Chlorine in PDB 8q4w: Crystal Structure of YTHDC1 in Complex with Compound 40 (CS_3A)

The structure of Crystal Structure of YTHDC1 in Complex with Compound 40 (CS_3A), PDB code: 8q4w 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)	38.58 / 1.61
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.84, 103.97, 42.07, 90, 104.42, 90
R / Rfree (%)	20.6 / 23.8

The binding sites of Chlorine atom in the Crystal Structure of YTHDC1 in Complex with Compound 40 (CS_3A) (pdb code 8q4w). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of YTHDC1 in Complex with Compound 40 (CS_3A), PDB code: 8q4w:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of YTHDC1 in Complex with Compound 40 (CS_3A)


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 in Complex with Compound 40 (CS_3A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:42.3 occ:1.00 CL06 A:JNC601 0.0 42.3 1.0 C05 A:JNC601 1.8 36.5 1.0 N07 A:JNC601 2.7 35.3 1.0 N04 A:JNC601 2.8 34.4 1.0 ND2 A:ASN364 3.0 46.7 1.0 CG A:PRO431 3.3 57.0 1.0 ND2 A:ASN367 3.3 38.2 1.0 CG A:ASN364 3.3 42.4 1.0 N A:ASN363 3.3 34.3 1.0 N A:ASN364 3.4 35.0 1.0 OG A:SER362 3.5 34.5 1.0 OD1 A:ASN364 3.6 41.2 1.0 CB A:ASN363 3.6 39.8 1.0 CA A:ASN363 3.8 37.3 1.0 C A:ASN363 3.8 37.2 1.0 CD A:PRO431 3.8 55.6 1.0 C08 A:JNC601 4.0 35.7 1.0 C03 A:JNC601 4.0 33.9 1.0 O A:VAL429 4.1 54.0 1.0 CB A:ASN364 4.1 40.6 1.0 CG A:ASN367 4.2 40.6 1.0 CA A:ASN364 4.3 37.3 1.0 C A:SER362 4.3 34.1 1.0 CB A:PRO431 4.5 60.5 1.0 CB A:ASN367 4.5 32.5 1.0 C20 A:JNC601 4.6 34.4 1.0 O A:ASN364 4.6 33.2 1.0 CG A:ASN363 4.7 43.7 1.0 CA A:SER362 4.7 30.9 1.0 CB A:SER362 4.7 33.8 1.0 N A:PRO431 4.8 61.4 1.0 O A:ASN363 4.8 40.2 1.0 C A:ASN364 4.9 38.0 1.0 OD1 A:ASN363 5.0 46.3 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of YTHDC1 in Complex with Compound 40 (CS_3A)


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 in Complex with Compound 40 (CS_3A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:63.5 occ:1.00 CL14 A:JNC601 0.0 63.5 1.0 C13 A:JNC601 1.8 53.8 1.0 C12 A:JNC601 2.8 47.7 1.0 C15 A:JNC601 2.8 50.0 1.0 O A:ALA432 3.2 70.2 1.0 CB A:MET434 3.7 67.5 1.0 CB A:PRO431 3.9 60.5 1.0 ND2 A:ASN363 3.9 46.1 1.0 C16 A:JNC601 4.1 48.4 1.0 C11 A:JNC601 4.2 44.8 1.0 CG A:PRO431 4.2 57.0 1.0 C A:ALA432 4.4 68.2 1.0 N A:MET434 4.5 69.2 1.0 CA A:MET434 4.6 70.6 1.0 C A:GLY433 4.6 70.5 1.0 CG A:ASN363 4.6 43.7 1.0 C17 A:JNC601 4.7 44.8 1.0 O A:GLY433 4.8 72.0 1.0 C A:PRO431 4.8 65.6 1.0 CD A:PRO431 4.9 55.6 1.0 N A:ALA432 4.9 68.7 1.0 OD1 A:ASN363 5.0 46.3 1.0 CA A:PRO431 5.0 63.5 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of YTHDC1 in Complex with Compound 40 (CS_3A)


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 in Complex with Compound 40 (CS_3A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:34.5 occ:1.00 CL06 B:JNC601 0.0 34.5 1.0 C05 B:JNC601 1.8 30.1 1.0 N07 B:JNC601 2.6 30.2 1.0 N04 B:JNC601 2.7 29.5 1.0 ND2 B:ASN367 3.2 31.1 1.0 ND2 B:ASN364 3.2 34.8 1.0 CG B:ASN364 3.3 36.6 1.0 OD1 B:ASN364 3.4 36.1 1.0 N B:ASN364 3.4 30.6 1.0 N B:ASN363 3.5 32.4 1.0 OG B:SER362 3.6 30.6 1.0 CG B:PRO431 3.8 47.0 1.0 CD B:PRO431 3.9 43.1 1.0 CB B:ASN363 3.9 36.5 1.0 CA B:ASN363 3.9 34.6 1.0 C08 B:JNC601 3.9 29.3 1.0 C B:ASN363 4.0 32.8 1.0 C03 B:JNC601 4.0 27.0 1.0 CG B:ASN367 4.1 32.1 1.0 O B:VAL429 4.1 34.0 1.0 CB B:ASN364 4.2 31.5 1.0 CA B:ASN364 4.3 31.6 1.0 CB B:ASN367 4.4 28.0 1.0 CB B:PRO431 4.4 50.2 1.0 C B:SER362 4.4 29.6 1.0 C20 B:JNC601 4.5 32.5 1.0 O B:ASN364 4.7 33.2 1.0 CA B:SER362 4.7 29.2 1.0 CB B:SER362 4.7 29.4 1.0 N B:PRO431 4.9 44.1 1.0 CE B:MET434 4.9 45.9 1.0 C B:ASN364 4.9 31.5 1.0 O B:ASN363 4.9 36.5 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of YTHDC1 in Complex with Compound 40 (CS_3A)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of YTHDC1 in Complex with Compound 40 (CS_3A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:49.8 occ:1.00 CL14 B:JNC601 0.0 49.8 1.0 C13 B:JNC601 1.8 49.4 1.0 C15 B:JNC601 2.8 47.1 1.0 C12 B:JNC601 2.8 42.4 1.0 CE B:MET434 3.8 45.9 1.0 CG B:PRO431 4.0 47.0 1.0 O B:GLY433 4.0 63.5 1.0 O B:ALA432 4.1 63.6 1.0 C B:GLY433 4.1 63.3 1.0 C16 B:JNC601 4.1 40.9 1.0 C11 B:JNC601 4.1 40.5 1.0 CB B:MET434 4.2 56.9 1.0 ND2 B:ASN363 4.2 44.0 1.0 CA B:GLY433 4.5 63.2 1.0 SD B:MET434 4.5 58.4 1.0 N B:MET434 4.6 60.8 1.0 C17 B:JNC601 4.6 45.0 1.0 CB B:PRO431 4.6 50.2 1.0 C B:ALA432 4.7 59.1 1.0 O B:PRO431 4.8 52.1 1.0 CA B:MET434 4.8 58.9 1.0 N B:GLY433 4.9 61.2 1.0 CG B:ASN363 4.9 36.4 1.0

R.K.Bedi, F.Zalesak, A.Caflisch. Crystal Structure of YTHDC1 in Complex with Compound 40 (CS_3A) To Be Published.