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

Enzymatic activity of Halotag with Traq-G Ligand

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

Protein crystallography data

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

Other elements in 7zbd:

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

Chlorine (Cl) 2 atoms

Silicon Binding Sites:

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 7zbd

Go back to Silicon Binding Sites List in 7zbd
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 7zbd

Go back to Silicon Binding Sites List in 7zbd
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

Reference:

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
Page generated: Fri Apr 7 20:00:15 2023

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