Zinc in PDB 8sy5: E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Ds-Btp Base Pair in the Active Site

All present enzymatic activity of E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Ds-Btp Base Pair in the Active Site:
2.7.7.6;

The structure of E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Ds-Btp Base Pair in the Active Site also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Ds-Btp Base Pair in the Active Site (pdb code 8sy5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Ds-Btp Base Pair in the Active Site, PDB code: 8sy5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Ds-Btp Base Pair in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Ds-Btp Base Pair in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1501 b:91.3 occ:1.00 SG J:CYS88 2.3 63.6 1.0 SG J:CYS72 2.3 60.6 1.0 SG J:CYS85 2.3 61.6 1.0 SG J:CYS70 2.3 55.5 1.0 CB J:CYS72 3.1 60.6 1.0 CB J:CYS88 3.1 63.6 1.0 CB J:CYS85 3.3 61.6 1.0 N J:CYS72 3.6 60.6 1.0 CB J:CYS70 3.8 55.5 1.0 CA J:CYS72 3.9 60.6 1.0 CG J:LYS87 4.0 69.5 1.0 N J:CYS88 4.0 63.6 1.0 CG J:LYS74 4.1 63.5 1.0 CA J:CYS88 4.2 63.6 1.0 N J:GLY73 4.5 54.3 1.0 N J:LEU71 4.5 53.0 1.0 CD J:LYS87 4.6 69.5 1.0 C J:CYS72 4.7 60.6 1.0 C J:LEU71 4.7 53.0 1.0 CD J:LYS74 4.8 63.5 1.0 CA J:CYS85 4.8 61.6 1.0 CE J:LYS74 4.8 63.5 1.0 N J:LYS74 4.9 63.5 1.0 CA J:CYS70 5.0 55.5 1.0 C J:CYS70 5.0 55.5 1.0

Zinc binding site 2 out of 2 in the E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Ds-Btp Base Pair in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Ds-Btp Base Pair in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1502 b:83.0 occ:1.00 CB J:CYS814 1.4 41.0 1.0 SG J:CYS888 2.3 33.5 1.0 SG J:CYS895 2.3 24.3 1.0 SG J:CYS814 2.3 41.0 1.0 CA J:CYS814 2.8 41.0 1.0 N J:CYS814 3.3 41.0 1.0 SG J:CYS898 3.3 28.4 1.0 CB J:CYS895 3.6 24.3 1.0 CB J:CYS888 3.9 33.5 1.0 C J:CYS814 3.9 41.0 1.0 OG1 J:THR890 4.0 33.4 1.0 CA J:CYS888 4.4 33.5 1.0 N J:GLY815 4.5 45.1 1.0 N J:ASP889 4.5 42.0 1.0 C J:ASP813 4.5 36.6 1.0 CB J:CYS898 4.6 28.4 1.0 O J:CYS814 4.6 41.0 1.0 NH2 J:ARG883 4.7 36.8 1.0 CA J:CYS895 4.8 24.3 1.0 N J:CYS895 4.8 24.3 1.0 N J:THR890 4.8 33.4 1.0 CB J:THR890 4.9 33.4 1.0 C J:CYS888 4.9 33.5 1.0

J.Oh, Z.Shan, S.Hoshika, J.Xu, J.Chong, S.A.Benner, D.Lyumkis, D.Wang. A Unified Watson-Crick Geometry Drives Transcription of Six-Letter Expanded Dna Alphabets By E. Coli Rna Polymerase. Nat Commun V. 14 8219 2023.
ISSN: ESSN 2041-1723
PubMed: 38086811
DOI: 10.1038/S41467-023-43735-9