Zinc in PDB 8to6: Escherichia Coli Rna Polymerase Unwinding Intermediate (I1D) at the Lambda Pr Promoter

All present enzymatic activity of Escherichia Coli Rna Polymerase Unwinding Intermediate (I1D) at the Lambda Pr Promoter:
2.7.7.6;

The structure of Escherichia Coli Rna Polymerase Unwinding Intermediate (I1D) at the Lambda Pr Promoter also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Escherichia Coli Rna Polymerase Unwinding Intermediate (I1D) at the Lambda Pr Promoter (pdb code 8to6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Escherichia Coli Rna Polymerase Unwinding Intermediate (I1D) at the Lambda Pr Promoter, PDB code: 8to6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Escherichia Coli Rna Polymerase Unwinding Intermediate (I1D) at the Lambda Pr Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Escherichia Coli Rna Polymerase Unwinding Intermediate (I1D) at the Lambda Pr Promoter within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1502 b:129.2 occ:1.00 SG J:CYS85 2.3 75.8 1.0 SG J:CYS88 2.3 77.1 1.0 SG J:CYS70 2.3 71.1 1.0 SG J:CYS72 2.3 77.1 1.0 CB J:CYS88 2.6 66.5 1.0 CB J:CYS85 3.1 69.1 1.0 N J:CYS88 3.2 68.9 1.0 CA J:CYS88 3.5 67.3 1.0 CB J:CYS72 3.6 61.9 1.0 CB J:CYS70 3.7 56.6 1.0 N J:CYS72 4.0 66.1 1.0 C J:LYS87 4.1 80.7 1.0 CB J:LYS87 4.4 81.4 1.0 CA J:CYS72 4.4 65.5 1.0 N J:LYS87 4.5 82.0 1.0 N J:LEU71 4.5 57.8 1.0 CA J:CYS85 4.5 66.0 1.0 C J:CYS88 4.5 68.8 1.0 CA J:LYS87 4.5 83.6 1.0 N J:GLY89 4.6 62.5 1.0 CA J:CYS70 4.9 60.2 1.0 C J:CYS85 4.9 69.9 1.0 CG J:LYS87 5.0 83.0 1.0

Zinc binding site 2 out of 2 in the Escherichia Coli Rna Polymerase Unwinding Intermediate (I1D) at the Lambda Pr Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Escherichia Coli Rna Polymerase Unwinding Intermediate (I1D) at the Lambda Pr Promoter within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1503 b:95.7 occ:1.00 SG J:CYS814 2.2 70.5 1.0 SG J:CYS898 2.2 57.6 1.0 SG J:CYS888 2.3 36.1 1.0 SG J:CYS895 2.3 58.8 1.0 CB J:CYS814 2.9 57.1 1.0 CB J:CYS895 3.0 35.8 1.0 CB J:CYS898 3.4 37.3 1.0 CB J:CYS888 3.6 44.7 1.0 N J:CYS895 3.9 30.1 1.0 N J:CYS814 3.9 55.3 1.0 CA J:CYS895 4.0 28.3 1.0 OG1 J:THR890 4.0 57.9 1.0 CA J:CYS888 4.0 49.0 1.0 CA J:CYS814 4.0 57.2 1.0 N J:ASP889 4.2 61.3 1.0 NH2 J:ARG883 4.2 55.0 1.0 N J:CYS898 4.5 38.2 1.0 CA J:CYS898 4.5 36.5 1.0 C J:CYS888 4.5 53.8 1.0 N J:THR890 4.6 56.2 1.0 CB J:THR890 4.7 53.5 1.0 C J:CYS895 4.7 32.3 1.0 O J:CYS895 4.8 40.6 1.0

S.A.Darst, R.M.Saecker, A.U.Mueller, B.Malone, J.Chen, W.C.Budell, V.P.Dandey, K.Maruthi, J.H.Mendez, N.Molina, E.T.Eng, L.Y.Yen, C.S.Potter, B.Carragher. Early Intermediates in Bacterial Rna Polymerase Promoter Melting Visualized By Time-Resolved Cryo-Electron Microscopy Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
DOI: 0.1038/S41594-024-01349-9