Chlorine in PDB 8q39: Crystal Structure of YTHDC1 in Complex with Compound 21 (ZA_515)

The structure of Crystal Structure of YTHDC1 in Complex with Compound 21 (ZA_515), PDB code: 8q39 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)	37.83 / 1.42
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.11, 103.84, 41.93, 90, 104.36, 90
R / Rfree (%)	22.7 / 25

The binding sites of Chlorine atom in the Crystal Structure of YTHDC1 in Complex with Compound 21 (ZA_515) (pdb code 8q39). 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 in Complex with Compound 21 (ZA_515), PDB code: 8q39:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of YTHDC1 in Complex with Compound 21 (ZA_515)


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 21 (ZA_515) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:56.0 occ:1.00 CL23 A:K1O601 0.0 56.0 1.0 C22 A:K1O601 1.8 42.1 1.0 ND2 A:ASN364 2.6 46.7 1.0 N24 A:K1O601 2.8 37.4 1.0 N21 A:K1O601 2.8 40.3 1.0 ND2 A:ASN367 3.0 38.2 1.0 CG A:ASN364 3.2 42.0 1.0 N A:ASN364 3.4 39.5 1.0 N A:ASN363 3.4 38.9 1.0 CB A:ASN363 3.5 46.5 1.0 OD1 A:ASN364 3.7 42.6 1.0 CA A:ASN363 3.7 41.5 1.0 OG A:SER362 3.8 39.8 1.0 O A:VAL429 3.8 50.3 1.0 CD A:PRO431 3.8 58.3 1.0 C A:ASN363 3.8 40.5 1.0 CG A:PRO431 3.9 60.1 1.0 CG A:ASN367 4.0 39.2 1.0 C03 A:K1O601 4.1 35.2 1.0 CB A:ASN364 4.1 42.8 1.0 C20 A:K1O601 4.2 40.0 1.0 CA A:ASN364 4.3 40.2 1.0 C A:SER362 4.5 36.0 1.0 CB A:ASN367 4.6 35.4 1.0 O A:ASN364 4.7 37.6 1.0 C04 A:K1O601 4.7 37.4 1.0 CA A:SER362 4.8 36.2 1.0 CG A:ASN363 4.8 48.9 1.0 O A:ASN363 4.8 42.5 1.0 OD1 A:ASN367 4.9 38.7 1.0 CB A:SER362 4.9 37.9 1.0 N A:PRO431 4.9 61.1 1.0 CB A:PRO431 4.9 63.0 1.0 C A:ASN364 4.9 38.8 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of YTHDC1 in Complex with Compound 21 (ZA_515)


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 21 (ZA_515) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:49.0 occ:1.00 CL23 B:K1O601 0.0 49.0 1.0 C22 B:K1O601 1.8 32.7 1.0 N21 B:K1O601 2.8 32.7 1.0 N24 B:K1O601 2.8 33.6 1.0 ND2 B:ASN364 2.9 34.7 1.0 CG B:ASN364 3.1 34.7 1.0 ND2 B:ASN367 3.3 31.8 1.0 N B:ASN364 3.3 31.7 1.0 OD1 B:ASN364 3.4 35.1 1.0 N B:ASN363 3.5 33.1 1.0 OG B:SER362 3.5 32.0 1.0 CG B:PRO431 3.7 45.6 1.0 CB B:ASN363 3.8 36.2 1.0 CA B:ASN363 3.9 34.0 1.0 C B:ASN363 3.9 33.9 1.0 CB B:ASN364 4.0 33.5 1.0 O B:VAL429 4.0 34.6 1.0 C03 B:K1O601 4.1 28.8 1.0 C20 B:K1O601 4.1 30.7 1.0 CA B:ASN364 4.1 36.0 1.0 CG B:ASN367 4.2 31.4 1.0 CD B:PRO431 4.2 45.0 1.0 CB B:ASN367 4.4 26.8 1.0 C B:SER362 4.5 31.0 1.0 O B:ASN364 4.5 32.2 1.0 C04 B:K1O601 4.6 29.5 1.0 CB B:SER362 4.7 30.9 1.0 CA B:SER362 4.8 28.9 1.0 C B:ASN364 4.8 32.1 1.0 CB B:PRO431 4.8 51.1 1.0 N B:PRO431 4.9 45.6 1.0 O B:ASN363 4.9 38.4 1.0

R.K.Bedi, F.Zalesak, A.Caflisch. Crystal Structure of YTHDC1 in Complex with Compound 21 (ZA_515) To Be Published.