Zinc in PDB 7szj: Cryo-Em Structure of Rifamycin Bound to E. Coli Rnap and RRNBP1 Promoter Complex

All present enzymatic activity of Cryo-Em Structure of Rifamycin Bound to E. Coli Rnap and RRNBP1 Promoter Complex:
2.7.7.6;

The structure of Cryo-Em Structure of Rifamycin Bound to E. Coli Rnap and RRNBP1 Promoter Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Cryo-Em Structure of Rifamycin Bound to E. Coli Rnap and RRNBP1 Promoter Complex (pdb code 7szj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of Rifamycin Bound to E. Coli Rnap and RRNBP1 Promoter Complex, PDB code: 7szj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of Rifamycin Bound to E. Coli Rnap and RRNBP1 Promoter Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Rifamycin Bound to E. Coli Rnap and RRNBP1 Promoter Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:121.9 occ:1.00 SG D:CYS85 2.2 39.2 1.0 SG D:CYS88 2.3 40.0 1.0 SG D:CYS72 2.3 36.5 1.0 SG D:CYS70 2.5 34.6 1.0 CB D:CYS85 2.5 39.2 1.0 CB D:CYS70 2.7 34.6 1.0 CB D:CYS72 3.6 36.5 1.0 O D:CYS88 3.8 40.0 1.0 CB D:CYS88 3.9 40.0 1.0 N D:CYS88 4.0 40.0 1.0 CA D:CYS85 4.1 39.2 1.0 CA D:CYS70 4.1 34.6 1.0 N D:CYS72 4.1 36.5 1.0 CA D:CYS88 4.4 40.0 1.0 CA D:CYS72 4.5 36.5 1.0 C D:CYS88 4.5 40.0 1.0 N D:LEU71 4.6 29.4 1.0 CB D:LYS74 4.6 36.6 1.0 C D:CYS85 4.7 39.2 1.0 C D:CYS70 4.7 34.6 1.0 N D:CYS85 4.8 39.2 1.0 N D:LYS74 4.9 36.6 1.0 N D:GLY73 4.9 35.5 1.0 O D:VAL90 4.9 24.7 1.0 CB D:LYS87 4.9 48.8 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Rifamycin Bound to E. Coli Rnap and RRNBP1 Promoter Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Rifamycin Bound to E. Coli Rnap and RRNBP1 Promoter Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2003 b:71.2 occ:1.00 SG D:CYS898 2.2 15.2 1.0 SG D:CYS895 2.2 14.9 1.0 SG D:CYS888 2.2 23.2 1.0 SG D:CYS814 2.3 28.2 1.0 CB D:CYS898 3.0 15.2 1.0 CB D:CYS814 3.5 28.2 1.0 CB D:CYS888 3.5 23.2 1.0 CB D:CYS895 3.7 14.9 1.0 CA D:CYS888 3.9 23.2 1.0 N D:CYS814 4.1 28.2 1.0 CA D:CYS898 4.2 15.2 1.0 N D:CYS898 4.2 15.2 1.0 N D:CYS895 4.2 14.9 1.0 N D:ASP889 4.3 33.5 1.0 CA D:CYS814 4.4 28.2 1.0 CA D:CYS895 4.5 14.9 1.0 NH2 D:ARG883 4.5 16.6 1.0 C D:CYS888 4.6 23.2 1.0 OG1 D:THR890 4.6 33.3 1.0 CG2 D:THR816 4.8 37.6 1.0 N D:THR890 4.8 33.3 1.0 O D:CYS895 4.9 14.9 1.0 C D:CYS895 5.0 14.9 1.0

W.Rajeswaran, S.R.Ashkar, P.H.Lee, L.Yeomans, Y.Shin, S.G.Franzblau, K.S.Murakami, H.D.Showalter, G.A.Garcia. Optimization of Benzoxazinorifamycins to Improve Mycobacterium Tuberculosis Rna Polymerase Inhibition and Treatment of Tuberculosis. Acs Infect Dis. V. 8 1422 2022.
ISSN: ESSN 2373-8227
PubMed: 35772744
DOI: 10.1021/ACSINFECDIS.1C00636