Zinc in PDB 8sy7: E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Db-Stp Base Pair in the Active Site

All present enzymatic activity of E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Db-Stp 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-Stp 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-Stp Base Pair in the Active Site (pdb code 8sy7). 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-Stp Base Pair in the Active Site, PDB code: 8sy7:
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-Stp 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-Stp Base Pair in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1501 b:225.3 occ:1.00 SG J:CYS88 2.3 134.5 1.0 SG J:CYS85 2.3 134.1 1.0 CB J:CYS70 2.5 145.4 1.0 SG J:CYS70 3.0 145.4 1.0 CB J:CYS85 3.1 134.1 1.0 CB J:VAL90 3.1 128.7 1.0 CG2 J:VAL90 3.5 128.7 1.0 N J:VAL90 3.9 128.7 1.0 CA J:CYS70 3.9 145.4 1.0 CA J:VAL90 3.9 128.7 1.0 O J:VAL90 4.0 128.7 1.0 CB J:CYS88 4.1 134.5 1.0 CG1 J:VAL90 4.1 128.7 1.0 N J:LEU71 4.3 133.8 1.0 C J:CYS70 4.4 145.4 1.0 N J:CYS72 4.4 143.8 1.0 C J:VAL90 4.4 128.7 1.0 CA J:CYS85 4.5 134.1 1.0 CB J:CYS72 4.5 143.8 1.0 N J:GLY89 4.8 126.2 1.0 N J:CYS85 4.8 134.1 1.0 C J:GLY89 4.9 126.2 1.0 C J:CYS88 4.9 134.5 1.0 CA J:CYS88 4.9 134.5 1.0 N J:CYS70 5.0 145.4 1.0 N J:GLY73 5.0 142.2 1.0

Zinc binding site 2 out of 2 in the E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Db-Stp 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-Stp Base Pair in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1502 b:84.2 occ:1.00 SG J:CYS895 2.3 28.3 1.0 SG J:CYS888 2.3 36.8 1.0 SG J:CYS898 2.3 39.0 1.0 SG J:CYS814 2.3 64.4 1.0 CB J:CYS898 3.2 39.0 1.0 CB J:CYS814 3.3 64.4 1.0 CB J:CYS895 3.7 28.3 1.0 CB J:CYS888 3.7 36.8 1.0 NH2 J:ARG883 3.8 51.7 1.0 CA J:CYS888 4.1 36.8 1.0 N J:CYS814 4.1 64.4 1.0 OG1 J:THR890 4.3 40.6 1.0 N J:CYS895 4.3 28.3 1.0 CA J:CYS898 4.4 39.0 1.0 CA J:CYS814 4.4 64.4 1.0 N J:CYS898 4.4 39.0 1.0 CA J:CYS895 4.5 28.3 1.0 CZ J:ARG883 4.6 51.7 1.0 CG2 J:THR816 4.6 73.5 1.0 O J:CYS895 4.6 28.3 1.0 N J:ASP889 4.7 44.6 1.0 C J:CYS888 4.8 36.8 1.0 C J:CYS895 4.9 28.3 1.0 O J:SER887 4.9 39.1 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