Fluorine in PDB 8q33: Crystal Structure of YTHDC1 in Complex with Compound 15 (ZA_343)

The structure of Crystal Structure of YTHDC1 in Complex with Compound 15 (ZA_343), PDB code: 8q33 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)	40.75 / 1.43
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.17, 103.47, 42.12, 90, 104.66, 90
R / Rfree (%)	20.6 / 22.9

The structure of Crystal Structure of YTHDC1 in Complex with Compound 15 (ZA_343) 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 15 (ZA_343) (pdb code 8q33). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of YTHDC1 in Complex with Compound 15 (ZA_343), PDB code: 8q33:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of YTHDC1 in Complex with Compound 15 (ZA_343)


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 15 (ZA_343) within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:54.2 occ:1.00 F20 B:IWV601 0.0 54.2 1.0 C19 B:IWV601 1.4 48.5 1.0 F22 B:IWV601 2.2 55.7 1.0 F21 B:IWV601 2.2 46.4 1.0 C18 B:IWV601 2.4 51.1 1.0 O B:HOH716 2.5 39.9 1.0 N17 B:IWV601 2.8 50.9 1.0 CB B:ASP476 3.2 27.2 1.0 N B:ASP476 3.3 28.3 1.0 O23 B:IWV601 3.4 51.4 1.0 O B:HOH756 3.5 42.6 1.0 CA B:ASP476 3.8 27.4 1.0 CB B:ARG475 3.9 35.2 1.0 O B:ASP476 4.0 27.9 1.0 C16 B:IWV601 4.3 47.3 1.0 C B:ARG475 4.3 27.2 1.0 C B:ASP476 4.4 27.9 1.0 CA B:ARG475 4.4 31.2 1.0 CG B:ASP476 4.5 31.0 1.0 OD2 B:ASP476 4.7 33.1 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of YTHDC1 in Complex with Compound 15 (ZA_343)


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 15 (ZA_343) within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:46.4 occ:1.00 F21 B:IWV601 0.0 46.4 1.0 C19 B:IWV601 1.4 48.5 1.0 F22 B:IWV601 2.2 55.7 1.0 F20 B:IWV601 2.2 54.2 1.0 C18 B:IWV601 2.4 51.1 1.0 O23 B:IWV601 2.6 51.4 1.0 N B:ASP476 2.8 28.3 1.0 O B:HOH715 3.4 45.9 1.0 CB B:ASP476 3.5 27.2 1.0 CA B:ARG475 3.5 31.2 1.0 C B:ARG475 3.6 27.2 1.0 CB B:ARG475 3.7 35.2 1.0 N17 B:IWV601 3.7 50.9 1.0 CA B:ASP476 3.7 27.4 1.0 CB B:LYS361 4.2 27.3 1.0 O B:HOH716 4.3 39.9 1.0 CG B:LYS361 4.5 31.9 1.0 O B:ARG475 4.8 25.5 1.0 C B:ASP476 4.8 27.9 1.0 N B:ARG475 4.9 29.0 1.0 O B:ASP476 4.9 27.9 1.0 CG B:ASP476 4.9 31.0 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of YTHDC1 in Complex with Compound 15 (ZA_343)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of YTHDC1 in Complex with Compound 15 (ZA_343) within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:55.7 occ:1.00 F22 B:IWV601 0.0 55.7 1.0 C19 B:IWV601 1.4 48.5 1.0 F20 B:IWV601 2.2 54.2 1.0 F21 B:IWV601 2.2 46.4 1.0 C18 B:IWV601 2.4 51.1 1.0 N17 B:IWV601 3.1 50.9 1.0 O23 B:IWV601 3.2 51.4 1.0 O B:HOH715 4.2 45.9 1.0 O B:HOH716 4.4 39.9 1.0 CB B:ARG475 4.4 35.2 1.0 C16 B:IWV601 4.5 47.3 1.0 N B:ASP476 4.6 28.3 1.0 CA B:ARG475 4.9 31.2 1.0 CB B:ASP476 5.0 27.2 1.0

R.K.Bedi, F.Zalesak, A.Caflisch. Crystal Structure of YTHDC1 in Complex with Compound 15 (ZA_343) To Be Published.