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

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

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 5 Nt, PDB code: 6kqf 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)	48.85 / 2.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	183.644, 103.640, 296.186, 90.00, 98.95, 90.00
R / Rfree (%)	19.9 / 23

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

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 5 Nt (pdb code 6kqf). 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 5 Nt, PDB code: 6kqf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 5 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 5 Nt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2001 b:36.2 occ:1.00 SG D:CYS1201 2.3 32.1 1.0 SG D:CYS1194 2.3 35.8 1.0 SG D:CYS1112 2.3 35.9 1.0 SG D:CYS1204 2.4 31.5 1.0 CB D:CYS1204 3.2 33.8 1.0 CB D:CYS1194 3.3 34.3 1.0 CB D:CYS1112 3.3 28.0 1.0 CB D:CYS1201 3.4 36.9 1.0 CA D:CYS1194 3.6 36.9 1.0 N D:CYS1201 3.8 36.1 1.0 N D:CYS1112 3.9 36.1 1.0 NH2 D:ARG1189 4.0 43.0 1.0 OG1 D:THR1196 4.0 40.5 1.0 N D:GLN1195 4.1 40.1 1.0 CA D:CYS1201 4.1 31.2 1.0 CA D:CYS1112 4.2 33.7 1.0 N D:CYS1204 4.3 32.4 1.0 CA D:CYS1204 4.3 35.6 1.0 C D:CYS1194 4.3 38.3 1.0 CG2 D:THR1114 4.5 33.9 1.0 N D:THR1196 4.7 32.8 1.0 C D:CYS1201 4.8 33.8 1.0 O D:CYS1201 4.8 31.3 1.0 N D:CYS1194 4.8 33.2 1.0 C D:VAL1200 4.9 32.2 1.0 CZ D:ARG1189 5.0 46.4 1.0 NE D:ARG1189 5.0 53.2 1.0

Zinc binding site 2 out of 2 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 5 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 5 Nt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:71.5 occ:1.00 SG D:CYS76 2.2 70.0 1.0 SG D:CYS73 2.3 69.9 1.0 SG D:CYS60 2.3 72.2 1.0 SG D:CYS58 2.3 61.4 1.0 CB D:CYS58 3.0 71.2 1.0 CB D:CYS73 3.2 77.0 1.0 CB D:CYS76 3.4 72.3 1.0 CB D:CYS60 3.7 62.6 1.0 N D:CYS60 3.7 70.3 1.0 N D:CYS76 3.8 81.0 1.0 N D:GLY61 4.1 70.1 1.0 CA D:CYS60 4.2 73.3 1.0 CA D:CYS76 4.2 74.0 1.0 N D:ALA59 4.2 59.6 1.0 N D:LYS62 4.3 75.1 1.0 CB D:LYS62 4.3 79.3 1.0 CA D:CYS58 4.3 66.9 1.0 C D:CYS58 4.4 60.8 1.0 CB D:ARG75 4.6 71.2 1.0 CA D:CYS73 4.6 73.5 1.0 C D:CYS60 4.7 74.8 1.0 CD2 D:TYR63 4.7 76.9 1.0 C D:ARG75 4.8 80.7 1.0 C D:ALA59 4.8 72.9 1.0 CA D:LYS62 4.9 79.0 1.0 C D:CYS76 4.9 66.7 1.0 N D:GLY77 4.9 65.1 1.0 N D:ARG75 5.0 74.2 1.0 CA D:ALA59 5.0 63.7 1.0

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