Zinc in PDB 6kql: Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 4 Nt

All present enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 4 Nt:
2.7.7.6;

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 4 Nt, PDB code: 6kql 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)	44.84 / 2.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	183.802, 103.166, 295.560, 90.00, 99.12, 90.00
R / Rfree (%)	20.7 / 24.6

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 4 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 4 Nt (pdb code 6kql). 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 4 Nt, PDB code: 6kql:
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 4 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 4 Nt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2001 b:53.6 occ:1.00 SG D:CYS1194 2.3 57.2 1.0 SG D:CYS1112 2.3 48.7 1.0 SG D:CYS1201 2.3 48.1 1.0 SG D:CYS1204 2.4 40.5 1.0 CB D:CYS1204 3.2 44.3 1.0 CB D:CYS1194 3.3 51.4 1.0 CB D:CYS1112 3.3 44.3 1.0 CB D:CYS1201 3.4 49.8 1.0 CA D:CYS1194 3.6 46.9 1.0 OG1 D:THR1196 3.9 52.6 1.0 N D:CYS1201 3.9 51.9 1.0 N D:GLN1195 4.0 49.5 1.0 N D:CYS1112 4.0 52.7 1.0 C D:CYS1194 4.3 48.1 1.0 NH2 D:ARG1189 4.3 54.4 1.0 CA D:CYS1201 4.3 48.4 1.0 CA D:CYS1112 4.3 48.0 1.0 CG2 D:THR1114 4.4 53.4 1.0 N D:CYS1204 4.4 49.7 1.0 CA D:CYS1204 4.4 47.6 1.0 N D:THR1196 4.5 47.3 1.0 N D:CYS1194 4.8 47.4 1.0 CB D:THR1196 4.8 50.5 1.0 O D:HOH2186 4.9 49.2 1.0 OD1 D:ASP1111 4.9 63.0 1.0 C D:CYS1201 5.0 45.7 1.0

Zinc binding site 2 out of 2 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 4 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 4 Nt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:0.6 occ:1.00 SG D:CYS76 2.3 85.7 1.0 SG D:CYS60 2.3 96.1 1.0 SG D:CYS73 2.3 98.9 1.0 SG D:CYS58 2.3 0.3 1.0 CB D:CYS58 3.2 93.0 1.0 CB D:CYS73 3.3 95.3 1.0 CB D:CYS76 3.6 86.8 1.0 N D:CYS60 3.8 92.8 1.0 CB D:LYS62 3.8 0.1 1.0 CB D:CYS60 3.8 87.2 1.0 N D:LYS62 3.8 0.9 1.0 N D:GLY61 4.0 91.3 1.0 N D:CYS76 4.1 0.5 1.0 CA D:CYS60 4.2 93.8 1.0 N D:ALA59 4.3 82.8 1.0 CA D:CYS58 4.4 82.0 1.0 CA D:LYS62 4.4 0.3 1.0 CA D:CYS76 4.4 96.7 1.0 C D:CYS58 4.5 79.8 1.0 C D:CYS60 4.5 94.0 1.0 CD2 D:TYR63 4.7 0.5 1.0 CA D:CYS73 4.7 93.7 1.0 C D:ALA59 4.8 91.9 1.0 N D:TYR63 4.8 0.1 1.0 C D:GLY61 4.9 0.1 1.0 CB D:ARG75 4.9 0.7 1.0 CA D:GLY61 4.9 98.8 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