Chlorine 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:

Fluorine

(F)

2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of YTHDC1 with Compound DHU_DC1_135, PDB code: 6ynn:
Jump to Chlorine binding site number: 1; 2;

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl601 b:32.1 occ:1.00 CL1 A:P0B601 0.0 32.1 1.0 CAO A:P0B601 1.8 26.4 1.0 CAQ A:P0B601 2.8 26.6 1.0 CAH A:P0B601 2.8 29.2 1.0 CAK A:P0B601 3.1 28.8 1.0 NAT A:P0B601 3.3 26.5 1.0 CD2 A:LEU439 3.3 35.8 1.0 C A:THR379 3.3 18.7 1.0 CA A:THR379 3.5 17.7 1.0 N A:LEU380 3.5 19.9 1.0 NAL A:P0B601 3.5 18.6 1.0 O A:SER378 3.7 14.4 1.0 O A:THR379 3.8 19.2 1.0 CAS A:P0B601 3.9 20.4 1.0 CAP A:P0B601 3.9 18.1 1.0 N A:THR379 4.0 15.7 1.0 CAN A:P0B601 4.0 27.7 1.0 CAF A:P0B601 4.1 33.5 1.0 C A:SER378 4.1 14.4 1.0 CG A:LEU380 4.1 25.2 1.0 CD2 A:LEU380 4.2 27.7 1.0 OAC A:P0B601 4.2 24.2 1.0 CAA A:P0B601 4.3 26.9 1.0 CAJ A:P0B601 4.3 20.7 1.0 CA A:LEU380 4.3 19.3 1.0 O A:HOH809 4.5 21.8 1.0 NAM A:P0B601 4.6 18.6 1.0 CG A:LEU439 4.6 34.5 1.0 CAG A:P0B601 4.6 28.5 1.0 CAI A:P0B601 4.6 19.7 1.0 CB A:LEU380 4.8 20.6 1.0 CB A:THR379 4.8 18.4 1.0 CAR A:P0B601 4.9 20.4 1.0 CD1 A:LEU439 4.9 30.5 1.0 CB A:LEU439 5.0 29.3 1.0 SD A:MET434 5.0 38.5 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl601 b:31.7 occ:1.00 CL1 B:P0B601 0.0 31.7 1.0 CAO B:P0B601 1.8 22.4 1.0 CAQ B:P0B601 2.7 17.5 1.0 CAH B:P0B601 2.8 20.7 1.0 CAK B:P0B601 3.1 21.9 1.0 NAT B:P0B601 3.3 18.7 1.0 C B:THR379 3.3 14.8 1.0 O B:SER378 3.3 12.5 1.0 CA B:THR379 3.4 13.2 1.0 CD2 B:LEU439 3.4 31.2 1.0 O B:THR379 3.5 17.1 1.0 C B:SER378 3.6 13.2 1.0 NAL B:P0B601 3.6 14.3 1.0 N B:THR379 3.6 13.5 1.0 N B:LEU380 3.7 15.8 1.0 CAP B:P0B601 4.0 12.3 1.0 CAN B:P0B601 4.0 16.9 1.0 CAF B:P0B601 4.1 20.9 1.0 CAS B:P0B601 4.1 15.1 1.0 CAJ B:P0B601 4.2 15.8 1.0 CAA B:P0B601 4.3 23.0 1.0 OG B:SER378 4.3 14.6 0.3 CB B:SER378 4.4 13.8 0.7 CB B:SER378 4.4 13.9 0.3 CG B:LEU439 4.4 30.6 1.0 OAC B:P0B601 4.4 16.6 1.0 CD2 B:LEU380 4.5 25.6 1.0 CAG B:P0B601 4.6 22.5 1.0 CA B:LEU380 4.6 17.4 1.0 CD1 B:LEU439 4.6 27.7 1.0 CA B:SER378 4.7 11.0 0.7 CA B:SER378 4.7 11.1 0.3 CG B:LEU380 4.7 21.5 1.0 CAI B:P0B601 4.7 13.9 1.0 CB B:LEU439 4.7 23.0 1.0 NAM B:P0B601 4.8 13.0 1.0 CB B:THR379 4.8 13.8 1.0 CA B:LEU439 4.9 24.9 1.0 CE B:MET434 4.9 29.0 1.0

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