Chlorine in PDB 8q4v: Crystal Structure of YTHDC1 in Complex with Compound 37 (ZA_356)

The structure of Crystal Structure of YTHDC1 in Complex with Compound 37 (ZA_356), PDB code: 8q4v 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)	40.51 / 1.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.8, 103.84, 41.91, 90, 104.85, 90
R / Rfree (%)	20.7 / 22.1

The binding sites of Chlorine atom in the Crystal Structure of YTHDC1 in Complex with Compound 37 (ZA_356) (pdb code 8q4v). 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 in Complex with Compound 37 (ZA_356), PDB code: 8q4v:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of YTHDC1 in Complex with Compound 37 (ZA_356)


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 37 (ZA_356) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:56.7 occ:1.00 CL01 A:JO0601 0.0 56.7 1.0 C02 A:JO0601 1.8 44.5 1.0 ND2 A:ASN364 2.6 45.2 1.0 N22 A:JO0601 2.8 44.6 1.0 N03 A:JO0601 2.8 43.0 1.0 ND2 A:ASN367 2.9 39.0 1.0 N A:ASN363 3.2 36.3 1.0 CG A:ASN364 3.3 38.1 1.0 CB A:ASN363 3.4 44.6 1.0 N A:ASN364 3.4 31.7 1.0 CA A:ASN363 3.6 39.0 1.0 OG A:SER362 3.7 35.4 1.0 C A:ASN363 3.8 36.8 1.0 OD1 A:ASN364 3.9 39.4 1.0 CD A:PRO431 3.9 60.9 1.0 O A:VAL429 3.9 54.0 1.0 CG A:PRO431 4.0 62.8 1.0 CG A:ASN367 4.0 36.8 1.0 C04 A:JO0601 4.1 38.6 1.0 CB A:ASN364 4.2 37.4 1.0 C10 A:JO0601 4.2 45.7 1.0 C A:SER362 4.3 29.4 1.0 CA A:ASN364 4.3 35.0 1.0 CB A:PRO431 4.5 62.0 1.0 CB A:ASN367 4.6 29.4 1.0 CG A:ASN363 4.6 47.1 1.0 CA A:SER362 4.6 31.1 1.0 C09 A:JO0601 4.7 43.7 1.0 O A:ASN364 4.7 30.4 1.0 N A:PRO431 4.7 62.8 1.0 O A:ASN363 4.8 37.2 1.0 CB A:SER362 4.8 31.8 1.0 OD1 A:ASN367 4.9 36.5 1.0 C A:ASN364 5.0 33.7 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of YTHDC1 in Complex with Compound 37 (ZA_356)


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 37 (ZA_356) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:50.0 occ:1.00 CL01 B:JO0601 0.0 50.0 1.0 C02 B:JO0601 1.8 35.7 1.0 N22 B:JO0601 2.8 33.9 1.0 N03 B:JO0601 2.8 38.5 1.0 ND2 B:ASN364 3.0 37.4 1.0 CG B:ASN364 3.3 34.3 1.0 N B:ASN364 3.3 29.7 1.0 N B:ASN363 3.3 29.7 1.0 ND2 B:ASN367 3.4 29.7 1.0 OG B:SER362 3.6 29.6 1.0 CB B:ASN363 3.6 37.5 1.0 CA B:ASN363 3.7 30.9 1.0 OD1 B:ASN364 3.7 32.1 1.0 C B:ASN363 3.7 30.5 1.0 CG B:PRO431 3.8 54.6 1.0 CB B:ASN364 3.9 32.9 1.0 CA B:ASN364 4.1 33.3 1.0 C04 B:JO0601 4.1 32.7 1.0 C10 B:JO0601 4.2 36.7 1.0 CG B:ASN367 4.3 27.0 1.0 C B:SER362 4.4 24.4 1.0 O B:VAL429 4.4 32.5 1.0 CD B:PRO431 4.5 51.8 1.0 CB B:ASN367 4.5 21.7 1.0 O B:ASN364 4.5 30.8 1.0 O B:ASN363 4.7 34.0 1.0 CA B:SER362 4.7 28.0 1.0 C09 B:JO0601 4.7 35.9 1.0 CB B:SER362 4.7 26.9 1.0 C B:ASN364 4.8 28.1 1.0 CG B:ASN363 4.9 37.6 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of YTHDC1 in Complex with Compound 37 (ZA_356)


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 37 (ZA_356) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:65.9 occ:1.00 CL16 B:JO0601 0.0 65.9 1.0 C15 B:JO0601 1.8 57.3 1.0 C17 B:JO0601 2.9 60.5 1.0 C14 B:JO0601 2.9 49.6 1.0 CB B:PRO431 3.5 58.6 1.0 CB B:MET434 3.7 63.9 1.0 O B:ALA432 3.9 63.8 1.0 CG B:PRO431 4.0 54.6 1.0 C18 B:JO0601 4.3 54.6 1.0 C13 B:JO0601 4.3 46.9 1.0 ND2 B:ASN363 4.6 47.6 1.0 CA B:MET434 4.8 64.8 1.0 CA B:PRO431 4.8 57.6 1.0 N B:MET434 4.8 64.7 1.0 C19 B:JO0601 4.8 50.3 1.0 CD B:PRO431 4.9 51.8 1.0 C B:PRO431 4.9 59.3 1.0

R.K.Bedi, F.Zalesak, A.Caflisch. Crystal Structure of YTHDC1 in Complex with Compound 37 (ZA_356) To Be Published.