Zinc in PDB 8pdy: E. Coli Rna Polymerase Paused at Ops Site

All present enzymatic activity of E. Coli Rna Polymerase Paused at Ops Site:
2.7.7.6;

The structure of E. Coli Rna Polymerase Paused at Ops Site also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the E. Coli Rna Polymerase Paused at Ops Site (pdb code 8pdy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the E. Coli Rna Polymerase Paused at Ops Site, PDB code: 8pdy:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the E. Coli Rna Polymerase Paused at Ops Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E. Coli Rna Polymerase Paused at Ops Site within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1501 b:215.2 occ:1.00 SG J:CYS70 2.3 180.7 1.0 SG J:CYS72 2.3 176.9 1.0 SG J:CYS88 2.3 172.7 1.0 SG J:CYS85 2.3 174.2 1.0 CB J:CYS72 3.1 176.9 1.0 CB J:CYS85 3.2 174.2 1.0 N J:CYS72 3.6 176.9 1.0 N J:CYS88 3.7 172.7 1.0 CB J:CYS88 3.8 172.7 1.0 CA J:CYS72 3.9 176.9 1.0 CB J:CYS70 4.0 180.7 1.0 CB J:LYS74 4.2 173.2 1.0 CB J:LYS87 4.3 175.7 1.0 CA J:CYS88 4.3 172.7 1.0 N J:LEU71 4.5 169.6 1.0 C J:CYS72 4.5 176.9 1.0 C J:LYS87 4.6 175.7 1.0 N J:LYS74 4.6 173.2 1.0 N J:GLY89 4.6 165.0 1.0 N J:LYS87 4.6 175.7 1.0 CA J:CYS85 4.7 174.2 1.0 N J:GLY73 4.7 172.3 1.0 C J:LEU71 4.7 169.6 1.0 CA J:LYS87 4.7 175.7 1.0 C J:CYS88 4.7 172.7 1.0 C J:CYS70 4.9 180.7 1.0 N J:VAL90 5.0 160.9 1.0 CA J:CYS70 5.0 180.7 1.0

Zinc binding site 2 out of 2 in the E. Coli Rna Polymerase Paused at Ops Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E. Coli Rna Polymerase Paused at Ops Site within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1502 b:177.0 occ:1.00 SG J:CYS814 2.3 141.8 1.0 SG J:CYS888 2.3 137.4 1.0 SG J:CYS898 2.3 136.4 1.0 SG J:CYS895 2.3 141.2 1.0 CB J:CYS898 2.6 136.4 1.0 CB J:CYS895 3.0 141.2 1.0 CB J:CYS814 3.4 141.8 1.0 CB J:CYS888 3.5 137.4 1.0 N J:CYS895 3.7 141.2 1.0 CA J:CYS888 3.7 137.4 1.0 NH2 J:ARG883 3.7 132.6 1.0 CA J:CYS898 3.8 136.4 1.0 CA J:CYS895 3.8 141.2 1.0 N J:CYS898 3.9 136.4 1.0 N J:CYS814 4.1 141.8 1.0 N J:ASP889 4.3 139.5 1.0 CA J:CYS814 4.4 141.8 1.0 C J:CYS888 4.4 137.4 1.0 C J:CYS895 4.4 141.2 1.0 O J:CYS895 4.4 141.2 1.0 OG1 J:THR890 4.6 141.1 1.0 CZ J:ARG883 4.8 132.6 1.0 C J:VAL894 4.9 132.6 1.0 N J:CYS888 4.9 137.4 1.0 C J:CYS898 5.0 136.4 1.0 NE J:ARG883 5.0 132.6 1.0

P.K.Zuber, N.Said, T.Hilal, B.Wang, B.Loll, J.Gonzalez-Higueras, C.A.Ramirez-Sarmiento, G.A.Belogurov, I.Artsimovitch, M.C.Wahl, S.H.Knauer. Concerted Transformation of A Hyper-Paused Transcription Complex and Its Reinforcing Protein. Nat Commun V. 15 3040 2024.
ISSN: ESSN 2041-1723
PubMed: 38589445
DOI: 10.1038/S41467-024-47368-4