Zinc in PDB 9msf: De Novo Sign Rna Polymerase Transcription Initiation Intermediate with Post-Catalytic Bebp State (RPI1 Closed Ring)

All present enzymatic activity of De Novo Sign Rna Polymerase Transcription Initiation Intermediate with Post-Catalytic Bebp State (RPI1 Closed Ring):
2.7.7.6;

The structure of De Novo Sign Rna Polymerase Transcription Initiation Intermediate with Post-Catalytic Bebp State (RPI1 Closed Ring) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the De Novo Sign Rna Polymerase Transcription Initiation Intermediate with Post-Catalytic Bebp State (RPI1 Closed Ring) (pdb code 9msf). 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 Transcription Initiation Intermediate with Post-Catalytic Bebp State (RPI1 Closed Ring), PDB code: 9msf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the De Novo Sign Rna Polymerase Transcription Initiation Intermediate with Post-Catalytic Bebp State (RPI1 Closed Ring)


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 Transcription Initiation Intermediate with Post-Catalytic Bebp State (RPI1 Closed Ring) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1503 b:84.0 occ:1.00 SG J:CYS72 2.2 66.5 1.0 SG J:CYS85 2.4 73.3 1.0 SG J:CYS88 2.4 52.5 1.0 SG J:CYS70 2.5 53.5 1.0 CB J:CYS85 3.1 54.3 1.0 CB J:CYS70 3.3 42.9 1.0 CB J:CYS72 3.5 54.7 1.0 N J:CYS72 3.7 60.7 1.0 CB J:CYS88 3.8 52.9 1.0 N J:GLY73 4.0 60.3 1.0 CA J:CYS72 4.1 55.7 1.0 N J:CYS88 4.1 60.7 1.0 N J:LYS74 4.3 54.7 1.0 N J:LEU71 4.3 47.8 1.0 C J:CYS72 4.5 58.3 1.0 CA J:CYS70 4.5 43.6 1.0 C J:CYS70 4.5 47.9 1.0 CA J:CYS88 4.6 57.4 1.0 CB J:LYS74 4.6 60.6 1.0 CB J:LYS87 4.6 67.6 1.0 CG J:LYS74 4.6 65.2 1.0 CA J:CYS85 4.6 58.0 1.0 C J:LEU71 4.8 57.5 1.0 CD1 J:TYR75 4.8 64.7 1.0

Zinc binding site 2 out of 2 in the De Novo Sign Rna Polymerase Transcription Initiation Intermediate with Post-Catalytic Bebp State (RPI1 Closed Ring)


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 Transcription Initiation Intermediate with Post-Catalytic Bebp State (RPI1 Closed Ring) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1504 b:84.4 occ:1.00 SG J:CYS895 2.2 57.9 1.0 SG J:CYS898 2.3 70.6 1.0 SG J:CYS814 2.4 71.4 1.0 SG J:CYS888 2.4 54.5 1.0 CB J:CYS898 3.1 46.5 1.0 CB J:CYS814 3.5 69.3 1.0 CB J:CYS888 3.5 59.6 1.0 CB J:CYS895 3.6 49.9 1.0 CA J:CYS888 3.9 60.9 1.0 NH2 J:ARG883 4.0 67.9 1.0 N J:CYS814 4.2 57.7 1.0 N J:ASP889 4.2 72.1 1.0 CA J:CYS898 4.2 42.2 1.0 N J:CYS898 4.2 41.9 1.0 N J:CYS895 4.3 37.2 1.0 CA J:CYS814 4.4 63.0 1.0 CA J:CYS895 4.5 39.6 1.0 C J:CYS888 4.5 68.6 1.0 CG2 J:THR816 4.6 77.9 1.0 OG1 J:THR890 4.6 65.0 1.0 N J:THR890 4.9 73.0 1.0 O J:CYS895 4.9 41.4 1.0 C J:CYS895 5.0 37.3 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