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Zinc in PDB 6kop: Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 9 Nt

Enzymatic activity of Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 9 Nt

All present enzymatic activity of Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 9 Nt:
2.7.7.6;

Protein crystallography data

The structure of Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 9 Nt, PDB code: 6kop 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) 49.25 / 3.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 127.371, 162.637, 133.421, 90.00, 117.95, 90.00
R / Rfree (%) 21.7 / 25.5

Other elements in 6kop:

The structure of Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 9 Nt also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 9 Nt (pdb code 6kop). 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 9 Nt, PDB code: 6kop:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6kop

Go back to Zinc Binding Sites List in 6kop
Zinc binding site 1 out of 2 in the Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 9 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 9 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:0.4
occ:1.00
SG D:CYS62 2.3 0.5 1.0
SG D:CYS78 2.3 0.8 1.0
SG D:CYS75 2.3 0.9 1.0
SG D:CYS60 2.3 0.3 1.0
CB D:CYS75 3.4 0.7 1.0
CB D:CYS60 3.4 0.4 1.0
N D:CYS62 3.4 0.6 1.0
CB D:CYS78 3.6 0.4 1.0
CB D:CYS62 3.6 0.3 1.0
N D:TYR61 3.9 0.6 1.0
CA D:CYS62 3.9 0.2 1.0
N D:GLY63 4.1 0.8 1.0
N D:CYS78 4.2 0.2 1.0
N D:LYS64 4.2 0.1 1.0
CB D:LYS64 4.3 0.9 1.0
C D:CYS62 4.4 0.9 1.0
C D:CYS60 4.4 0.2 1.0
C D:TYR61 4.4 0.7 1.0
CA D:CYS78 4.5 0.1 1.0
CA D:CYS60 4.5 0.7 1.0
CA D:TYR61 4.6 0.1 1.0
CB D:ARG77 4.7 0.2 1.0
CA D:CYS75 4.8 0.1 1.0
CA D:LYS64 4.9 0.9 1.0
CB D:TYR61 4.9 0.6 1.0
C D:ARG77 4.9 0.8 1.0

Zinc binding site 2 out of 2 in 6kop

Go back to Zinc Binding Sites List in 6kop
Zinc binding site 2 out of 2 in the Mycobacterium Tuberculosis Initial Transcription Complex Comprising Sigma H and 5'-Oh Rna of 9 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 9 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:0.8
occ:1.00
SG D:CYS968 2.1 0.6 1.0
SG D:CYS978 2.1 0.8 1.0
SG D:CYS975 2.4 1.0 1.0
SG D:CYS891 2.4 0.2 1.0
CB D:CYS891 2.5 0.9 1.0
CB D:CYS978 2.6 0.7 1.0
CB D:CYS968 2.7 1.0 1.0
CA D:CYS968 3.2 0.7 1.0
CA D:CYS891 3.9 0.4 1.0
OG1 D:THR970 4.0 0.0 1.0
CB D:CYS975 4.0 0.8 1.0
CG2 D:THR893 4.1 0.0 1.0
CA D:CYS978 4.1 0.1 1.0
N D:ALA969 4.2 0.4 1.0
C D:CYS968 4.2 0.2 1.0
N D:CYS891 4.2 0.8 1.0
N D:CYS968 4.3 0.2 1.0
N D:CYS978 4.5 0.9 1.0
N D:CYS975 4.5 0.6 1.0
NH1 D:ARG963 4.7 0.0 1.0
O D:SER964 4.8 0.3 1.0
CA D:CYS975 4.8 0.4 1.0
C D:CYS891 5.0 0.9 1.0

Reference:

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
Page generated: Wed Dec 16 12:08:50 2020

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