 4.1 56.7 1.0
CG2 D:THR1114 4.1 53.1 1.0
N D:GLN1195 4.1 48.1 1.0
N D:CYS1204 4.2 48.1 1.0
N D:CYS1112 4.2 56.0 1.0
CA D:CYS1204 4.2 48.4 1.0
N D:CYS1201 4.3 48.7 1.0
C D:CYS1194 4.4 51.6 1.0
CA D:CYS1201 4.4 49.1 1.0
CA D:CYS1112 4.5 55.4 1.0
N D:CYS1194 4.8 40.4 1.0
N D:THR1196 4.9 52.0 1.0
O D:CYS1201 4.9 48.8 1.0
NE D:ARG1189 4.9 49.8 1.0
C D:CYS1201 5.0 48.9 1.0
CZ D:ARG1189 5.0 46.2 1.0

Zinc binding site 2 out of 4 in 6kqd

Go back to Zinc Binding Sites List in 6kqd
Zinc binding site 2 out of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:88.7
occ:1.00
 SG D:CYS76 2.3 82.1 1.0
SG D:CYS60 2.4 92.3 1.0
SG D:CYS73 2.4 87.3 1.0
SG D:CYS58 2.7 95.6 1.0
CB D:CYS58 3.2 86.1 1.0
CB D:CYS73 3.2 82.1 1.0
CB D:CYS76 3.6 78.0 1.0
N D:CYS60 3.7 97.6 1.0
CB D:CYS60 3.8 94.0 1.0
N D:ALA59 4.1 75.9 1.0
N D:LYS62 4.1 0.8 1.0
CB D:LYS62 4.1 98.0 1.0
N D:CYS76 4.1 99.1 1.0
N D:GLY61 4.1 0.1 1.0
CA D:CYS60 4.2 92.5 1.0
C D:CYS58 4.4 85.1 1.0
CA D:CYS58 4.4 84.6 1.0
CA D:CYS76 4.5 90.7 1.0
C D:CYS60 4.5 0.5 1.0
C D:ALA59 4.7 92.8 1.0
CA D:LYS62 4.7 99.4 1.0
CA D:CYS73 4.7 84.0 1.0
CD2 D:TYR63 4.7 95.2 1.0
CB D:ARG75 4.8 91.7 1.0
CA D:ALA59 4.9 74.2 1.0

Zinc binding site 3 out of 4 in 6kqd

Go back to Zinc Binding Sites List in 6kqd
Zinc binding site 3 out of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn2001

b:55.8
occ:1.00
 SG N:CYS1201 2.2 55.5 1.0
SG N:CYS1204 2.3 49.7 1.0
SG N:CYS1112 2.3 54.0 1.0
SG N:CYS1194 2.5 43.5 1.0
CB N:CYS1204 3.0 50.5 1.0
CB N:CYS1194 3.3 45.5 1.0
CB N:CYS1201 3.5 47.0 1.0
CB N:CYS1112 3.6 52.1 1.0
CA N:CYS1194 3.7 45.5 1.0
N N:GLN1195 4.1 51.5 1.0
OG1 N:THR1196 4.1 55.9 1.0
NH2 N:ARG1189 4.2 53.1 1.0
N N:CYS1204 4.2 53.5 1.0
CA N:CYS1204 4.2 52.1 1.0
CG2 N:THR1114 4.2 54.3 1.0
N N:CYS1201 4.2 56.7 1.0
N N:CYS1112 4.3 57.6 1.0
CA N:CYS1201 4.4 51.0 1.0
C N:CYS1194 4.4 52.2 1.0
CA N:CYS1112 4.6 55.0 1.0
O N:CYS1201 4.7 50.4 1.0
C N:CYS1201 4.8 49.7 1.0
N N:THR1196 4.8 54.0 1.0
N N:CYS1194 4.9 39.5 1.0

Zinc binding site 4 out of 4 in 6kqd

Go back to Zinc Binding Sites List in 6kqd
Zinc binding site 4 out of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn2002

b:0.2
occ:1.00
 SG N:CYS60 2.4 0.5 1.0
SG N:CYS58 2.4 0.2 1.0
SG N:CYS73 2.5 0.4 1.0
SG N:CYS76 2.5 0.6 1.0
CB N:CYS58 3.2 0.0 1.0
CB N:CYS73 3.3 0.7 1.0
CB N:CYS76 3.8 0.4 1.0
N N:LYS62 3.8 0.1 1.0
N N:CYS60 3.8 0.6 1.0
CB N:LYS62 3.9 0.3 1.0
CB N:CYS60 3.9 0.4 1.0
N N:GLY61 3.9 0.5 1.0
CA N:CYS60 4.2 0.6 1.0
N N:ALA59 4.3 94.5 1.0
N N:CYS76 4.3 0.2 1.0
C N:CYS60 4.3 0.2 1.0
CA N:LYS62 4.4 0.1 1.0
CA N:CYS58 4.4 0.9 1.0
C N:CYS58 4.5 0.3 1.0
CA N:CYS76 4.6 0.1 1.0
CA N:CYS73 4.8 1.0 1.0
C N:GLY61 4.8 0.1 1.0
C N:ALA59 4.8 0.4 1.0
CA N:GLY61 4.8 0.4 1.0
N N:TYR63 4.9 0.3 1.0
CD1 N:TYR63 5.0 0.8 1.0

Reference:

L.Li, V.Molodtsov, W.Lin, R.H.Ebright, Y.Zhang. Rna Extension Drives A Stepwise Displacement of An Initiation-Factor Structural Module in Initial Transcription. Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1920747117
Page generated: Tue Oct 29 01:57:41 2024

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