Zinc in PDB 8txo: E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound to the Unnatural Dz-Ptp Base Pair in the Active Site

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

The structure of E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound to the Unnatural Dz-Ptp 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 to the Unnatural Dz-Ptp Base Pair in the Active Site (pdb code 8txo). 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 to the Unnatural Dz-Ptp Base Pair in the Active Site, PDB code: 8txo:
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 to the Unnatural Dz-Ptp 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 to the Unnatural Dz-Ptp Base Pair in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1501 b:101.6 occ:1.00 N J:LYS74 2.3 93.9 1.0 SG J:CYS72 2.3 90.1 1.0 SG J:CYS70 2.3 89.4 1.0 SG J:CYS85 2.3 83.3 1.0 N J:GLY73 2.4 92.5 1.0 CA J:GLY73 2.9 92.5 1.0 C J:GLY73 2.9 92.5 1.0 CA J:LYS74 3.3 93.9 1.0 CB J:CYS70 3.4 89.4 1.0 C J:CYS72 3.4 90.1 1.0 N J:TYR75 3.5 95.5 1.0 CB J:LYS74 3.6 93.9 1.0 CB J:CYS85 3.7 83.3 1.0 CB J:CYS72 3.7 90.1 1.0 C J:LYS74 3.9 93.9 1.0 CA J:CYS72 4.0 90.1 1.0 O J:GLY73 4.0 92.5 1.0 N J:CYS72 4.1 90.1 1.0 SG J:CYS88 4.2 80.0 1.0 O J:TYR75 4.2 95.5 1.0 O J:CYS72 4.4 90.1 1.0 C J:CYS70 4.6 89.4 1.0 CA J:CYS70 4.6 89.4 1.0 CA J:TYR75 4.6 95.5 1.0 O J:CYS70 4.6 89.4 1.0 C J:TYR75 4.7 95.5 1.0

Zinc binding site 2 out of 2 in the E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound to the Unnatural Dz-Ptp 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 to the Unnatural Dz-Ptp Base Pair in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1502 b:62.5 occ:1.00 SG J:CYS895 2.3 26.7 1.0 SG J:CYS814 2.3 34.2 1.0 SG J:CYS898 2.3 25.3 1.0 SG J:CYS888 2.3 26.1 1.0 CB J:CYS898 2.9 25.3 1.0 CB J:CYS814 3.5 34.2 1.0 OG1 J:THR890 3.5 29.4 1.0 CB J:CYS895 3.6 26.7 1.0 CB J:CYS888 3.6 26.1 1.0 CA J:CYS888 4.0 26.1 1.0 N J:CYS814 4.0 34.2 1.0 N J:ASP889 4.1 28.0 1.0 N J:CYS895 4.1 26.7 1.0 CA J:CYS898 4.2 25.3 1.0 N J:CYS898 4.3 25.3 1.0 CA J:CYS814 4.3 34.2 1.0 C J:CYS888 4.4 26.1 1.0 CA J:CYS895 4.4 26.7 1.0 N J:THR890 4.4 29.4 1.0 CB J:THR890 4.6 29.4 1.0 NH2 J:ARG883 4.6 23.7 1.0 CG2 J:THR816 4.8 32.4 1.0 O J:CYS895 4.9 26.7 1.0 C J:CYS895 4.9 26.7 1.0 NE J:ARG883 5.0 23.7 1.0

S.Aiyer, P.R.Baldwin, S.M.Tan, Z.Shan, J.Oh, A.Mehrani, M.E.Bowman, G.Louie, D.O.Passos, S.Dordevic-Marquardt, M.Mietzsch, J.A.Hull, S.Hoshika, B.A.Barad, D.A.Grotjahn, R.Mckenna, M.Agbandje-Mckenna, S.A.Benner, J.A.P.Noel, D.Wang, Y.Z.Tan, D.Lyumkis. Overcoming Resolution Attenuation During Tilted Cryo-Em Data Collection. Nat Commun V. 15 389 2024.
ISSN: ESSN 2041-1723
PubMed: 38195598
DOI: 10.1038/S41467-023-44555-7