Atomistry » Zinc » PDB 6km3-6ksm » 6kqd
Atomistry »
  Zinc »
    PDB 6km3-6ksm »
      6kqd »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy