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

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

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 4 Nt, PDB code: 6kqe 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)	48.95 / 3.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	184.567, 103.757, 295.981, 90.00, 98.70, 90.00
R / Rfree (%)	21.8 / 25.8

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 4 Nt also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Zinc atom in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 4 Nt (pdb code 6kqe). 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 4 Nt, PDB code: 6kqe:
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 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'-Oh Rna of 4 Nt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2001 b:71.3 occ:1.00 SG D:CYS1112 2.2 67.2 1.0 SG D:CYS1204 2.3 63.8 1.0 SG D:CYS1201 2.3 62.7 1.0 SG D:CYS1194 2.4 63.8 1.0 CB D:CYS1204 3.3 62.5 1.0 CB D:CYS1194 3.3 61.4 1.0 CB D:CYS1112 3.3 66.5 1.0 CA D:CYS1194 3.5 55.5 1.0 CB D:CYS1201 3.6 63.4 1.0 OG1 D:THR1196 3.8 69.6 1.0 N D:GLN1195 4.0 58.5 1.0 N D:CYS1112 4.1 79.8 1.0 N D:CYS1201 4.2 65.3 1.0 C D:CYS1194 4.2 61.4 1.0 NH2 D:ARG1189 4.2 75.4 1.0 CA D:CYS1112 4.3 74.9 1.0 CG2 D:THR1114 4.3 69.5 1.0 N D:CYS1204 4.4 69.7 1.0 CA D:CYS1204 4.4 67.8 1.0 CA D:CYS1201 4.5 65.4 1.0 N D:THR1196 4.6 59.5 1.0 N D:CYS1194 4.7 53.3 1.0 OD1 D:ASP1111 4.9 76.1 1.0 NE D:ARG1189 4.9 76.2 1.0 CB D:THR1196 5.0 65.4 1.0

Zinc binding site 2 out of 2 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh 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'-Oh Rna of 4 Nt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:0.4 occ:1.00 SG D:CYS76 2.2 94.1 1.0 SG D:CYS73 2.3 0.8 1.0 SG D:CYS60 2.3 0.2 1.0 SG D:CYS58 2.4 0.6 1.0 CB D:CYS58 2.9 0.8 1.0 CB D:CYS73 3.2 0.6 1.0 CB D:CYS76 3.8 94.8 1.0 CB D:LYS62 3.8 0.7 1.0 CB D:CYS60 3.9 96.2 1.0 N D:CYS60 3.9 0.1 1.0 N D:LYS62 3.9 0.8 1.0 N D:CYS76 4.0 0.9 1.0 N D:GLY61 4.1 0.9 1.0 CA D:CYS58 4.2 98.6 1.0 N D:ALA59 4.3 92.2 1.0 C D:CYS58 4.3 93.0 1.0 CA D:CYS60 4.3 0.9 1.0 CA D:LYS62 4.4 0.4 1.0 CA D:CYS76 4.5 0.1 1.0 CD2 D:TYR63 4.5 0.4 1.0 C D:CYS60 4.6 0.6 1.0 CA D:CYS73 4.7 0.5 1.0 N D:TYR63 4.7 0.8 1.0 CB D:ARG75 4.7 0.3 1.0 CE2 D:TYR63 4.8 0.3 1.0 C D:ALA59 4.9 0.1 1.0 O D:CYS58 4.9 90.5 1.0 C D:GLY61 4.9 0.4 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