Chlorine in PDB 6ynj: Crystal Structure of YTHDC1 with Compound DHU_DC1_046

The structure of Crystal Structure of YTHDC1 with Compound DHU_DC1_046, PDB code: 6ynj 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)	40.81 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.830, 103.990, 42.360, 90.00, 105.53, 90.00
R / Rfree (%)	17 / 19.9

The binding sites of Chlorine atom in the Crystal Structure of YTHDC1 with Compound DHU_DC1_046 (pdb code 6ynj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of YTHDC1 with Compound DHU_DC1_046, PDB code: 6ynj:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of YTHDC1 with Compound DHU_DC1_046


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_046 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:89.6 occ:1.00 CL1 A:P0N601 0.0 89.6 1.0 C12 A:P0N601 1.8 51.3 1.0 C11 A:P0N601 2.8 41.1 1.0 C07 A:P0N601 2.8 44.8 1.0 C06 A:P0N601 3.1 43.1 1.0 C05 A:P0N601 3.3 35.5 1.0 CG A:PRO431 3.7 52.6 1.0 C10 A:P0N601 4.1 43.4 1.0 C08 A:P0N601 4.1 49.6 1.0 CD A:PRO431 4.2 49.9 1.0 O3 A:SO4605 4.2 46.3 1.0 CD1 A:LEU380 4.3 30.9 1.0 O14 A:P0N601 4.5 39.7 1.0 N04 A:P0N601 4.5 33.6 1.0 C09 A:P0N601 4.6 51.5 1.0 CG A:LEU380 4.7 38.1 1.0 O2 A:SO4605 4.9 48.4 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of YTHDC1 with Compound DHU_DC1_046


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_046 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl602 b:38.4 occ:1.00 CL1 A:P0N602 0.0 38.4 1.0 C12 A:P0N602 1.8 31.8 1.0 C11 A:P0N602 2.7 24.9 1.0 C07 A:P0N602 2.8 29.0 1.0 C06 A:P0N602 3.1 28.9 1.0 O B:HOH946 3.4 26.5 1.0 CA B:HIS427 3.5 25.7 1.0 CB B:HIS427 3.7 25.8 1.0 C B:HIS427 3.9 16.9 1.0 O A:HOH871 4.0 39.0 1.0 CG B:HIS427 4.1 31.1 1.0 C10 A:P0N602 4.1 28.5 1.0 C08 A:P0N602 4.1 24.7 1.0 O B:TRP428 4.1 20.1 1.0 C05 A:P0N602 4.1 30.8 1.0 CD2 B:HIS427 4.1 34.2 1.0 O14 A:P0N602 4.2 34.1 1.0 O B:HIS427 4.3 20.3 1.0 N B:TRP428 4.5 19.9 1.0 C09 A:P0N602 4.6 22.9 1.0 O B:ILE426 4.7 25.7 1.0 N B:HIS427 4.7 26.6 1.0 O B:HOH960 5.0 24.5 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of YTHDC1 with Compound DHU_DC1_046


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of YTHDC1 with Compound DHU_DC1_046 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl701 b:46.5 occ:1.00 CL1 B:P0N701 0.0 46.5 1.0 C12 B:P0N701 1.8 36.2 1.0 C11 B:P0N701 2.8 33.7 1.0 O B:HOH983 2.8 43.3 1.0 C07 B:P0N701 2.8 34.6 1.0 C06 B:P0N701 3.1 31.3 1.0 C05 B:P0N701 3.4 32.3 1.0 CG B:PRO431 3.8 31.8 1.0 CD1 B:LEU380 4.1 36.6 1.0 C10 B:P0N701 4.1 38.0 1.0 C08 B:P0N701 4.1 39.0 1.0 O14 B:P0N701 4.4 30.0 1.0 O3 B:SO4703 4.5 45.0 1.0 O B:HOH892 4.5 33.3 1.0 CD B:PRO431 4.6 29.8 1.0 O B:HOH958 4.6 34.3 1.0 C09 B:P0N701 4.6 43.3 1.0 N04 B:P0N701 4.6 29.6 1.0 O B:HOH810 4.6 35.7 1.0 CG B:LEU380 4.7 29.8 1.0 O2 B:SO4703 4.7 41.5 1.0 CB B:PRO431 4.9 36.1 1.0

R.K.Bedi, D.Huang, L.Wiedmer, A.Caflisch. Crystal Structure of YTHDC1 with Compound DHU_DC1_046 To Be Published.