Zinc in PDB 7rdq: Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna

All present enzymatic activity of Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna:
2.7.7.6;

The structure of Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna (pdb code 7rdq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna, PDB code: 7rdq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2001 b:39.9 occ:1.00 SG D:CYS1204 2.3 19.5 1.0 SG D:CYS1194 2.3 21.3 1.0 SG D:CYS1201 2.4 19.3 1.0 SG D:CYS1112 2.4 21.9 1.0 CB D:CYS1204 3.2 19.5 1.0 CB D:CYS1194 3.2 21.3 1.0 CB D:CYS1112 3.5 21.9 1.0 CA D:CYS1194 3.6 21.3 1.0 CB D:CYS1201 3.7 19.3 1.0 OG1 D:THR1196 4.0 22.0 1.0 N D:GLN1195 4.2 21.8 1.0 N D:CYS1201 4.2 19.3 1.0 NH2 D:ARG1189 4.3 14.7 1.0 N D:CYS1204 4.3 19.5 1.0 CA D:CYS1204 4.3 19.5 1.0 C D:CYS1194 4.4 21.3 1.0 N D:CYS1112 4.4 21.9 1.0 CG2 D:THR1114 4.5 22.7 1.0 CA D:CYS1201 4.5 19.3 1.0 CA D:CYS1112 4.6 21.9 1.0 N D:CYS1194 4.7 21.3 1.0 N D:THR1196 5.0 22.0 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:98.3 occ:1.00 SG D:CYS76 2.3 76.5 1.0 SG D:CYS60 2.3 85.1 1.0 SG D:CYS58 2.8 80.0 1.0 N D:CYS60 2.9 85.1 1.0 CB D:CYS58 2.9 80.0 1.0 SG D:CYS73 2.9 81.1 1.0 CB D:CYS60 3.3 85.1 1.0 CB D:CYS76 3.4 76.5 1.0 N D:ALA59 3.4 77.0 1.0 CA D:CYS60 3.5 85.1 1.0 CB D:CYS73 3.6 81.1 1.0 C D:CYS58 3.8 80.0 1.0 C D:ALA59 3.9 77.0 1.0 N D:GLY61 3.9 82.8 1.0 CA D:CYS58 3.9 80.0 1.0 CA D:ALA59 4.1 77.0 1.0 C D:CYS60 4.1 85.1 1.0 N D:CYS76 4.2 76.5 1.0 N D:LYS62 4.4 84.8 1.0 CA D:CYS76 4.4 76.5 1.0 CB D:ALA59 4.5 77.0 1.0 O D:CYS58 4.6 80.0 1.0 CB D:LYS62 4.7 84.8 1.0 CD2 D:TYR63 4.9 87.8 1.0 O D:ALA59 5.0 77.0 1.0

Y.Liu, L.Yu, C.Pukhrambam, J.T.Winkelman, E.Firlar, J.T.Kaelber, Y.Zhang, B.E.Nickels, R.H.Ebright. Structural and Mechanistic Basis of Reiterative Transcription Initiation. Proc.Natl.Acad.Sci.Usa V. 119 2022.
ISSN: ESSN 1091-6490
PubMed: 35082149
DOI: 10.1073/PNAS.2115746119