Zinc in PDB 6kon: Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 5 Nt

All present enzymatic activity of Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 5 Nt:
2.7.7.6;

The structure of Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 5 Nt, PDB code: 6kon was solved by L.Li, Y.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.65 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	129.330, 161.219, 129.469, 90.00, 117.78, 90.00
R / Rfree (%)	22 / 27.1

The structure of Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 5 Nt also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 5 Nt (pdb code 6kon). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 5 Nt, PDB code: 6kon:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H 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 Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 5 Nt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2001 b:0.8 occ:1.00 SG D:CYS75 2.3 0.8 1.0 SG D:CYS62 2.3 94.1 1.0 SG D:CYS78 2.3 0.4 1.0 SG D:CYS60 2.4 0.8 1.0 CB D:CYS75 3.4 0.2 1.0 CB D:CYS60 3.4 95.3 1.0 N D:CYS62 3.8 0.5 1.0 CB D:CYS62 3.9 0.5 1.0 CB D:CYS78 4.0 0.5 1.0 N D:GLY63 4.2 1.0 1.0 N D:CYS78 4.2 0.5 1.0 N D:TYR61 4.3 91.6 1.0 CA D:CYS62 4.4 0.7 1.0 CD1 D:TYR65 4.4 0.2 1.0 CB D:ARG77 4.4 0.7 1.0 N D:LYS64 4.5 0.8 1.0 CA D:CYS78 4.7 0.6 1.0 CA D:CYS60 4.7 88.6 1.0 C D:CYS60 4.7 92.0 1.0 C D:CYS62 4.8 0.5 1.0 CA D:CYS75 4.8 0.5 1.0 C D:TYR61 4.8 0.5 1.0 CB D:LYS64 4.9 0.3 1.0 N D:TYR65 4.9 0.4 1.0 CE1 D:TYR65 5.0 0.0 1.0 N D:ARG77 5.0 0.3 1.0

Zinc binding site 2 out of 2 in the Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H 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 Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 5 Nt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:90.0 occ:1.00 SG D:CYS968 2.2 86.2 1.0 SG D:CYS975 2.2 77.0 1.0 SG D:CYS978 2.2 76.7 1.0 SG D:CYS891 2.3 0.5 1.0 CB D:CYS978 3.0 91.7 1.0 CB D:CYS968 3.1 83.3 1.0 CB D:CYS975 3.3 91.5 1.0 CG2 D:THR970 3.3 90.4 1.0 CB D:CYS891 3.5 94.9 1.0 CA D:CYS968 3.6 84.2 1.0 N D:ALA969 3.7 94.6 1.0 N D:CYS975 3.7 91.1 1.0 CA D:CYS975 4.0 94.6 1.0 NH2 D:ARG963 4.0 89.1 1.0 C D:CYS968 4.1 93.7 1.0 N D:THR970 4.1 97.9 1.0 N D:CYS891 4.2 94.7 1.0 CA D:CYS978 4.3 90.9 1.0 N D:CYS978 4.4 86.3 1.0 CA D:CYS891 4.5 95.2 1.0 O D:CYS975 4.5 87.3 1.0 CB D:THR970 4.5 0.5 1.0 CG2 D:THR893 4.6 90.3 1.0 C D:CYS975 4.6 90.0 1.0 OG1 D:THR970 4.7 0.6 1.0 CA D:ALA969 4.8 97.8 1.0 C D:VAL974 4.9 88.9 1.0 N D:CYS968 4.9 78.5 1.0 C D:ALA969 4.9 97.0 1.0 CA D:THR970 5.0 0.1 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