Silicon in PDB 7zbd: Halotag with Traq-G Ligand

All present enzymatic activity of Halotag with Traq-G Ligand:
3.8.1.5;

The structure of Halotag with Traq-G Ligand, PDB code: 7zbd was solved by S.Hubner, P.Rivera-Fuentes, F.Pojer, K.Lau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.75 / 1.68
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	166.905, 50.46, 79.476, 90, 117.74, 90
R / Rfree (%)	18.6 / 22.2

The structure of Halotag with Traq-G Ligand also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Silicon atom in the Halotag with Traq-G Ligand (pdb code 7zbd). This binding sites where shown within 5.0 Angstroms radius around Silicon atom.
In total 2 binding sites of Silicon where determined in the Halotag with Traq-G Ligand, PDB code: 7zbd:
Jump to Silicon binding site number: 1; 2;

Silicon binding site 1 out of 2 in the Halotag with Traq-G Ligand


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 1 of Halotag with Traq-G Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Si402 b:23.2 occ:1.00 SI35 A:ILQ402 0.0 23.2 1.0 C34 A:ILQ402 1.8 18.6 1.0 C39 A:ILQ402 1.8 21.3 1.0 C36 A:ILQ402 1.9 21.5 1.0 C37 A:ILQ402 1.9 25.1 1.0 H363 A:ILQ402 2.4 25.8 1.0 H362 A:ILQ402 2.4 25.8 1.0 H361 A:ILQ402 2.4 25.8 1.0 H371 A:ILQ402 2.5 30.2 1.0 H372 A:ILQ402 2.5 30.2 1.0 H373 A:ILQ402 2.5 30.2 1.0 C33 A:ILQ402 2.8 21.2 1.0 C40 A:ILQ402 2.8 25.9 1.0 C27 A:ILQ402 2.8 20.7 1.0 C38 A:ILQ402 2.8 19.3 1.0 H331 A:ILQ402 2.9 25.4 1.0 H401 A:ILQ402 2.9 31.1 1.0 C26 A:ILQ402 3.3 19.0 1.0 H451 A:ILQ402 3.6 27.7 1.0 C30 A:ILQ402 4.1 21.3 1.0 C41 A:ILQ402 4.1 49.5 1.0 C28 A:ILQ402 4.1 20.2 1.0 C44 A:ILQ402 4.1 27.2 1.0 C25 A:ILQ402 4.2 20.4 1.0 C45 A:ILQ402 4.3 23.1 1.0 H322 A:ILQ402 4.4 36.1 1.0 N21 A:ILQ402 4.4 19.0 1.0 C29 A:ILQ402 4.6 21.6 1.0 C43 A:ILQ402 4.6 44.4 1.0 OG1 A:THR148 4.7 23.2 1.0 CG1 A:VAL167 4.7 29.2 1.0 C22 A:ILQ402 4.9 22.7 1.0 H281 A:ILQ402 5.0 24.3 1.0 H441 A:ILQ402 5.0 32.6 1.0

Silicon binding site 2 out of 2 in the Halotag with Traq-G Ligand


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 2 of Halotag with Traq-G Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Si402 b:30.2 occ:1.00 SI01 B:ILU402 0.0 30.2 1.0 C19 B:ILU402 1.9 32.5 1.0 C20 B:ILU402 1.9 31.4 1.0 C14 B:ILU402 1.9 31.0 1.0 C08 B:ILU402 1.9 27.2 1.0 H16 B:ILU402 2.5 39.0 1.0 H14 B:ILU402 2.5 39.0 1.0 H15 B:ILU402 2.5 39.0 1.0 H19 B:ILU402 2.5 37.7 1.0 H18 B:ILU402 2.5 37.7 1.0 H17 B:ILU402 2.5 37.7 1.0 C16 B:ILU402 2.8 34.0 1.0 C10 B:ILU402 2.8 27.4 1.0 C06 B:ILU402 2.9 27.3 1.0 C12 B:ILU402 2.9 32.0 1.0 H08 B:ILU402 2.9 40.8 1.0 H05 B:ILU402 2.9 32.9 1.0 C01 B:ILU402 3.2 29.2 1.0 C17 B:ILU402 4.1 33.5 1.0 C07 B:ILU402 4.1 26.0 1.0 C13 B:ILU402 4.2 31.7 1.0 C11 B:ILU402 4.2 30.9 1.0 CB B:GLU143 4.5 25.4 1.0 N B:GLU143 4.5 23.9 1.0 C15 B:ILU402 4.6 33.6 1.0 C09 B:ILU402 4.7 25.4 1.0 C03 B:ILU402 4.7 29.1 1.0 H02 B:ILU402 4.7 33.0 1.0 O B:TRP141 4.8 22.6 1.0 O01 B:ILU402 5.0 37.2 1.0 CA B:GLU143 5.0 24.1 1.0 H03 B:ILU402 5.0 31.2 1.0 CA B:PRO142 5.0 20.7 1.0

S.Hubner, G.Quargnali, S.Thallmair, P.Rivera-Fuentes. A Locally Activatable Sensor For Robust Quantification of Organellar Glutathione Biorxiv 2022.
ISSN: ISSN 2692-8205
DOI: 10.1101/2022.04.01.486692