Fluorine in PDB 8q35: Crystal Structure of YTHDC1 in Complex with Compound 16 (ZA_354)

The structure of Crystal Structure of YTHDC1 in Complex with Compound 16 (ZA_354), PDB code: 8q35 was solved by R.K.Bedi, F.Zalesak, A.Caflisch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.68 / 1.31
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.96, 103.53, 42.06, 90, 104.52, 90
R / Rfree (%)	21.1 / 22.9

The structure of Crystal Structure of YTHDC1 in Complex with Compound 16 (ZA_354) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of YTHDC1 in Complex with Compound 16 (ZA_354) (pdb code 8q35). 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 in Complex with Compound 16 (ZA_354), PDB code: 8q35:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of YTHDC1 in Complex with Compound 16 (ZA_354)


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 in Complex with Compound 16 (ZA_354) within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:49.9 occ:1.00 F14 B:IWM601 0.0 49.9 1.0 C13 B:IWM601 1.4 48.1 1.0 NH2 B:ARG404 2.2 46.1 1.0 F15 B:IWM601 2.2 49.0 1.0 C12 B:IWM601 2.4 50.5 1.0 O2 B:SO4604 2.8 42.0 1.0 O3 B:SO4604 2.8 57.6 1.0 C10 B:IWM601 2.9 38.5 1.0 C11 B:IWM601 3.0 43.7 1.0 O B:HOH702 3.2 50.4 1.0 CZ B:ARG404 3.3 42.7 1.0 S B:SO4604 3.4 60.8 1.0 C16 B:IWM601 3.6 52.5 1.0 CB B:ASP476 3.8 22.6 1.0 NE B:ARG404 3.9 44.3 1.0 N09 B:IWM601 4.2 35.0 1.0 NH1 B:ARG404 4.3 48.7 1.0 O B:HOH728 4.4 40.1 1.0 O4 B:SO4604 4.4 50.6 1.0 O1 B:SO4604 4.4 53.7 1.0 CG B:ASP476 4.4 29.2 1.0 C19 B:IWM601 4.4 45.3 1.0 OD2 B:ASP476 4.5 32.2 1.0 OD1 B:ASN363 4.5 41.0 1.0 O B:LYS361 4.6 34.0 1.0 C20 B:IWM601 4.7 34.8 1.0 C17 B:IWM601 4.9 56.7 1.0 N B:ASP476 5.0 25.2 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of YTHDC1 in Complex with Compound 16 (ZA_354)


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 in Complex with Compound 16 (ZA_354) within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:49.0 occ:1.00 F15 B:IWM601 0.0 49.0 1.0 C13 B:IWM601 1.4 48.1 1.0 F14 B:IWM601 2.2 49.9 1.0 C12 B:IWM601 2.3 50.5 1.0 O B:HOH728 2.4 40.1 1.0 OD2 B:ASP476 2.9 32.2 1.0 C11 B:IWM601 3.1 43.7 1.0 C10 B:IWM601 3.1 38.5 1.0 CB B:ASP476 3.3 22.6 1.0 O B:HOH702 3.4 50.4 1.0 CG B:ASP476 3.4 29.2 1.0 C16 B:IWM601 3.5 52.5 1.0 C20 B:IWM601 3.6 34.8 1.0 N09 B:IWM601 3.7 35.0 1.0 O2 B:SO4604 3.9 42.0 1.0 CD1 B:LEU380 4.0 42.4 1.0 NH2 B:ARG404 4.2 46.1 1.0 O B:HOH750 4.2 37.1 1.0 CD2 B:LEU380 4.4 45.0 1.0 C19 B:IWM601 4.5 45.3 1.0 O3 B:SO4604 4.5 57.6 1.0 OD1 B:ASP476 4.6 24.2 1.0 CG B:LEU380 4.8 41.2 1.0 CA B:ASP476 4.8 23.6 1.0 S B:SO4604 4.8 60.8 1.0 C17 B:IWM601 4.8 56.7 1.0 N21 B:IWM601 4.9 29.0 1.0 ND2 B:ASN383 5.0 28.1 1.0 O B:LYS361 5.0 34.0 1.0

R.K.Bedi, F.Zalesak, A.Caflisch. Crystal Structure of YTHDC1 in Complex with Compound 16 (ZA_354) To Be Published.