Zinc in PDB 8w8o: Thermus Thermophilus Initiation Complex in the Half-Translocated State

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

The structure of Thermus Thermophilus Initiation Complex in the Half-Translocated State, PDB code: 8w8o 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)	39.88 / 2.51
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	183.397, 103.796, 295.035, 90, 99.19, 90
R / Rfree (%)	18.7 / 22.6

The structure of Thermus Thermophilus Initiation Complex in the Half-Translocated State also contains other interesting chemical elements:

Magnesium

(Mg)

7 atoms

The binding sites of Zinc atom in the Thermus Thermophilus Initiation Complex in the Half-Translocated State (pdb code 8w8o). 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 Complex in the Half-Translocated State, PDB code: 8w8o:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Thermus Thermophilus Initiation Complex in the Half-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 Complex in the Half-Translocated State within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1601 b:37.8 occ:1.00 SG D:CYS1194 2.3 34.0 1.0 SG D:CYS1201 2.3 38.9 1.0 SG D:CYS1112 2.3 35.2 1.0 SG D:CYS1204 2.4 35.9 1.0 CB D:CYS1204 3.1 36.2 1.0 CB D:CYS1194 3.3 34.9 1.0 CB D:CYS1112 3.3 34.1 1.0 CB D:CYS1201 3.4 37.9 1.0 CA D:CYS1194 3.6 33.6 1.0 N D:CYS1201 3.9 38.6 1.0 N D:CYS1112 3.9 41.8 1.0 NH2 D:ARG1189 4.0 40.1 1.0 N D:GLN1195 4.1 41.2 1.0 OG1 D:THR1196 4.2 43.8 1.0 CA D:CYS1112 4.2 38.9 1.0 CA D:CYS1201 4.2 36.0 1.0 N D:CYS1204 4.3 34.0 1.0 CA D:CYS1204 4.3 33.2 1.0 C D:CYS1194 4.4 39.1 1.0 CG2 D:THR1114 4.6 37.7 1.0 N D:THR1196 4.7 35.8 1.0 N D:CYS1194 4.8 34.7 1.0 C D:CYS1201 4.9 34.8 1.0 CZ D:ARG1189 4.9 44.6 1.0 NE D:ARG1189 5.0 49.4 1.0

Zinc binding site 2 out of 2 in the Thermus Thermophilus Initiation Complex in the Half-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 Complex in the Half-Translocated State within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1602 b:76.5 occ:1.00 SG D:CYS73 2.2 69.7 1.0 SG D:CYS76 2.2 70.2 1.0 SG D:CYS58 2.3 67.5 1.0 SG D:CYS60 2.4 71.1 1.0 CB D:CYS58 3.1 74.0 1.0 CB D:CYS73 3.2 74.5 1.0 CB D:CYS76 3.5 72.0 1.0 CB D:CYS60 3.7 64.1 1.0 N D:CYS76 3.7 81.5 1.0 N D:CYS60 3.8 77.0 1.0 CB D:LYS62 4.2 81.2 1.0 CA D:CYS76 4.2 74.3 1.0 N D:LYS62 4.2 80.5 1.0 CA D:CYS60 4.2 75.7 1.0 N D:GLY61 4.2 74.6 1.0 N D:ALA59 4.3 60.4 1.0 CA D:CYS58 4.4 71.5 1.0 C D:CYS58 4.5 65.5 1.0 CB D:ARG75 4.5 78.2 1.0 CA D:CYS73 4.6 76.4 1.0 C D:CYS60 4.7 79.8 1.0 C D:ARG75 4.7 79.2 1.0 CD2 D:TYR63 4.7 83.5 1.0 CA D:LYS62 4.8 85.2 1.0 N D:ARG75 4.8 77.5 1.0 C D:ALA59 4.9 77.3 1.0 N D:GLY77 4.9 70.7 1.0 CA D:ARG75 4.9 75.2 1.0 C D:CYS76 5.0 69.1 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