Chlorine in PDB 8q4t: Crystal Structure of YTHDC1 in Complex with Compound 31 (ZA_400)

The structure of Crystal Structure of YTHDC1 in Complex with Compound 31 (ZA_400), PDB code: 8q4t 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)	38.77 / 1.51
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.13, 104.08, 41.99, 90, 104.94, 90
R / Rfree (%)	20.9 / 23.8

The binding sites of Chlorine atom in the Crystal Structure of YTHDC1 in Complex with Compound 31 (ZA_400) (pdb code 8q4t). 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 31 (ZA_400), PDB code: 8q4t:
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 31 (ZA_400)


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 31 (ZA_400) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:73.0 occ:1.00 CL01 A:JBD601 0.0 73.0 1.0 C02 A:JBD601 1.8 54.3 1.0 C03 A:JBD601 2.8 49.1 1.0 C25 A:JBD601 2.9 53.6 1.0 O A:ALA432 3.4 64.7 1.0 CB A:PRO431 3.7 57.3 1.0 CB A:MET434 3.7 62.4 1.0 CG A:PRO431 3.9 54.8 1.0 N A:MET434 4.2 66.8 1.0 C04 A:JBD601 4.3 46.9 1.0 C24 A:JBD601 4.3 51.4 1.0 CA A:MET434 4.3 65.1 1.0 C A:GLY433 4.6 68.4 1.0 CD A:PRO431 4.6 53.9 1.0 C A:ALA432 4.6 64.8 1.0 C A:PRO431 4.8 60.8 1.0 CA A:PRO431 4.8 57.4 1.0 C18 A:JBD601 4.8 47.8 1.0 O A:GLY433 4.9 71.1 1.0 ND2 A:ASN363 4.9 53.6 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of YTHDC1 in Complex with Compound 31 (ZA_400)


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 31 (ZA_400) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:56.1 occ:1.00 CL10 A:JBD601 0.0 56.1 1.0 C09 A:JBD601 1.8 38.6 1.0 ND2 A:ASN364 2.8 43.8 1.0 N11 A:JBD601 2.8 36.8 1.0 N08 A:JBD601 2.8 39.3 1.0 ND2 A:ASN367 3.0 38.1 1.0 CG A:ASN364 3.2 39.9 1.0 N A:ASN363 3.4 33.6 1.0 N A:ASN364 3.4 35.9 1.0 OD1 A:ASN364 3.6 42.1 1.0 CB A:ASN363 3.6 40.4 1.0 OG A:SER362 3.6 38.0 1.0 CG A:PRO431 3.6 54.8 1.0 CA A:ASN363 3.8 38.6 1.0 CG A:ASN367 3.9 38.7 1.0 C A:ASN363 3.9 35.5 1.0 O A:VAL429 3.9 47.3 1.0 CD A:PRO431 4.1 53.9 1.0 C12 A:JBD601 4.1 35.0 1.0 CB A:ASN364 4.2 41.3 1.0 C07 A:JBD601 4.2 38.1 1.0 CA A:ASN364 4.3 36.4 1.0 C A:SER362 4.4 33.3 1.0 CB A:ASN367 4.4 33.3 1.0 O A:ASN364 4.6 35.7 1.0 O A:HOH778 4.6 45.6 1.0 CA A:SER362 4.7 32.9 1.0 C15 A:JBD601 4.7 33.7 1.0 CB A:SER362 4.7 36.4 1.0 CG A:ASN363 4.7 46.1 1.0 OD1 A:ASN367 4.8 35.2 1.0 CB A:PRO431 4.9 57.3 1.0 ND2 A:ASN363 4.9 53.6 1.0 C A:ASN364 4.9 37.2 1.0 O A:ASN363 5.0 41.5 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of YTHDC1 in Complex with Compound 31 (ZA_400)


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 31 (ZA_400) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:65.5 occ:1.00 CL01 B:JBD601 0.0 65.5 1.0 C02 B:JBD601 1.8 49.4 1.0 C03 B:JBD601 2.9 42.7 1.0 C25 B:JBD601 2.9 48.7 1.0 CG B:PRO431 3.6 47.7 1.0 O B:ALA432 3.7 57.3 1.0 CB B:MET434 4.0 56.1 1.0 CB B:PRO431 4.2 48.6 1.0 C04 B:JBD601 4.3 39.2 1.0 ND2 B:ASN363 4.3 49.5 1.0 C24 B:JBD601 4.3 44.6 1.0 N B:MET434 4.5 62.7 1.0 O B:PRO431 4.7 48.7 1.0 CA B:MET434 4.7 62.3 1.0 C B:ALA432 4.7 56.3 1.0 C B:GLY433 4.7 65.5 1.0 CD B:PRO431 4.8 41.8 1.0 C18 B:JBD601 4.8 41.0 1.0 C B:PRO431 4.8 48.5 1.0 CG B:ASN363 5.0 42.7 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of YTHDC1 in Complex with Compound 31 (ZA_400)


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 31 (ZA_400) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:64.3 occ:1.00 CL10 B:JBD601 0.0 64.3 1.0 C09 B:JBD601 1.8 35.5 1.0 ND2 B:ASN364 2.8 39.9 1.0 N08 B:JBD601 2.8 34.5 1.0 N11 B:JBD601 2.8 31.8 1.0 CG B:ASN364 3.1 37.4 1.0 ND2 B:ASN367 3.2 33.6 1.0 N B:ASN364 3.3 37.6 1.0 OD1 B:ASN364 3.3 38.8 1.0 N B:ASN363 3.4 33.9 1.0 OG B:SER362 3.5 36.0 1.0 CB B:ASN363 3.5 37.3 1.0 CA B:ASN363 3.7 35.6 1.0 C B:ASN363 3.9 37.5 1.0 CD B:PRO431 4.0 41.8 1.0 CB B:ASN364 4.0 36.6 1.0 CG B:PRO431 4.1 47.7 1.0 O B:VAL429 4.1 34.1 1.0 C12 B:JBD601 4.1 30.7 1.0 C07 B:JBD601 4.1 34.1 1.0 CG B:ASN367 4.1 32.5 1.0 CA B:ASN364 4.2 38.6 1.0 C B:SER362 4.3 30.6 1.0 CB B:ASN367 4.4 30.1 1.0 O B:ASN364 4.5 36.4 1.0 CB B:SER362 4.6 31.6 1.0 CG B:ASN363 4.6 42.7 1.0 CA B:SER362 4.6 27.9 1.0 C15 B:JBD601 4.7 30.0 1.0 CB B:PRO431 4.8 48.6 1.0 C B:ASN364 4.8 36.2 1.0 O B:ASN363 5.0 39.9 1.0

R.K.Bedi, F.Zalesak, A.Caflisch. Crystal Structure of YTHDC1 in Complex with Compound 31 (ZA_400) To Be Published.