Fluorine in PDB 8k2e: Crystal Structure of YTHDC1 and Y3 Complex

The structure of Crystal Structure of YTHDC1 and Y3 Complex, PDB code: 8k2e was solved by H.L.Zhang, S.Y.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.71 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.644, 103.515, 41.815, 90, 102.43, 90
R / Rfree (%)	18.6 / 22.4

The structure of Crystal Structure of YTHDC1 and Y3 Complex also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of YTHDC1 and Y3 Complex (pdb code 8k2e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of YTHDC1 and Y3 Complex, PDB code: 8k2e:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of YTHDC1 and Y3 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of YTHDC1 and Y3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:53.1 occ:1.00 F14 B:VIM601 0.0 53.1 1.0 C11 B:VIM601 1.4 48.4 1.0 C12 B:VIM601 2.4 42.8 1.0 C10 B:VIM601 2.4 45.0 1.0 H121 B:VIM601 2.6 51.3 1.0 H101 B:VIM601 2.6 53.9 1.0 CB B:MET438 3.4 34.9 1.0 C13 B:VIM601 3.7 40.8 1.0 C9 B:VIM601 3.7 44.5 1.0 CD2 B:LEU439 3.7 26.4 1.0 CG B:LEU439 3.7 28.8 1.0 CD2 B:LEU380 3.8 34.1 1.0 O B:SER435 3.9 42.7 1.0 CE B:MET438 3.9 53.1 1.0 CB B:MET434 3.9 37.2 1.0 SD B:MET434 4.0 65.3 1.0 CG B:MET434 4.1 42.0 1.0 N B:LEU439 4.1 40.2 1.0 C B:MET438 4.1 46.1 1.0 C8 B:VIM601 4.1 37.3 1.0 CA B:MET438 4.3 41.0 1.0 SD B:MET438 4.3 59.8 1.0 CG B:MET438 4.3 33.1 1.0 H131 B:VIM601 4.4 48.8 1.0 H091 B:VIM601 4.4 53.2 1.0 N B:SER435 4.6 31.6 1.0 O B:MET438 4.6 36.6 1.0 CA B:LEU439 4.6 35.9 1.0 CB B:LEU439 4.7 34.5 1.0 CE B:MET434 4.7 45.8 1.0 CD1 B:LEU439 4.7 27.0 1.0 C B:SER435 4.8 36.7 1.0 N B:MET438 4.8 36.4 1.0 CA B:MET434 4.8 36.0 1.0 CG B:LEU380 4.9 30.9 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of YTHDC1 and Y3 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of YTHDC1 and Y3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:57.0 occ:1.00 F14 A:VIM601 0.0 57.0 1.0 C11 A:VIM601 1.4 51.5 1.0 C12 A:VIM601 2.4 60.2 1.0 C10 A:VIM601 2.4 48.0 1.0 H121 A:VIM601 2.6 72.1 1.0 H101 A:VIM601 2.6 57.5 1.0 O A:SER435 3.3 41.5 1.0 CB A:MET434 3.5 51.0 1.0 CB A:MET438 3.7 37.6 1.0 C9 A:VIM601 3.7 46.1 1.0 C13 A:VIM601 3.7 37.1 1.0 N A:SER435 3.8 44.6 1.0 C A:SER435 4.0 47.0 1.0 SD A:MET434 4.0 82.8 1.0 CD2 A:LEU439 4.1 21.4 1.0 CG A:LEU439 4.1 29.8 1.0 C8 A:VIM601 4.2 30.4 1.0 CA A:MET434 4.3 45.6 1.0 SD A:MET438 4.3 61.2 1.0 CG A:MET434 4.3 47.2 1.0 C A:MET434 4.4 41.6 1.0 H091 A:VIM601 4.4 55.2 1.0 H131 A:VIM601 4.4 44.4 1.0 CD2 A:LEU380 4.5 27.9 1.0 CG A:MET438 4.5 54.0 1.0 CA A:SER435 4.6 48.3 1.0 N A:LEU439 4.6 30.2 1.0 CA A:MET438 4.7 27.0 1.0 C A:MET438 4.7 36.9 1.0 CD2 A:LEU430 4.8 48.2 1.0 N A:ALA436 4.8 38.1 1.0 CD1 A:LEU439 4.9 28.0 1.0 N A:MET438 5.0 40.3 1.0

Y.Jiang, G.Zhang, J.You, H.Zhang, R.Yao, H.Xie, L.Zhang, Z.Xia, M.Dai, Y.Wu, L.Li, S.Yang. Pocketflow Is A Data-and-Knowledge-Driven Structure-Based Molecular Generative Model Nat. Mach. Intell. V. 6 326 2024.
DOI: 10.1038/S42256-024-00808-8