Fluorine in PDB 6ynn: Crystal Structure of YTHDC1 with Compound DHU_DC1_135

The structure of Crystal Structure of YTHDC1 with Compound DHU_DC1_135, PDB code: 6ynn was solved by R.K.Bedi, D.Huang, L.Wiedmer, A.Caflisch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.73 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.800, 103.810, 42.060, 90.00, 104.47, 90.00
R / Rfree (%)	19.3 / 21.4

The structure of Crystal Structure of YTHDC1 with Compound DHU_DC1_135 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of YTHDC1 with Compound DHU_DC1_135 (pdb code 6ynn). 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 with Compound DHU_DC1_135, PDB code: 6ynn:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of YTHDC1 with Compound DHU_DC1_135


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 with Compound DHU_DC1_135 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:25.4 occ:1.00 FAD A:P0B601 0.0 25.4 1.0 CAN A:P0B601 1.3 27.7 1.0 CAQ A:P0B601 2.3 26.6 1.0 CAG A:P0B601 2.4 28.5 1.0 CAK A:P0B601 2.8 28.8 1.0 OD1 A:ASN363 3.1 20.9 1.0 ND2 A:ASN363 3.1 29.4 1.0 CG A:ASN363 3.3 27.0 1.0 ND2 A:ASN367 3.3 21.8 1.0 CAJ A:P0B601 3.5 20.7 1.0 CD A:PRO431 3.5 33.5 1.0 O A:VAL429 3.6 31.5 1.0 CAO A:P0B601 3.6 26.4 1.0 CAF A:P0B601 3.6 33.5 1.0 NAT A:P0B601 3.7 26.5 1.0 CAI A:P0B601 3.9 19.7 1.0 CD2 A:LEU430 3.9 32.0 1.0 CA A:LEU430 3.9 31.8 1.0 CAP A:P0B601 4.0 18.1 1.0 CAH A:P0B601 4.1 29.2 1.0 CG A:PRO431 4.2 32.7 1.0 C A:VAL429 4.4 30.7 1.0 N A:PRO431 4.4 34.6 1.0 CB A:ASN363 4.5 22.2 1.0 CG A:ASN367 4.5 17.6 1.0 N A:LEU430 4.6 30.1 1.0 C A:LEU430 4.7 35.3 1.0 CB A:LEU430 4.7 32.0 1.0 CAA A:P0B601 4.7 26.9 1.0 SD A:MET434 4.8 38.5 1.0 CG A:LEU430 4.9 31.9 1.0 CAR A:P0B601 5.0 20.4 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of YTHDC1 with Compound DHU_DC1_135


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 with Compound DHU_DC1_135 within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:19.0 occ:1.00 FAD B:P0B601 0.0 19.0 1.0 CAN B:P0B601 1.3 16.9 1.0 CAQ B:P0B601 2.4 17.5 1.0 CAG B:P0B601 2.4 22.5 1.0 CAK B:P0B601 2.9 21.9 1.0 OD1 B:ASN363 3.0 13.8 1.0 CG B:ASN363 3.3 13.7 1.0 CAJ B:P0B601 3.4 15.8 1.0 CD B:PRO431 3.4 19.3 1.0 ND2 B:ASN363 3.5 15.8 1.0 CD2 B:LEU430 3.5 23.6 1.0 ND2 B:ASN367 3.6 12.5 1.0 CAF B:P0B601 3.6 20.9 1.0 CAO B:P0B601 3.6 22.4 1.0 NAT B:P0B601 3.7 18.7 1.0 O B:VAL429 3.9 14.9 1.0 CAI B:P0B601 3.9 13.9 1.0 CA B:LEU430 4.0 17.8 1.0 CAP B:P0B601 4.0 12.3 1.0 CAH B:P0B601 4.1 20.7 1.0 CG B:PRO431 4.3 23.5 1.0 CB B:ASN363 4.3 13.8 1.0 N B:PRO431 4.4 20.9 1.0 CB B:LEU430 4.6 19.9 1.0 SD B:MET434 4.6 29.5 1.0 C B:VAL429 4.6 16.1 1.0 CG B:LEU430 4.7 20.7 1.0 C B:LEU430 4.7 19.5 1.0 CAA B:P0B601 4.7 23.0 1.0 N B:LEU430 4.7 18.2 1.0 CG B:ASN367 4.8 11.8 1.0 O B:HOH910 5.0 34.0 1.0

R.K.Bedi, D.Huang, L.Wiedmer, A.Caflisch. Crystal Structure of YTHDC1 with Compound DHU_DC1_135 To Be Published.