Zinc in PDB 9msh: De Novo Sign Rna Polymerase Open Complex (Rpo)

All present enzymatic activity of De Novo Sign Rna Polymerase Open Complex (Rpo):
2.7.7.6;

The structure of De Novo Sign Rna Polymerase Open Complex (Rpo) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the De Novo Sign Rna Polymerase Open Complex (Rpo) (pdb code 9msh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the De Novo Sign Rna Polymerase Open Complex (Rpo), PDB code: 9msh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the De Novo Sign Rna Polymerase Open Complex (Rpo)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of De Novo Sign Rna Polymerase Open Complex (Rpo) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1502 b:107.0 occ:1.00 SG J:CYS72 2.1 91.2 1.0 SG J:CYS85 2.2 95.4 1.0 SG J:CYS88 2.3 79.8 1.0 SG J:CYS70 2.5 74.3 1.0 CB J:CYS85 3.0 75.2 1.0 CB J:CYS70 3.3 65.2 1.0 CB J:CYS72 3.5 73.3 1.0 CB J:CYS88 3.7 73.5 1.0 N J:CYS72 3.7 73.2 1.0 N J:CYS88 4.1 80.4 1.0 CA J:CYS72 4.1 73.2 1.0 N J:GLY73 4.1 74.2 1.0 N J:LYS74 4.2 73.3 1.0 N J:LEU71 4.3 66.5 1.0 CA J:CYS85 4.4 71.6 1.0 CB J:LYS74 4.4 77.2 1.0 CA J:CYS88 4.5 77.2 1.0 C J:CYS72 4.5 76.9 1.0 CA J:CYS70 4.6 61.1 1.0 C J:CYS70 4.6 65.6 1.0 CB J:LYS87 4.7 82.9 1.0 CD2 J:TYR75 4.7 74.4 1.0 C J:LEU71 4.8 67.9 1.0 C J:CYS85 4.9 78.1 1.0 CA J:LYS74 4.9 75.4 1.0 N J:TYR75 5.0 71.8 1.0

Zinc binding site 2 out of 2 in the De Novo Sign Rna Polymerase Open Complex (Rpo)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of De Novo Sign Rna Polymerase Open Complex (Rpo) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1503 b:85.7 occ:1.00 SG J:CYS895 2.0 53.5 1.0 SG J:CYS898 2.2 66.6 1.0 SG J:CYS814 2.3 56.2 1.0 SG J:CYS888 2.4 50.4 1.0 CB J:CYS898 3.0 36.5 1.0 CB J:CYS814 3.5 52.9 1.0 CB J:CYS888 3.6 51.1 1.0 CB J:CYS895 3.6 38.0 1.0 NH2 J:ARG883 4.0 52.9 1.0 CA J:CYS888 4.0 47.9 1.0 N J:CYS898 4.2 38.8 1.0 CA J:CYS898 4.2 33.5 1.0 N J:CYS895 4.2 38.1 1.0 N J:CYS814 4.2 53.7 1.0 N J:ASP889 4.4 54.7 1.0 CA J:CYS895 4.4 33.7 1.0 CA J:CYS814 4.5 51.3 1.0 OG1 J:THR890 4.6 55.4 1.0 CG2 J:THR816 4.6 56.3 1.0 C J:CYS888 4.6 55.7 1.0 CZ J:ARG883 4.9 49.2 1.0 O J:CYS895 4.9 36.3 1.0 C J:CYS895 5.0 33.3 1.0

A.U.Mueller, N.Molina, B.T.Nixon, S.A.Darst. Real-Time Capture of Sigma N Transcription Initiation Intermediates Reveals Mechanism of Atpase-Driven Activation By Limited Unfolding. Nat Commun V. 16 7138 2025.
ISSN: ESSN 2041-1723
PubMed: 40759887
DOI: 10.1038/S41467-025-61837-4