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Zinc in PDB 6dv9: Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) Containing 5NT Rna with 4NT Spacer

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) Containing 5NT Rna with 4NT Spacer

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) Containing 5NT Rna with 4NT Spacer:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) Containing 5NT Rna with 4NT Spacer, PDB code: 6dv9 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) 91.47 / 3.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 143.270, 161.440, 237.690, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.2

Other elements in 6dv9:

The structure of Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) Containing 5NT Rna with 4NT Spacer also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) Containing 5NT Rna with 4NT Spacer (pdb code 6dv9). 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) Containing 5NT Rna with 4NT Spacer, PDB code: 6dv9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6dv9

Go back to Zinc Binding Sites List in 6dv9
Zinc binding site 1 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) Containing 5NT Rna with 4NT Spacer


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) Containing 5NT Rna with 4NT Spacer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1402

b:0.8
occ:1.00
 SG D:CYS968 2.4 1.0 1.0
SG D:CYS975 2.4 0.2 1.0
SG D:CYS891 2.4 0.4 1.0
SG D:CYS978 2.4 0.1 1.0
CB D:CYS968 2.5 0.4 1.0
CB D:CYS978 2.8 99.2 1.0
CA D:CYS968 3.0 1.0 1.0
CB D:CYS975 3.6 0.9 1.0
CB D:CYS891 3.6 0.1 1.0
C D:CYS968 3.9 0.3 1.0
CA D:CYS978 4.1 1.0 1.0
N D:CYS975 4.1 0.2 1.0
N D:CYS968 4.1 0.5 1.0
N D:CYS978 4.2 1.0 1.0
N D:ALA969 4.2 0.3 1.0
CA D:CYS975 4.3 0.7 1.0
N D:CYS891 4.4 0.1 1.0
OG1 D:THR970 4.5 0.0 1.0
O D:CYS975 4.5 0.3 1.0
NH2 D:ARG963 4.6 0.6 1.0
CA D:CYS891 4.6 0.6 1.0
C D:CYS975 4.7 0.5 1.0
O D:SER964 4.8 0.7 1.0
OG1 D:THR893 4.8 0.2 1.0
O D:CYS968 4.8 0.5 1.0

Zinc binding site 2 out of 2 in 6dv9

Go back to Zinc Binding Sites List in 6dv9
Zinc binding site 2 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Transcription Initiation Complex(Ecf Sigma Factor L) Containing 5NT Rna with 4NT Spacer


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) Containing 5NT Rna with 4NT Spacer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1403

b:0.8
occ:1.00
 SG D:CYS78 2.4 0.2 1.0
SG D:CYS62 2.4 80.8 1.0
SG D:CYS60 2.4 0.8 1.0
SG D:CYS75 2.4 96.7 1.0
CB D:CYS60 3.0 0.7 1.0
CB D:CYS75 3.2 88.6 1.0
N D:CYS62 3.5 93.9 1.0
CB D:CYS62 3.5 0.6 1.0
CB D:CYS78 3.8 0.6 1.0
CA D:CYS62 4.0 0.8 1.0
N D:TYR61 4.0 0.8 1.0
N D:GLY63 4.2 0.2 1.0
CA D:CYS60 4.3 0.9 1.0
N D:CYS78 4.3 0.1 1.0
N D:LYS64 4.4 0.1 1.0
CD1 D:TYR65 4.4 0.2 1.0
C D:CYS60 4.4 1.0 1.0
C D:CYS62 4.4 0.6 1.0
C D:TYR61 4.5 98.2 1.0
CB D:LYS64 4.6 0.7 1.0
CA D:CYS78 4.6 0.2 1.0
CA D:CYS75 4.7 79.6 1.0
CA D:TYR61 4.7 0.5 1.0
N D:TYR65 4.8 1.0 1.0
CE1 D:TYR65 5.0 0.3 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 19:48:17 2024

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