Zinc in PDB 6koo: Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 7 Nt

All present enzymatic activity of Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 7 Nt:
2.7.7.6;

The structure of Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 7 Nt, PDB code: 6koo 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)	31.38 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	125.033, 162.314, 128.482, 90.00, 117.03, 90.00
R / Rfree (%)	20.6 / 24.8

The structure of Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 7 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 7 Nt (pdb code 6koo). 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 7 Nt, PDB code: 6koo:
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 7 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 7 Nt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2001 b:87.5 occ:1.00 SG D:CYS975 2.2 82.9 1.0 SG D:CYS978 2.3 86.2 1.0 SG D:CYS891 2.4 95.1 1.0 SG D:CYS968 2.5 80.1 1.0 CB D:CYS978 2.7 76.7 1.0 CB D:CYS968 3.3 82.1 1.0 CA D:CYS968 3.7 82.0 1.0 CB D:CYS975 3.7 85.8 1.0 NH2 D:ARG963 3.7 82.7 1.0 CB D:CYS891 3.8 89.2 1.0 CA D:CYS978 3.9 68.5 1.0 N D:CYS978 4.0 67.9 1.0 N D:ALA969 4.1 88.8 1.0 N D:CYS975 4.2 85.4 1.0 N D:CYS891 4.3 84.1 1.0 C D:CYS968 4.4 87.2 1.0 CG2 D:THR970 4.4 84.8 1.0 CA D:CYS975 4.4 83.2 1.0 CG2 D:THR893 4.5 90.0 1.0 O D:CYS975 4.6 72.1 1.0 CA D:CYS891 4.6 88.7 1.0 CZ D:ARG963 4.7 84.8 1.0 NE D:ARG963 4.8 81.7 1.0 C D:CYS975 4.8 77.3 1.0 N D:CYS968 4.9 79.3 1.0

Zinc binding site 2 out of 2 in the Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 7 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 7 Nt within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:0.3 occ:1.00 SG D:CYS75 2.2 91.7 1.0 SG D:CYS78 2.3 99.9 1.0 SG D:CYS60 2.4 0.7 1.0 SG D:CYS62 2.4 0.4 1.0 CB D:CYS78 3.0 90.3 1.0 CB D:CYS75 3.2 90.4 1.0 CB D:CYS60 3.4 93.2 1.0 N D:CYS62 3.8 0.8 1.0 N D:CYS78 3.8 95.8 1.0 CB D:CYS62 3.9 91.0 1.0 CA D:CYS78 4.0 94.7 1.0 N D:LYS64 4.1 0.1 1.0 CB D:LYS64 4.2 0.0 1.0 N D:GLY63 4.2 0.2 1.0 N D:TYR61 4.3 93.9 1.0 CA D:CYS62 4.3 0.6 1.0 CD2 D:TYR65 4.4 0.4 1.0 C D:CYS62 4.6 0.2 1.0 CA D:CYS75 4.6 95.8 1.0 CA D:CYS60 4.7 88.8 1.0 C D:CYS60 4.7 95.7 1.0 CB D:ARG77 4.7 0.5 1.0 C D:ARG77 4.7 94.3 1.0 CA D:LYS64 4.7 0.4 1.0 CE2 D:TYR65 4.9 0.4 1.0 C D:TYR61 4.9 99.0 1.0 N D:TYR65 4.9 0.2 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