Fluorine in PDB 8q4u: Crystal Structure of YTHDC1 in Complex with Compound 36 (ZA_540B)

The structure of Crystal Structure of YTHDC1 in Complex with Compound 36 (ZA_540B), PDB code: 8q4u 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)	38.70 / 1.37
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.1, 103.29, 42.16, 90, 105.16, 90
R / Rfree (%)	21.2 / 22.6

The structure of Crystal Structure of YTHDC1 in Complex with Compound 36 (ZA_540B) 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 36 (ZA_540B) (pdb code 8q4u). 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 36 (ZA_540B), PDB code: 8q4u:
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 36 (ZA_540B)


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 36 (ZA_540B) within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:36.7 occ:1.00 F19 A:JA0601 0.0 36.7 1.0 C18 A:JA0601 1.4 34.9 1.0 N17 A:JA0601 2.2 34.0 1.0 N20 A:JA0601 2.3 30.8 1.0 ND2 A:ASN367 3.1 35.4 1.0 N A:ASN363 3.2 32.0 1.0 OG A:SER362 3.3 29.5 1.0 ND2 A:ASN364 3.3 42.0 1.0 C16 A:JA0601 3.4 35.4 1.0 CG A:PRO431 3.5 56.0 1.0 C03 A:JA0601 3.5 32.5 1.0 CB A:ASN363 3.6 41.7 1.0 N A:ASN364 3.6 32.0 1.0 CG A:ASN364 3.7 38.3 1.0 CA A:ASN363 3.8 35.6 1.0 OD1 A:ASN364 3.8 36.5 1.0 C04 A:JA0601 4.0 32.0 1.0 CD A:PRO431 4.0 56.0 1.0 C A:ASN363 4.1 35.3 1.0 C A:SER362 4.1 29.1 1.0 CG A:ASN367 4.1 34.1 1.0 O A:VAL429 4.3 50.4 1.0 CA A:SER362 4.3 26.6 1.0 CB A:SER362 4.4 28.5 1.0 CB A:ASN367 4.5 31.9 1.0 CB A:ASN364 4.6 36.1 1.0 CA A:ASN364 4.6 32.5 1.0 CG A:ASN363 4.6 44.3 1.0 N02 A:JA0601 4.7 29.0 1.0 N07 A:JA0601 4.7 35.2 1.0 O A:ASN364 4.8 29.1 1.0 OD1 A:ASN363 4.9 45.0 1.0 CB A:PRO431 5.0 60.0 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of YTHDC1 in Complex with Compound 36 (ZA_540B)


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 36 (ZA_540B) within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:34.0 occ:1.00 F19 B:JA0601 0.0 34.0 1.0 C18 B:JA0601 1.4 28.2 1.0 N17 B:JA0601 2.2 30.1 1.0 N20 B:JA0601 2.3 32.0 1.0 ND2 B:ASN364 3.3 33.2 1.0 OG B:SER362 3.3 27.8 1.0 CG B:PRO431 3.3 41.7 1.0 ND2 B:ASN367 3.4 31.1 1.0 C16 B:JA0601 3.4 28.7 1.0 CG B:ASN364 3.5 36.5 1.0 N B:ASN363 3.5 31.6 1.0 C03 B:JA0601 3.5 26.1 1.0 OD1 B:ASN364 3.6 32.0 1.0 N B:ASN364 3.6 30.7 1.0 C04 B:JA0601 4.0 29.5 1.0 CD B:PRO431 4.1 43.1 1.0 CA B:ASN363 4.2 34.9 1.0 CG B:ASN367 4.2 31.2 1.0 CB B:ASN367 4.3 26.6 1.0 C B:ASN363 4.3 32.8 1.0 C B:SER362 4.4 25.3 1.0 CB B:ASN363 4.4 37.4 1.0 CB B:ASN364 4.4 26.6 1.0 CB B:SER362 4.4 25.9 1.0 CA B:SER362 4.4 28.0 1.0 CA B:ASN364 4.5 32.1 1.0 O B:VAL429 4.5 37.2 1.0 CB B:PRO431 4.6 49.9 1.0 O B:ASN364 4.7 30.1 1.0 N02 B:JA0601 4.7 26.6 1.0 N07 B:JA0601 4.7 32.3 1.0 OD1 B:ASN363 5.0 42.9 1.0

R.K.Bedi, F.Zalesak, A.Caflisch. Crystal Structure of YTHDC1 in Complex with Compound 36 (ZA_540B) To Be Published.