Zinc in PDB 6vvs: Crystal Structure of A Mycobacterium Smegmatis Rna Polymerase Transcription Initiation Complex with Antibiotic Sorangicin

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

The structure of Crystal Structure of A Mycobacterium Smegmatis Rna Polymerase Transcription Initiation Complex with Antibiotic Sorangicin, PDB code: 6vvs was solved by M.Lilic, N.Braffman, 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)	54.67 / 3.11
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	132.461, 162.908, 139.325, 90.00, 107.32, 90.00
R / Rfree (%)	21.6 / 25.8

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

Zinc binding site 1 out of 2 in the Crystal Structure of A Mycobacterium Smegmatis Rna Polymerase Transcription Initiation Complex with 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 Rna Polymerase Transcription Initiation Complex with Antibiotic Sorangicin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2001 b:77.2 occ:1.00 SG D:CYS977 2.1 76.3 1.0 SG D:CYS890 2.2 80.5 1.0 SG D:CYS967 2.3 73.8 1.0 SG D:CYS974 2.4 86.1 1.0 CB D:CYS977 3.1 81.2 1.0 CB D:CYS967 3.2 68.5 1.0 CB D:CYS890 3.3 73.8 1.0 NH1 D:ARG962 3.4 78.0 1.0 CB D:CYS974 3.6 71.8 1.0 CA D:CYS967 3.6 82.0 1.0 N D:CYS890 4.0 79.6 1.0 OG D:SER969 4.2 97.6 1.0 N D:THR968 4.2 79.5 1.0 CA D:CYS977 4.2 72.1 1.0 CA D:CYS890 4.2 71.1 1.0 N D:CYS977 4.3 66.9 1.0 N D:CYS974 4.4 59.9 1.0 C D:CYS967 4.4 88.8 1.0 CA D:CYS974 4.5 76.7 1.0 CZ D:ARG962 4.5 60.4 1.0 CG2 D:THR892 4.5 83.7 1.0 NH2 D:ARG962 4.7 75.9 1.0 N D:SER969 4.8 90.7 1.0 N D:CYS967 4.9 77.3 1.0 O D:CYS974 5.0 62.8 1.0 C D:CYS890 5.0 84.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of A Mycobacterium Smegmatis Rna Polymerase Transcription Initiation Complex with 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 Rna Polymerase Transcription Initiation Complex with Antibiotic Sorangicin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:0.1 occ:1.00 SG D:CYS75 2.1 0.4 1.0 SG D:CYS60 2.2 0.3 1.0 SG D:CYS62 2.2 88.5 1.0 SG D:CYS78 2.2 0.6 1.0 CB D:CYS75 2.8 88.4 1.0 CB D:CYS60 3.1 0.9 1.0 CB D:CYS78 3.7 0.8 1.0 CB D:CYS62 3.7 0.7 1.0 N D:CYS62 3.8 0.7 1.0 N D:GLY63 3.9 0.2 1.0 N D:CYS78 4.1 0.6 1.0 N D:LYS64 4.1 0.6 1.0 CA D:CYS62 4.2 0.6 1.0 CA D:CYS75 4.3 84.0 1.0 CA D:CYS60 4.3 0.1 1.0 N D:TYR61 4.3 0.8 1.0 C D:CYS60 4.4 0.2 1.0 CB D:LYS64 4.5 0.7 1.0 CA D:CYS78 4.5 0.9 1.0 C D:CYS62 4.5 1.0 1.0 C D:CYS75 4.8 99.7 1.0 CB D:ARG77 4.8 0.9 1.0 C D:TYR61 4.8 0.2 1.0 CA D:LYS64 4.9 0.6 1.0 CA D:GLY63 4.9 0.5 1.0 C D:GLY63 5.0 0.9 1.0 N D:TYR65 5.0 0.7 1.0 O D:CYS75 5.0 0.0 1.0 O D:CYS60 5.0 0.4 1.0

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