Chlorine in PDB 6yni: Crystal Structure of YTHDC1 with Compound DHU_DC1_036

The structure of Crystal Structure of YTHDC1 with Compound DHU_DC1_036, PDB code: 6yni 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)	40.30 / 1.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.250, 103.040, 42.040, 90.00, 106.55, 90.00
R / Rfree (%)	19.1 / 22.2

The binding sites of Chlorine atom in the Crystal Structure of YTHDC1 with Compound DHU_DC1_036 (pdb code 6yni). 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_036, PDB code: 6yni:
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_036


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_036 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl607 b:27.5 occ:0.48 CL1 B:P0Q607 0.0 27.5 0.5 CAL B:P0Q607 1.8 31.5 0.5 CAH B:P0Q607 2.8 26.2 0.5 CAF B:P0Q607 2.8 33.8 0.5 O B:SER435 3.2 27.4 1.0 N B:LEU439 3.7 25.8 1.0 CB B:MET438 3.8 27.7 1.0 CD2 B:LEU439 3.8 22.2 1.0 C B:MET438 3.8 24.2 1.0 CG B:LEU439 3.8 23.4 1.0 CAL B:P0Q607 3.9 31.1 0.5 CA B:LEU439 3.9 24.1 1.0 CAF B:P0Q607 4.0 35.5 0.5 O B:MET438 4.1 25.8 1.0 CB B:MET434 4.1 31.3 1.0 CAE B:P0Q607 4.1 34.0 0.5 CAM B:P0Q607 4.1 28.4 0.5 CAH B:P0Q607 4.1 27.7 0.5 C B:SER435 4.2 27.9 1.0 CD2 B:LEU430 4.3 18.3 1.0 CA B:MET438 4.3 25.0 1.0 CL1 B:P0Q607 4.3 26.6 0.5 CAE B:P0Q607 4.4 34.3 0.5 N B:SER435 4.4 34.2 1.0 CB B:LEU439 4.5 23.9 1.0 CAM B:P0Q607 4.5 28.4 0.5 CAG B:P0Q607 4.6 31.5 0.5 CAG B:P0Q607 4.6 31.5 0.5 N B:MET438 4.7 26.2 1.0 CD1 B:LEU430 4.7 22.4 1.0 CG B:MET434 4.8 36.8 1.0 CG B:MET438 4.9 27.8 1.0 OAK B:P0Q607 4.9 24.2 0.5 SD B:MET438 5.0 38.7 1.0 CG B:LEU430 5.0 17.8 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of YTHDC1 with Compound DHU_DC1_036


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_036 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl607 b:26.6 occ:0.52 CL1 B:P0Q607 0.0 26.6 0.5 CAL B:P0Q607 1.8 31.1 0.5 O B:HOH771 2.4 36.1 1.0 CAF B:P0Q607 2.8 35.5 0.5 CAH B:P0Q607 2.8 27.7 0.5 O B:HOH811 3.4 23.9 1.0 O B:MET438 3.6 25.8 1.0 CAF B:P0Q607 3.6 33.8 0.5 CAL B:P0Q607 3.7 31.5 0.5 CAE B:P0Q607 3.9 34.0 0.5 O B:THR379 4.0 18.8 1.0 O B:HOH830 4.0 27.7 1.0 N B:GLY440 4.0 22.8 1.0 CAE B:P0Q607 4.0 34.3 0.5 CAM B:P0Q607 4.1 28.4 0.5 CD2 B:LEU380 4.1 36.0 1.0 CAH B:P0Q607 4.1 26.2 0.5 CD B:PRO381 4.2 20.7 1.0 CAG B:P0Q607 4.3 31.5 0.5 CL1 B:P0Q607 4.3 27.5 0.5 CA B:LEU439 4.4 24.1 1.0 CAM B:P0Q607 4.4 28.4 0.5 CA B:LEU380 4.4 22.4 1.0 C B:MET438 4.5 24.2 1.0 C B:LEU439 4.5 25.1 1.0 CAG B:P0Q607 4.6 31.5 0.5 C B:THR379 4.7 18.6 1.0 CG B:PRO381 4.8 25.1 1.0 N B:LEU439 4.9 25.8 1.0 CA B:GLY440 4.9 22.2 1.0 N B:LEU380 4.9 21.4 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of YTHDC1 with Compound DHU_DC1_036


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_036 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl608 b:27.0 occ:1.00 CL1 B:P0Q608 0.0 27.0 1.0 CAL B:P0Q608 1.8 25.8 1.0 CAF B:P0Q608 2.8 26.1 1.0 CAH B:P0Q608 2.8 31.5 1.0 O B:HOH781 3.4 21.2 1.0 CE1 A:HIS468 3.8 23.0 1.0 CZ3 A:TRP465 3.9 20.6 1.0 CB A:PRO464 3.9 18.2 1.0 CAE B:P0Q608 4.1 22.9 1.0 CAM B:P0Q608 4.1 33.6 1.0 O A:PRO464 4.4 17.3 1.0 NE2 A:HIS468 4.4 25.7 1.0 CE3 A:TRP465 4.5 19.2 1.0 CAG B:P0Q608 4.6 29.7 1.0 O B:HIS427 4.6 19.9 1.0 CH2 A:TRP465 4.6 23.0 1.0 CA A:PRO464 4.7 16.5 1.0 CG2 B:VAL429 4.7 21.9 1.0 C A:PRO464 4.8 17.0 1.0 ND1 A:HIS468 4.8 22.6 1.0 O B:HOH841 4.9 23.1 1.0

R.K.Bedi, D.Huang, L.Wiedmer, A.Caflisch. Crystal Structure of YTHDC1 with Compound DHU_DC1_036 To Be Published.