Zinc in PDB 8w8n: Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State

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

The structure of Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State, PDB code: 8w8n 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)	48.86 / 2.69
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	184.422, 103.704, 295.444, 90, 98.67, 90
R / Rfree (%)	21.2 / 26

The structure of Thermus Thermophilus Initiation Transcription Complex in the Pre- 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 in the Pre- Translocated State (pdb code 8w8n). 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 in the Pre- Translocated State, PDB code: 8w8n:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Thermus Thermophilus Initiation Transcription Complex in the Pre- 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 in the Pre- Translocated State within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1601 b:23.9 occ:1.00 SG D:CYS1194 2.2 19.0 1.0 SG D:CYS1204 2.2 13.8 1.0 SG D:CYS1201 2.3 17.7 1.0 SG D:CYS1112 2.4 19.7 1.0 CB D:CYS1194 3.1 18.9 1.0 CB D:CYS1204 3.1 15.5 1.0 CA D:CYS1194 3.4 14.8 1.0 CB D:CYS1201 3.5 21.1 1.0 CB D:CYS1112 3.5 18.3 1.0 N D:GLN1195 4.0 19.1 1.0 N D:CYS1201 4.1 22.3 1.0 N D:CYS1112 4.1 22.0 1.0 OG1 D:THR1196 4.2 26.5 1.0 C D:CYS1194 4.3 14.3 1.0 N D:CYS1204 4.3 24.7 1.0 CA D:CYS1204 4.3 19.7 1.0 CA D:CYS1201 4.3 19.1 1.0 CG2 D:THR1114 4.3 22.9 1.0 NH2 D:ARG1189 4.4 18.3 1.0 CA D:CYS1112 4.4 18.1 1.0 N D:CYS1194 4.6 12.6 1.0 N D:THR1196 4.8 16.9 1.0 C D:CYS1201 4.9 14.2 1.0 NE D:ARG1189 5.0 33.1 1.0

Zinc binding site 2 out of 2 in the Thermus Thermophilus Initiation Transcription Complex in the Pre- 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 in the Pre- Translocated State within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1602 b:58.8 occ:1.00 SG D:CYS73 2.3 56.0 1.0 SG D:CYS76 2.3 44.5 1.0 SG D:CYS60 2.3 51.7 1.0 SG D:CYS58 2.3 63.9 1.0 CB D:CYS73 2.9 62.0 1.0 CB D:CYS58 3.0 54.1 1.0 CB D:CYS76 3.9 51.3 1.0 CB D:CYS60 3.9 51.6 1.0 N D:CYS60 4.0 60.8 1.0 N D:LYS62 4.0 60.3 1.0 N D:GLY61 4.1 59.1 1.0 CB D:LYS62 4.1 65.7 1.0 CD1 D:TYR63 4.2 64.5 1.0 CA D:CYS58 4.3 47.4 1.0 N D:ALA59 4.3 39.8 1.0 N D:CYS76 4.3 73.1 1.0 CA D:CYS73 4.4 55.2 1.0 CA D:CYS60 4.4 58.1 1.0 C D:CYS58 4.4 43.9 1.0 CE1 D:TYR63 4.6 65.4 1.0 CA D:LYS62 4.6 65.3 1.0 CA D:CYS76 4.7 61.4 1.0 C D:CYS60 4.7 62.9 1.0 N D:TYR63 4.8 65.5 1.0 CB D:ARG75 4.9 61.8 1.0 C D:ALA59 4.9 57.8 1.0 C D:GLY61 5.0 56.7 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