Zinc in PDB 9mse: De Novo Sign Rna Polymerase Transcription Initiation Intermediate with Pre-Catalytic Bebp State (RPI1 Open Ring)

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

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

Magnesium

(Mg)

3 atoms

The binding sites of Zinc atom in the De Novo Sign Rna Polymerase Transcription Initiation Intermediate with Pre-Catalytic Bebp State (RPI1 Open Ring) (pdb code 9mse). 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 Pre-Catalytic Bebp State (RPI1 Open Ring), PDB code: 9mse:
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 Pre-Catalytic Bebp State (RPI1 Open 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 Pre-Catalytic Bebp State (RPI1 Open Ring) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1502 b:120.3 occ:1.00 SG J:CYS72 2.1 100.1 1.0 SG J:CYS85 2.3 100.3 1.0 SG J:CYS88 2.4 85.8 1.0 SG J:CYS70 2.5 88.5 1.0 CB J:CYS85 3.0 91.3 1.0 CB J:CYS70 3.2 79.0 1.0 CB J:CYS72 3.6 85.3 1.0 CB J:CYS88 3.7 85.4 1.0 N J:CYS72 3.7 90.0 1.0 N J:GLY73 4.0 92.0 1.0 N J:CYS88 4.0 95.3 1.0 CA J:CYS72 4.1 89.0 1.0 N J:LYS74 4.2 89.3 1.0 N J:LEU71 4.3 82.2 1.0 CB J:LYS74 4.4 89.0 1.0 CA J:CYS70 4.5 75.9 1.0 CA J:CYS85 4.5 91.4 1.0 CA J:CYS88 4.5 87.5 1.0 C J:CYS70 4.5 83.3 1.0 C J:CYS72 4.5 92.1 1.0 CG J:LYS74 4.6 95.5 1.0 CB J:LYS87 4.7 98.0 1.0 C J:LEU71 4.8 87.6 1.0 CA J:LYS74 4.9 86.3 1.0 C J:CYS85 5.0 96.1 1.0

Zinc binding site 2 out of 2 in the De Novo Sign Rna Polymerase Transcription Initiation Intermediate with Pre-Catalytic Bebp State (RPI1 Open 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 Pre-Catalytic Bebp State (RPI1 Open Ring) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1503 b:124.7 occ:1.00 SG J:CYS895 2.1 87.2 1.0 SG J:CYS814 2.3 102.9 1.0 SG J:CYS898 2.3 101.5 1.0 SG J:CYS888 2.4 78.9 1.0 CB J:CYS898 3.0 71.8 1.0 CB J:CYS814 3.5 98.2 1.0 CB J:CYS888 3.5 80.9 1.0 CB J:CYS895 3.6 76.0 1.0 NH2 J:ARG883 3.7 95.1 1.0 CA J:CYS888 3.9 88.5 1.0 CA J:CYS898 4.2 69.4 1.0 N J:CYS898 4.2 70.8 1.0 N J:CYS814 4.2 92.7 1.0 N J:CYS895 4.2 66.5 1.0 N J:ASP889 4.3 97.4 1.0 CA J:CYS895 4.4 64.3 1.0 CA J:CYS814 4.5 96.7 1.0 OG1 J:THR890 4.6 94.5 1.0 C J:CYS888 4.6 95.2 1.0 CZ J:ARG883 4.7 94.7 1.0 CG2 J:THR816 4.7 104.6 1.0 O J:CYS895 4.9 65.4 1.0 C J:CYS895 4.9 61.6 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