Fluorine in PDB 7y5t: Cryoem Structure of PS1-Containing Gamma-Secretase in Complex with Mrk-560

The structure of Cryoem Structure of PS1-Containing Gamma-Secretase in Complex with Mrk-560 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Cryoem Structure of PS1-Containing Gamma-Secretase in Complex with Mrk-560 (pdb code 7y5t). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Cryoem Structure of PS1-Containing Gamma-Secretase in Complex with Mrk-560, PDB code: 7y5t:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in the Cryoem Structure of PS1-Containing Gamma-Secretase in Complex with Mrk-560


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryoem Structure of PS1-Containing Gamma-Secretase in Complex with Mrk-560 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:108.6 occ:1.00 F04 B:IGD502 0.0 108.6 1.0 C22 B:IGD502 1.4 108.6 1.0 C27 B:IGD502 2.3 108.6 1.0 C20 B:IGD502 2.4 108.6 1.0 O09 B:IGD502 2.6 108.6 1.0 C14 B:IGD502 3.0 108.6 1.0 C15 B:IGD502 3.1 108.6 1.0 O B:LEU432 3.3 101.0 1.0 S02 B:IGD502 3.3 108.6 1.0 C29 B:IGD502 3.6 108.6 1.0 C23 B:IGD502 3.7 108.6 1.0 CB B:ALA431 3.8 104.4 1.0 N B:LEU432 3.9 101.0 1.0 C B:LEU432 4.0 101.0 1.0 C26 B:IGD502 4.1 108.6 1.0 CG1 B:VAL261 4.2 103.9 1.0 C B:ALA431 4.3 104.4 1.0 CG2 B:VAL272 4.3 107.4 1.0 CA B:ALA431 4.4 104.4 1.0 C24 B:IGD502 4.4 108.6 1.0 C21 B:IGD502 4.4 108.6 1.0 O10 B:IGD502 4.4 108.6 1.0 C18 B:IGD502 4.5 108.6 1.0 C16 B:IGD502 4.5 108.6 1.0 CA B:LEU432 4.6 101.0 1.0 N B:PRO433 4.8 97.3 1.0 CG2 B:VAL261 4.9 103.9 1.0 O B:ALA431 5.0 104.4 1.0

Fluorine binding site 2 out of 5 in the Cryoem Structure of PS1-Containing Gamma-Secretase in Complex with Mrk-560


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryoem Structure of PS1-Containing Gamma-Secretase in Complex with Mrk-560 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:108.6 occ:1.00 F05 B:IGD502 0.0 108.6 1.0 C26 B:IGD502 1.4 108.6 1.0 OD2 B:ASP385 2.4 85.0 1.0 C23 B:IGD502 2.4 108.6 1.0 C29 B:IGD502 2.4 108.6 1.0 CG B:ASP385 3.3 85.0 1.0 OD1 B:ASP385 3.5 85.0 1.0 C27 B:IGD502 3.6 108.6 1.0 C20 B:IGD502 3.7 108.6 1.0 N B:GLY382 3.7 87.1 1.0 CA B:GLY382 3.9 87.1 1.0 C22 B:IGD502 4.1 108.6 1.0 CB B:ALA434 4.2 91.3 1.0 CD1 B:LEU381 4.5 87.9 1.0 CB B:ASP385 4.6 85.0 1.0 C B:GLY382 4.7 87.1 1.0 O B:GLY382 4.8 87.1 1.0 C16 B:IGD502 4.8 108.6 1.0 C14 B:IGD502 4.9 108.6 1.0 C B:LEU381 4.9 87.9 1.0 N B:ALA434 4.9 91.3 1.0

Fluorine binding site 3 out of 5 in the Cryoem Structure of PS1-Containing Gamma-Secretase in Complex with Mrk-560


