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Zinc in PDB 6kqh: Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt

Enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt

All present enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt, PDB code: 6kqh 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) 39.82 / 3.18
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.007, 103.566, 294.935, 90.00, 99.20, 90.00
R / Rfree (%) 20.3 / 24.7

Other elements in 6kqh:

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt also contains other interesting chemical elements:

Magnesium (Mg) 4 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 7 Nt (pdb code 6kqh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt, PDB code: 6kqh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6kqh

Go back to Zinc Binding Sites List in 6kqh
Zinc binding site 1 out of 2 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 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 7 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:32.9
occ:1.00
SG D:CYS1201 2.3 27.3 1.0
SG D:CYS1204 2.4 30.9 1.0
SG D:CYS1112 2.4 25.0 1.0
SG D:CYS1194 2.4 21.4 1.0
CB D:CYS1194 3.3 30.6 1.0
CB D:CYS1204 3.3 33.3 1.0
CA D:CYS1194 3.4 28.7 1.0
CB D:CYS1112 3.5 25.9 1.0
CB D:CYS1201 3.6 31.6 1.0
OG1 D:THR1196 3.8 35.5 1.0
N D:GLN1195 4.0 26.2 1.0
NH2 D:ARG1189 4.0 34.6 1.0
N D:CYS1112 4.1 31.2 1.0
C D:CYS1194 4.2 29.5 1.0
N D:CYS1201 4.2 31.3 1.0
CA D:CYS1112 4.4 27.5 1.0
CG2 D:THR1114 4.4 34.3 1.0
N D:CYS1204 4.4 32.5 1.0
CA D:CYS1204 4.5 32.6 1.0
CA D:CYS1201 4.5 32.1 1.0
N D:CYS1194 4.6 27.0 1.0
N D:THR1196 4.6 30.2 1.0
OD1 D:ASP1111 4.7 39.1 1.0
CB D:THR1196 5.0 30.6 1.0

Zinc binding site 2 out of 2 in 6kqh

Go back to Zinc Binding Sites List in 6kqh
Zinc binding site 2 out of 2 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 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 7 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:73.4
occ:1.00
SG D:CYS60 2.3 69.9 1.0
SG D:CYS76 2.3 64.2 1.0
SG D:CYS73 2.3 81.4 1.0
SG D:CYS58 2.5 87.2 1.0
CB D:CYS58 3.1 71.2 1.0
CB D:CYS73 3.1 71.1 1.0
CB D:CYS76 3.7 63.4 1.0
CB D:CYS60 3.7 73.2 1.0
CB D:LYS62 3.7 93.8 1.0
N D:CYS60 3.8 70.2 1.0
N D:LYS62 3.9 86.5 1.0
N D:CYS76 3.9 79.0 1.0
N D:GLY61 4.1 66.9 1.0
CA D:CYS60 4.2 70.9 1.0
CA D:CYS76 4.4 74.3 1.0
CA D:CYS58 4.4 69.4 1.0
CA D:LYS62 4.4 93.4 1.0
N D:ALA59 4.4 60.6 1.0
C D:CYS58 4.5 62.7 1.0
C D:CYS60 4.5 63.9 1.0
CA D:CYS73 4.6 73.3 1.0
CD1 D:TYR63 4.6 89.4 1.0
CB D:ARG75 4.6 76.8 1.0
N D:TYR63 4.9 88.1 1.0
C D:GLY61 4.9 78.8 1.0
CE1 D:TYR63 4.9 86.9 1.0
C D:ALA59 4.9 73.9 1.0
C D:ARG75 5.0 79.7 1.0
CG D:LYS62 5.0 93.1 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: Wed Dec 16 12:09:14 2020

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