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

All present enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 6 Nt:
2.7.7.6;

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 6 Nt, PDB code: 6kqn 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)	48.79 / 3.49
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	184.621, 101.920, 296.110, 90.00, 98.83, 90.00
R / Rfree (%)	21.3 / 25.8

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 6 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'-Triphosphate Rna of 6 Nt (pdb code 6kqn). 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'-Triphosphate Rna of 6 Nt, PDB code: 6kqn:
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'-Triphosphate Rna of 6 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'-Triphosphate Rna of 6 Nt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2001 b:0.0 occ:1.00 SG D:CYS1112 2.3 0.2 1.0 SG D:CYS1201 2.3 90.2 1.0 SG D:CYS1194 2.3 89.6 1.0 SG D:CYS1204 2.4 93.4 1.0 CB D:CYS1194 3.4 86.9 1.0 CB D:CYS1112 3.4 0.8 1.0 CB D:CYS1201 3.4 99.9 1.0 CB D:CYS1204 3.4 92.4 1.0 CA D:CYS1194 3.7 88.3 1.0 OG1 D:THR1196 3.8 0.3 1.0 N D:GLN1195 4.0 96.8 1.0 N D:CYS1112 4.1 0.6 1.0 N D:CYS1201 4.2 96.4 1.0 CG2 D:THR1114 4.2 0.1 1.0 C D:CYS1194 4.3 99.4 1.0 CA D:CYS1112 4.4 0.8 1.0 CA D:CYS1201 4.4 0.0 1.0 N D:CYS1204 4.5 98.1 1.0 NH2 D:ARG1189 4.5 0.2 1.0 CA D:CYS1204 4.6 97.5 1.0 N D:THR1196 4.7 93.4 1.0 OD1 D:ASP1111 4.8 0.4 1.0 N D:CYS1194 4.9 84.0 1.0 CB D:THR1196 5.0 0.1 1.0

Zinc binding site 2 out of 2 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 6 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'-Triphosphate Rna of 6 Nt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:0.8 occ:1.00 SG D:CYS76 2.3 0.7 1.0 SG D:CYS60 2.3 0.3 1.0 SG D:CYS73 2.3 0.8 1.0 CB D:CYS73 3.2 0.9 1.0 SG D:CYS58 3.3 0.9 1.0 CB D:CYS58 3.4 0.5 1.0 CB D:CYS76 3.6 0.5 1.0 CB D:CYS60 3.7 0.6 1.0 N D:CYS76 3.8 0.5 1.0 N D:CYS60 3.8 0.7 1.0 CB D:LYS62 3.9 0.2 1.0 N D:LYS62 4.2 0.8 1.0 CA D:CYS76 4.2 0.2 1.0 CA D:CYS60 4.3 0.9 1.0 N D:GLY61 4.3 0.8 1.0 N D:ALA59 4.4 0.5 1.0 CB D:ARG75 4.6 1.0 1.0 CA D:LYS62 4.7 0.9 1.0 CA D:CYS73 4.7 0.1 1.0 C D:CYS60 4.7 0.7 1.0 CA D:CYS58 4.7 0.7 1.0 C D:CYS58 4.8 0.1 1.0 C D:ARG75 4.9 0.5 1.0 C D:ALA59 4.9 0.6 1.0 C D:CYS76 5.0 1.0 1.0 N D:ARG75 5.0 0.5 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