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryoem Structure of PS1-Containing Gamma-Secretase in Complex with Mrk-560 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:108.6 occ:1.00 F06 B:IGD502 0.0 108.6 1.0 C28 B:IGD502 1.4 108.6 1.0 F07 B:IGD502 2.2 108.6 1.0 F08 B:IGD502 2.2 108.6 1.0 S03 B:IGD502 2.6 108.6 1.0 O12 B:IGD502 2.8 108.6 1.0 O B:GLU280 3.4 108.5 1.0 O11 B:IGD502 3.4 108.6 1.0 CA B:THR281 3.8 105.8 1.0 N13 B:IGD502 3.9 108.6 1.0 CG2 B:THR281 4.1 105.8 1.0 CB B:THR281 4.2 105.8 1.0 C B:GLU280 4.3 108.5 1.0 CG B:GLN276 4.3 110.4 1.0 CB B:ALA275 4.4 110.0 1.0 N B:THR281 4.5 105.8 1.0 N B:LEU282 4.5 101.8 1.0 C B:THR281 4.6 105.8 1.0 CD2 B:LEU282 4.7 101.8 1.0 NE2 B:GLN276 4.8 110.4 1.0 C B:ALA275 4.9 110.0 1.0 N B:GLN276 4.9 110.4 1.0 O B:VAL272 5.0 107.4 1.0 C17 B:IGD502 5.0 108.6 1.0

Fluorine binding site 4 out of 5 in the Cryoem Structure of PS1-Containing Gamma-Secretase in Complex with Mrk-560


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cryoem Structure of PS1-Containing Gamma-Secretase in Complex with Mrk-560 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:108.6 occ:1.00 F07 B:IGD502 0.0 108.6 1.0 C28 B:IGD502 1.4 108.6 1.0 F06 B:IGD502 2.2 108.6 1.0 F08 B:IGD502 2.2 108.6 1.0 S03 B:IGD502 2.6 108.6 1.0 N13 B:IGD502 2.9 108.6 1.0 C18 B:IGD502 3.4 108.6 1.0 O12 B:IGD502 3.5 108.6 1.0 NE2 B:GLN276 3.5 110.4 1.0 C17 B:IGD502 3.8 108.6 1.0 O11 B:IGD502 3.8 108.6 1.0 CG1 B:VAL272 4.0 107.4 1.0 CG B:GLN276 4.2 110.4 1.0 CD B:GLN276 4.3 110.4 1.0 O B:VAL272 4.8 107.4 1.0 C15 B:IGD502 4.9 108.6 1.0 C19 B:IGD502 4.9 108.6 1.0

Fluorine binding site 5 out of 5 in the Cryoem Structure of PS1-Containing Gamma-Secretase in Complex with Mrk-560


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Cryoem Structure of PS1-Containing Gamma-Secretase in Complex with Mrk-560 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:108.6 occ:1.00 F08 B:IGD502 0.0 108.6 1.0 C28 B:IGD502 1.4 108.6 1.0 F07 B:IGD502 2.2 108.6 1.0 F06 B:IGD502 2.2 108.6 1.0 S03 B:IGD502 2.6 108.6 1.0 O11 B:IGD502 2.9 108.6 1.0 CD2 B:LEU282 3.4 101.8 1.0 N13 B:IGD502 3.5 108.6 1.0 C18 B:IGD502 3.7 108.6 1.0 O12 B:IGD502 3.8 108.6 1.0 CG1 B:VAL272 3.8 107.4 1.0 O B:VAL272 3.8 107.4 1.0 C17 B:IGD502 3.9 108.6 1.0 CB B:ALA275 4.0 110.0 1.0 CA B:VAL272 4.2 107.4 1.0 CB B:VAL272 4.4 107.4 1.0 C B:VAL272 4.5 107.4 1.0 CG B:LEU282 4.7 101.8 1.0 CG2 B:VAL272 4.8 107.4 1.0 N B:LEU282 4.8 101.8 1.0 CG B:GLN276 4.8 110.4 1.0 C15 B:IGD502 4.8 108.6 1.0 O B:GLU280 4.9 108.5 1.0 NE2 B:GLN276 4.9 110.4 1.0

X.Guo, Y.Wang, J.Zhou, C.Jin, J.Wang, B.Jia, D.Jing, C.Yan, J.Lei, R.Zhou, Y.Shi. Molecular Basis For Isoform-Selective Inhibition of Presenilin-1 By Mrk-560. Nat Commun V. 13 6299 2022.
ISSN: ESSN 2041-1723
PubMed: 36272978
DOI: 10.1038/S41467-022-33817-5