Silicon in PDB 7zba: Halotag with Me-Traq-G Ligand

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

The structure of Halotag with Me-Traq-G Ligand, PDB code: 7zba 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)	44.56 / 1.23
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.363, 81.499, 159.652, 90, 90, 90
R / Rfree (%)	23.5 / 25.5

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

Chlorine

(Cl)

2 atoms

The binding sites of Silicon atom in the Halotag with Me-Traq-G Ligand (pdb code 7zba). 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 Me-Traq-G Ligand, PDB code: 7zba:
Jump to Silicon binding site number: 1; 2;

Silicon binding site 1 out of 2 in the Halotag with Me-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 Me-Traq-G Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Si405 b:33.1 occ:1.00 SI01 A:IL7405 0.0 33.1 1.0 C32 A:IL7405 1.9 34.7 1.0 C33 A:IL7405 1.9 35.2 1.0 C10 A:IL7405 1.9 36.2 1.0 C16 A:IL7405 1.9 39.6 1.0 H36 A:IL7405 2.5 41.7 1.0 H38 A:IL7405 2.5 41.7 1.0 H37 A:IL7405 2.5 41.7 1.0 H39 A:IL7405 2.5 42.2 1.0 H41 A:IL7405 2.5 42.2 1.0 H40 A:IL7405 2.5 42.2 1.0 C08 A:IL7405 2.8 35.2 1.0 C12 A:IL7405 2.8 37.0 1.0 C18 A:IL7405 2.8 36.9 1.0 C14 A:IL7405 2.9 33.9 1.0 H09 A:IL7405 2.9 44.2 1.0 H06 A:IL7405 2.9 44.4 1.0 C01 A:IL7405 3.2 36.4 1.0 H02 B:IL7401 4.1 35.6 1.0 C09 A:IL7405 4.1 36.4 1.0 C13 A:IL7405 4.1 38.0 1.0 C19 A:IL7405 4.1 36.0 1.0 C15 A:IL7405 4.2 36.5 1.0 HG1 B:THR148 4.2 33.8 1.0 HG22 A:VAL167 4.2 20.6 1.0 H03 B:IL7401 4.3 40.0 1.0 HB3 B:GLU147 4.4 25.3 1.0 OE1 B:GLU147 4.4 29.0 1.0 HA3 A:GLY171 4.5 18.0 1.0 H43 A:IL7405 4.5 42.0 1.0 HG13 A:VAL167 4.6 23.9 1.0 C11 A:IL7405 4.6 36.0 1.0 O B:HOH628 4.6 27.7 1.0 C17 A:IL7405 4.6 36.3 1.0 C03 A:IL7405 4.7 38.6 1.0 OG1 B:THR148 4.7 28.2 1.0 O B:HOH503 4.7 30.5 1.0 CD B:GLU147 4.8 29.6 1.0 HG2 B:GLU147 4.8 32.2 1.0 C05 B:IL7401 4.8 29.7 1.0 C07 B:IL7401 4.9 33.4 1.0 HA2 A:GLY171 5.0 18.0 1.0 H04 A:IL7405 5.0 43.7 1.0 HG11 A:VAL167 5.0 23.9 1.0

Silicon binding site 2 out of 2 in the Halotag with Me-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 Me-Traq-G Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Si401 b:26.6 occ:1.00 SI01 B:IL7401 0.0 26.6 1.0 C32 B:IL7401 1.9 33.9 1.0 C33 B:IL7401 1.9 29.8 1.0 C16 B:IL7401 1.9 27.9 1.0 C10 B:IL7401 1.9 29.4 1.0 H36 B:IL7401 2.5 40.7 1.0 H37 B:IL7401 2.5 40.7 1.0 H38 B:IL7401 2.5 40.7 1.0 H41 B:IL7401 2.5 35.7 1.0 H40 B:IL7401 2.5 35.7 1.0 H39 B:IL7401 2.5 35.7 1.0 C18 B:IL7401 2.8 28.4 1.0 C12 B:IL7401 2.8 28.0 1.0 H09 B:IL7401 2.8 34.1 1.0 H06 B:IL7401 2.9 33.6 1.0 C14 B:IL7401 2.9 25.5 1.0 C08 B:IL7401 2.9 31.5 1.0 C01 B:IL7401 3.3 30.1 1.0 H02 A:IL7405 4.0 48.1 1.0 H03 A:IL7405 4.1 42.8 1.0 C19 B:IL7401 4.1 26.4 1.0 C13 B:IL7401 4.1 32.6 1.0 C15 B:IL7401 4.2 21.4 1.0 C09 B:IL7401 4.2 27.8 1.0 HD22 B:LEU161 4.2 24.7 1.0 HG22 B:VAL167 4.2 36.0 1.0 HG21 B:VAL167 4.3 36.0 1.0 C05 A:IL7405 4.5 40.0 1.0 C07 A:IL7405 4.6 35.6 1.0 C17 B:IL7401 4.6 27.4 1.0 C11 B:IL7401 4.6 28.5 1.0 CG2 B:VAL167 4.7 30.0 1.0 C03 B:IL7401 4.8 26.9 1.0 HD21 B:LEU161 4.8 24.7 1.0 H07 A:IL7405 4.9 43.8 1.0 HG1 A:THR148 4.9 29.1 1.0 CD2 B:LEU161 5.0 20.6 1.0 H42 B:IL7401 5.0 31.6 1.0 OE2 A:GLU147 5.0 31.4 1.0 O A:HOH529 5.0 29.9 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