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Zinc in PDB 6vvt: Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Antibiotic Sorangicin

Enzymatic activity of Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Antibiotic Sorangicin

All present enzymatic activity of Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Antibiotic Sorangicin:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Antibiotic Sorangicin, PDB code: 6vvt was solved by M.Lilic, S.A.Darst, E.A.Campbell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.75 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 129.217, 162.212, 136.295, 90.00, 111.36, 90.00
R / Rfree (%) 24 / 27.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Antibiotic Sorangicin (pdb code 6vvt). 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 A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Antibiotic Sorangicin, PDB code: 6vvt:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6vvt

Go back to Zinc Binding Sites List in 6vvt
Zinc binding site 1 out of 2 in the Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Antibiotic Sorangicin


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 A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Antibiotic Sorangicin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:85.1
occ:1.00
SG D:CYS977 2.2 80.5 1.0
SG D:CYS967 2.2 81.0 1.0
SG D:CYS890 2.3 89.1 1.0
SG D:CYS974 2.4 82.6 1.0
CB D:CYS967 2.7 70.0 1.0
CB D:CYS977 2.7 78.9 1.0
CA D:CYS967 3.1 76.8 1.0
CB D:CYS890 3.6 85.2 1.0
NH1 D:ARG962 3.8 87.9 1.0
CB D:CYS974 3.8 83.1 1.0
C D:CYS967 4.0 73.9 1.0
N D:THR968 4.0 80.0 1.0
CA D:CYS977 4.1 76.6 1.0
OG D:SER969 4.1 0.2 1.0
N D:CYS974 4.3 59.6 1.0
N D:CYS967 4.3 70.0 1.0
N D:CYS977 4.3 72.2 1.0
CG2 D:THR892 4.4 84.9 1.0
N D:CYS890 4.5 77.1 1.0
CA D:CYS974 4.6 68.8 1.0
CA D:CYS890 4.7 89.5 1.0
N D:SER969 4.8 85.4 1.0
CZ D:ARG962 5.0 75.2 1.0
O D:CYS974 5.0 66.3 1.0

Zinc binding site 2 out of 2 in 6vvt

Go back to Zinc Binding Sites List in 6vvt
Zinc binding site 2 out of 2 in the Crystal Structure of A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Antibiotic Sorangicin


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 A Mycobacterium Smegmatis Transcription Initiation Complex with Rifampicin-Resistant Rna Polymerase and Antibiotic Sorangicin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:0.3
occ:1.00
SG D:CYS78 2.2 0.1 1.0
SG D:CYS62 2.2 0.9 1.0
SG D:CYS60 2.2 97.6 1.0
SG D:CYS75 2.3 96.6 1.0
CB D:CYS60 3.1 93.8 1.0
CB D:CYS75 3.2 85.0 1.0
N D:CYS62 3.2 0.4 1.0
CB D:CYS78 3.3 93.3 1.0
CB D:CYS62 3.4 0.2 1.0
N D:CYS78 3.6 72.6 1.0
CA D:CYS62 3.8 89.4 1.0
N D:TYR61 3.8 88.5 1.0
N D:GLY63 3.9 0.9 1.0
CA D:CYS78 4.0 80.4 1.0
C D:CYS60 4.2 75.2 1.0
C D:TYR61 4.3 94.8 1.0
CA D:CYS60 4.3 77.4 1.0
C D:CYS62 4.4 85.1 1.0
CB D:ARG77 4.5 0.8 1.0
CA D:TYR61 4.5 85.2 1.0
N D:LYS64 4.6 88.0 1.0
CA D:CYS75 4.6 84.8 1.0
C D:ARG77 4.7 93.6 1.0
CB D:TYR61 4.8 81.0 1.0
C D:CYS78 4.8 84.8 1.0
N D:GLY79 4.9 81.3 1.0
O D:CYS60 5.0 76.4 1.0
CA D:ARG77 5.0 92.7 1.0

Reference:

M.Lilic, J.Chen, H.Boyaci, N.Braffman, E.A.Hubin, J.Herrmann, R.Muller, R.Mooney, R.Landick, S.A.Darst, E.A.Campbell. The Antibiotic Sorangicin A Inhibits Promoter Dna Unwinding in A Mycobacterium Tuberculosis Rifampicin-Resistant Rna Polymerase. Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
PubMed: 33199626
DOI: 10.1073/PNAS.2013706117
Page generated: Tue Oct 29 09:07:55 2024

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