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Zinc in PDB 6dvd: Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) with 6 Nt Spacer and Bromine Labelled in Position "-11

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) with 6 Nt Spacer and Bromine Labelled in Position "-11

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) with 6 Nt Spacer and Bromine Labelled in Position "-11:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) with 6 Nt Spacer and Bromine Labelled in Position "-11, PDB code: 6dvd was solved by W.Lin, K.Das, Y.Feng, R.H.Ebright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.90 / 3.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 142.135, 161.485, 239.367, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 24.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) with 6 Nt Spacer and Bromine Labelled in Position "-11 (pdb code 6dvd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) with 6 Nt Spacer and Bromine Labelled in Position "-11, PDB code: 6dvd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6dvd

Go back to Zinc Binding Sites List in 6dvd
Zinc binding site 1 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) with 6 Nt Spacer and Bromine Labelled in Position "-11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) with 6 Nt Spacer and Bromine Labelled in Position "-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:60.3
occ:1.00
 SG D:CYS968 2.4 72.4 1.0
SG D:CYS978 2.4 74.9 1.0
SG D:CYS975 2.4 74.1 1.0
SG D:CYS891 2.5 85.1 1.0
CB D:CYS968 2.6 66.3 1.0
CB D:CYS978 2.8 69.8 1.0
CA D:CYS968 3.0 65.2 1.0
CB D:CYS975 3.7 76.4 1.0
CB D:CYS891 3.8 79.7 1.0
C D:CYS968 4.0 66.1 1.0
CA D:CYS978 4.1 68.3 1.0
N D:CYS968 4.2 64.9 1.0
N D:CYS975 4.2 60.7 1.0
N D:CYS978 4.2 64.2 1.0
N D:ALA969 4.2 75.7 1.0
NH2 D:ARG963 4.4 81.7 1.0
CA D:CYS975 4.5 68.2 1.0
OG1 D:THR970 4.5 72.8 1.0
N D:CYS891 4.5 80.6 1.0
O D:CYS975 4.7 59.4 1.0
OG1 D:THR893 4.7 84.4 1.0
CA D:CYS891 4.8 83.2 1.0
O D:SER964 4.8 82.0 1.0
O D:CYS968 4.9 64.8 1.0
C D:CYS975 4.9 65.5 1.0

Zinc binding site 2 out of 2 in 6dvd

Go back to Zinc Binding Sites List in 6dvd
Zinc binding site 2 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) with 6 Nt Spacer and Bromine Labelled in Position "-11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) with 6 Nt Spacer and Bromine Labelled in Position "-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:68.3
occ:1.00
 SG D:CYS62 2.4 55.6 1.0
SG D:CYS78 2.4 80.7 1.0
SG D:CYS60 2.5 92.3 1.0
CB D:CYS60 2.9 80.5 1.0
SG D:CYS75 2.9 65.0 1.0
N D:CYS62 3.3 74.0 1.0
CB D:CYS62 3.5 70.5 1.0
CB D:CYS78 3.6 75.3 1.0
CB D:CYS75 3.7 69.9 1.0
N D:TYR61 3.8 66.5 1.0
CA D:CYS62 3.9 73.3 1.0
N D:GLY63 4.1 87.2 1.0
CA D:CYS60 4.1 84.6 1.0
C D:CYS60 4.1 85.4 1.0
N D:LYS64 4.3 84.7 1.0
C D:CYS62 4.3 80.0 1.0
C D:TYR61 4.3 74.3 1.0
N D:CYS78 4.5 79.9 1.0
CA D:TYR61 4.5 67.3 1.0
CB D:LYS64 4.6 91.4 1.0
CD1 D:TYR65 4.6 87.2 1.0
CA D:CYS78 4.7 74.6 1.0
N D:TYR65 4.9 90.2 1.0
CA D:LYS64 5.0 86.4 1.0
CB D:TYR61 5.0 70.1 1.0
O D:CYS60 5.0 88.7 1.0

Reference:

W.Lin, S.Mandal, D.Degen, M.S.Cho, Y.Feng, K.Das, R.H.Ebright. Structural Basis of Ecf-Sigma-Factor-Dependent Transcription Initiation. Nat Commun V. 10 710 2019.
ISSN: ESSN 2041-1723
PubMed: 30755604
DOI: 10.1038/S41467-019-08443-3
Page generated: Mon Oct 28 19:50:22 2024

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