Zinc in PDB 8w8p: Thermus Thermophilus Initiation Transcription Complex Containing Cmpcpp in the Post-Translocated State

All present enzymatic activity of Thermus Thermophilus Initiation Transcription Complex Containing Cmpcpp in the Post-Translocated State:
2.7.7.6;

The structure of Thermus Thermophilus Initiation Transcription Complex Containing Cmpcpp in the Post-Translocated State, PDB code: 8w8p was solved by L.Li, Y.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.76 / 3.17
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	184.681, 103.891, 294.614, 90, 98.97, 90
R / Rfree (%)	21.1 / 25.7

The structure of Thermus Thermophilus Initiation Transcription Complex Containing Cmpcpp in the Post-Translocated State also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Zinc atom in the Thermus Thermophilus Initiation Transcription Complex Containing Cmpcpp in the Post-Translocated State (pdb code 8w8p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Thermus Thermophilus Initiation Transcription Complex Containing Cmpcpp in the Post-Translocated State, PDB code: 8w8p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Thermus Thermophilus Initiation Transcription Complex Containing Cmpcpp in the Post-Translocated State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermus Thermophilus Initiation Transcription Complex Containing Cmpcpp in the Post-Translocated State within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1601 b:46.6 occ:1.00 SG D:CYS1194 2.3 47.5 1.0 SG D:CYS1201 2.4 40.0 1.0 SG D:CYS1112 2.5 33.1 1.0 SG D:CYS1204 2.5 46.3 1.0 CB D:CYS1194 3.0 44.0 1.0 CB D:CYS1112 3.0 41.2 1.0 CB D:CYS1204 3.3 42.9 1.0 CB D:CYS1201 3.5 46.5 1.0 CA D:CYS1194 3.5 46.5 1.0 N D:CYS1112 3.8 41.7 1.0 OG1 D:THR1196 3.9 50.5 1.0 CA D:CYS1112 4.0 39.5 1.0 N D:CYS1201 4.0 39.8 1.0 N D:GLN1195 4.1 41.0 1.0 N D:CYS1204 4.2 45.1 1.0 CA D:CYS1201 4.3 42.2 1.0 C D:CYS1194 4.3 45.3 1.0 CA D:CYS1204 4.4 44.4 1.0 NH2 D:ARG1189 4.5 36.7 1.0 N D:THR1196 4.6 45.9 1.0 N D:CYS1194 4.7 45.0 1.0 O D:CYS1201 4.8 46.9 1.0 CG2 D:THR1114 4.8 41.7 1.0 C D:CYS1201 4.9 43.9 1.0 C D:ASP1111 5.0 43.0 1.0 CB D:THR1196 5.0 47.0 1.0

Zinc binding site 2 out of 2 in the Thermus Thermophilus Initiation Transcription Complex Containing Cmpcpp in the Post-Translocated State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermus Thermophilus Initiation Transcription Complex Containing Cmpcpp in the Post-Translocated State within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1602 b:58.0 occ:1.00 SG D:CYS76 2.2 57.1 1.0 SG D:CYS60 2.3 62.4 1.0 SG D:CYS73 2.3 71.8 1.0 SG D:CYS58 2.6 74.5 1.0 CB D:CYS73 2.7 67.8 1.0 CB D:CYS58 3.3 69.3 1.0 CB D:CYS60 3.5 57.9 1.0 N D:CYS60 3.6 70.3 1.0 CB D:CYS76 3.7 61.2 1.0 N D:GLY61 4.0 66.0 1.0 CA D:CYS60 4.1 66.1 1.0 CD2 D:TYR63 4.1 77.9 1.0 N D:CYS76 4.2 69.9 1.0 N D:LYS62 4.2 75.8 1.0 CA D:CYS73 4.2 63.0 1.0 CB D:LYS62 4.2 75.0 1.0 N D:ALA59 4.3 52.7 1.0 CE2 D:TYR63 4.4 74.2 1.0 C D:CYS58 4.5 60.7 1.0 CA D:CYS76 4.5 67.8 1.0 C D:CYS60 4.5 68.5 1.0 CA D:CYS58 4.5 68.2 1.0 C D:ALA59 4.7 68.5 1.0 CA D:LYS62 4.8 77.8 1.0 CB D:ARG75 4.9 67.1 1.0 C D:CYS73 4.9 71.3 1.0 N D:TYR63 4.9 78.5 1.0 CA D:ALA59 5.0 55.0 1.0 N D:GLY77 5.0 61.0 1.0

I.C.Nova, J.M.Craig, A.Mazumder, A.H.Laszlo, I.M.Derrington, M.T.Noakes, H.Brinkerhoff, S.Yang, H.Vahedian-Movahed, L.Li, Y.Zhang, J.L.Bowman, J.R.Huang, J.W.Mount, R.H.Ebright, J.H.Gundlach. Nanopore Tweezers Show Fractional-Nucleotide Translocation in Sequence-Dependent Pausing By Rna Polymerase. Proc.Natl.Acad.Sci.Usa V. 121 17121 2024.
ISSN: ESSN 1091-6490
PubMed: 38990947
DOI: 10.1073/PNAS.2321017121