Zinc in PDB 7dy6: A Refined Cryo-Em Structure of An Escherichia Coli Rnap-Promoter Open Complex (Rpo) with Sspa

All present enzymatic activity of A Refined Cryo-Em Structure of An Escherichia Coli Rnap-Promoter Open Complex (Rpo) with Sspa:
2.7.7.6;

The structure of A Refined Cryo-Em Structure of An Escherichia Coli Rnap-Promoter Open Complex (Rpo) with Sspa also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the A Refined Cryo-Em Structure of An Escherichia Coli Rnap-Promoter Open Complex (Rpo) with Sspa (pdb code 7dy6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the A Refined Cryo-Em Structure of An Escherichia Coli Rnap-Promoter Open Complex (Rpo) with Sspa, PDB code: 7dy6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the A Refined Cryo-Em Structure of An Escherichia Coli Rnap-Promoter Open Complex (Rpo) with Sspa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Refined Cryo-Em Structure of An Escherichia Coli Rnap-Promoter Open Complex (Rpo) with Sspa within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:74.8 occ:1.00 SG D:CYS70 2.3 42.2 1.0 SG D:CYS85 2.4 47.4 1.0 SG D:CYS88 2.4 49.9 1.0 SG D:CYS72 2.4 51.1 1.0 CB D:CYS72 3.1 51.1 1.0 CB D:CYS85 3.5 47.4 1.0 N D:CYS72 3.5 51.1 1.0 N D:CYS88 3.7 49.9 1.0 O D:CYS88 3.8 49.9 1.0 CB D:LYS87 3.9 53.4 1.0 CA D:CYS72 3.9 51.1 1.0 CB D:CYS88 4.0 49.9 1.0 CB D:CYS70 4.0 42.2 1.0 CA D:CYS88 4.3 49.9 1.0 N D:LEU71 4.3 45.2 1.0 C D:CYS88 4.5 49.9 1.0 N D:GLY73 4.6 49.6 1.0 C D:LYS87 4.6 53.4 1.0 C D:LEU71 4.6 45.2 1.0 CA D:LYS87 4.7 53.4 1.0 C D:CYS72 4.8 51.1 1.0 N D:LYS87 4.8 53.4 1.0 CB D:LYS74 4.8 48.5 1.0 CA D:CYS85 4.9 47.4 1.0 CE D:LYS74 4.9 48.5 1.0 CA D:LEU71 4.9 45.2 1.0 CG D:LYS87 5.0 53.4 1.0 N D:LYS74 5.0 48.5 1.0

Zinc binding site 2 out of 2 in the A Refined Cryo-Em Structure of An Escherichia Coli Rnap-Promoter Open Complex (Rpo) with Sspa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Refined Cryo-Em Structure of An Escherichia Coli Rnap-Promoter Open Complex (Rpo) with Sspa within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2003 b:65.4 occ:1.00 CB D:CYS814 2.3 53.0 1.0 SG D:CYS898 2.3 38.0 1.0 SG D:CYS888 2.3 47.9 1.0 SG D:CYS895 2.4 37.5 1.0 SG D:CYS814 3.1 53.0 1.0 NH2 D:ARG883 3.2 48.8 1.0 CB D:CYS898 3.4 38.0 1.0 CB D:CYS888 3.5 47.9 1.0 CB D:CYS895 3.5 37.5 1.0 CA D:CYS814 3.5 53.0 1.0 N D:CYS814 3.6 53.0 1.0 CA D:CYS888 4.0 47.9 1.0 N D:ASP889 4.1 54.1 1.0 N D:CYS895 4.4 37.5 1.0 C D:CYS814 4.4 53.0 1.0 OG1 D:THR890 4.5 48.4 1.0 CA D:CYS898 4.5 38.0 1.0 CZ D:ARG883 4.5 48.8 1.0 N D:GLY815 4.5 56.9 1.0 N D:CYS898 4.5 38.0 1.0 CA D:CYS895 4.5 37.5 1.0 C D:CYS888 4.6 47.9 1.0 C D:ASP813 4.9 48.5 1.0

F.Wang, Y.Feng, Z.Shang, W.Lin. A Unique Binding Between Sspa and Rnap Beta' Nth Across Low-Gc Gram-Negative Bacteria Facilitates Sspa-Mediated Transcription Regulation. Biochem.Biophys.Res.Commun. V. 583 86 2021.
ISSN: ESSN 1090-2104
PubMed: 34735884
DOI: 10.1016/J.BBRC.2021.10.048