Zinc in PDB 9msj: De Novo Sign Rna Polymerase Ntp-Bound Open Complex (Rpo+2A)

All present enzymatic activity of De Novo Sign Rna Polymerase Ntp-Bound Open Complex (Rpo+2A):
2.7.7.6;

The structure of De Novo Sign Rna Polymerase Ntp-Bound Open Complex (Rpo+2A) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the De Novo Sign Rna Polymerase Ntp-Bound Open Complex (Rpo+2A) (pdb code 9msj). 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 Ntp-Bound Open Complex (Rpo+2A), PDB code: 9msj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the De Novo Sign Rna Polymerase Ntp-Bound Open Complex (Rpo+2A)


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 Ntp-Bound Open Complex (Rpo+2A) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1502 b:156.2 occ:1.00 SG J:CYS72 2.1 127.1 1.0 SG J:CYS85 2.2 133.9 1.0 SG J:CYS88 2.4 114.4 1.0 SG J:CYS70 2.5 111.3 1.0 CB J:CYS85 2.9 111.2 1.0 CB J:CYS70 3.3 90.0 1.0 CB J:CYS72 3.6 103.6 1.0 CB J:CYS88 3.7 103.2 1.0 N J:CYS72 3.7 98.7 1.0 N J:GLY73 3.8 102.8 1.0 N J:CYS88 4.1 113.5 1.0 CA J:CYS72 4.1 102.5 1.0 N J:LYS74 4.1 102.7 1.0 N J:LEU71 4.3 92.8 1.0 CA J:CYS85 4.4 104.2 1.0 C J:CYS72 4.4 104.5 1.0 C J:CYS70 4.5 93.4 1.0 CB J:LYS74 4.5 106.1 1.0 CA J:CYS88 4.5 108.6 1.0 CA J:CYS70 4.5 89.2 1.0 C J:LEU71 4.8 91.7 1.0 CB J:LYS87 4.8 110.2 1.0 CA J:GLY73 4.9 98.8 1.0 C J:CYS85 4.9 107.9 1.0 CA J:LYS74 5.0 104.7 1.0

Zinc binding site 2 out of 2 in the De Novo Sign Rna Polymerase Ntp-Bound Open Complex (Rpo+2A)


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 Ntp-Bound Open Complex (Rpo+2A) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1503 b:127.0 occ:1.00 SG J:CYS814 2.0 83.4 1.0 SG J:CYS895 2.1 71.9 1.0 SG J:CYS898 2.2 88.4 1.0 SG J:CYS888 2.4 77.1 1.0 CB J:CYS898 2.9 53.8 1.0 NH2 J:ARG883 3.3 67.0 1.0 CB J:CYS814 3.3 74.3 1.0 CB J:CYS895 3.6 55.9 1.0 CB J:CYS888 3.6 61.7 1.0 CA J:CYS888 4.0 66.1 1.0 CA J:CYS898 4.1 50.6 1.0 N J:CYS814 4.1 76.3 1.0 N J:CYS898 4.2 60.5 1.0 N J:CYS895 4.2 52.6 1.0 CA J:CYS814 4.4 72.4 1.0 CA J:CYS895 4.4 50.9 1.0 N J:ASP889 4.5 76.6 1.0 CZ J:ARG883 4.5 60.6 1.0 OG1 J:THR890 4.6 70.6 1.0 C J:CYS888 4.7 75.6 1.0 OG1 J:THR816 4.8 82.8 1.0 CG2 J:THR816 4.8 84.6 1.0 O J:SER887 4.9 77.0 1.0 C J:CYS895 5.0 49.0 1.0 NE J:ARG883 5.0 61.0 1.0 O J:CYS895 5.0 49.2 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