Zinc in PDB 8sy6: E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Db-Utp Base Pair in the Active Site

All present enzymatic activity of E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Db-Utp 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 Db-Utp 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 Db-Utp Base Pair in the Active Site (pdb code 8sy6). 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 Db-Utp Base Pair in the Active Site, PDB code: 8sy6:
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 Db-Utp 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 Db-Utp Base Pair in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1501 b:114.7 occ:1.00 SG J:CYS898 2.3 97.0 1.0 SG J:CYS895 2.3 94.3 1.0 SG J:CYS814 2.3 104.4 1.0 SG J:CYS888 2.3 99.0 1.0 CB J:CYS814 3.2 104.4 1.0 CB J:CYS898 3.3 97.0 1.0 CB J:CYS888 3.6 99.0 1.0 CB J:CYS895 3.7 94.3 1.0 N J:CYS814 4.1 104.4 1.0 CA J:CYS888 4.2 99.0 1.0 CA J:CYS814 4.3 104.4 1.0 N J:CYS898 4.4 97.0 1.0 CA J:CYS898 4.4 97.0 1.0 CG2 J:THR890 4.4 98.7 1.0 N J:CYS895 4.5 94.3 1.0 NH2 J:ARG883 4.6 108.2 1.0 CA J:CYS895 4.6 94.3 1.0 N J:ASP889 4.7 102.9 1.0 CG2 J:THR816 4.7 109.5 1.0 C J:CYS888 5.0 99.0 1.0

Zinc binding site 2 out of 2 in the E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Db-Utp 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 Db-Utp Base Pair in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1502 b:154.5 occ:1.00 SG J:CYS72 2.3 142.0 1.0 N J:GLU86 2.4 138.3 1.0 N J:LYS87 2.4 140.8 1.0 CB J:CYS85 2.9 134.6 1.0 CB J:CYS72 3.1 142.0 1.0 C J:GLU86 3.1 138.3 1.0 C J:CYS85 3.2 134.6 1.0 CA J:GLU86 3.2 138.3 1.0 CA J:CYS85 3.4 134.6 1.0 CA J:LYS87 3.4 140.8 1.0 N J:CYS88 3.4 137.9 1.0 CB J:LYS87 3.6 140.8 1.0 CB J:GLU86 3.9 138.3 1.0 C J:LYS87 3.9 140.8 1.0 O J:CYS85 4.2 134.6 1.0 O J:GLU86 4.3 138.3 1.0 N J:GLY89 4.3 134.3 1.0 CB J:LYS74 4.5 141.2 1.0 CA J:CYS88 4.6 137.9 1.0 CA J:CYS72 4.6 142.0 1.0 N J:CYS85 4.8 134.6 1.0 SG J:CYS70 4.9 134.0 1.0 CB J:CYS88 5.0 137.9 1.0 C J:CYS88 5.0 137.9 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