Chlorine in PDB 8q4m: Crystal Structure of YTHDC1 in Complex with Compound 25 (ZA_349)

The structure of Crystal Structure of YTHDC1 in Complex with Compound 25 (ZA_349), PDB code: 8q4m 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)	38.70 / 1.43
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.1, 103.62, 42.04, 90, 105.18, 90
R / Rfree (%)	20.9 / 22.8

The binding sites of Chlorine atom in the Crystal Structure of YTHDC1 in Complex with Compound 25 (ZA_349) (pdb code 8q4m). 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 25 (ZA_349), PDB code: 8q4m:
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 25 (ZA_349)


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 25 (ZA_349) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:61.9 occ:1.00 CL01 A:J9B601 0.0 61.9 1.0 C02 A:J9B601 1.8 45.9 1.0 N20 A:J9B601 2.8 44.6 1.0 N03 A:J9B601 2.8 40.3 1.0 ND2 A:ASN364 2.9 51.6 1.0 ND2 A:ASN367 3.1 42.2 1.0 CG A:ASN364 3.3 45.5 1.0 N A:ASN363 3.3 40.1 1.0 CG A:PRO431 3.4 63.9 1.0 N A:ASN364 3.4 36.4 1.0 OD1 A:ASN364 3.5 44.0 1.0 CB A:ASN363 3.5 46.1 1.0 OG A:SER362 3.6 39.5 1.0 CA A:ASN363 3.7 41.4 1.0 O A:VAL429 3.9 56.0 1.0 C A:ASN363 3.9 43.4 1.0 CD A:PRO431 3.9 63.8 1.0 CG A:ASN367 4.0 41.5 1.0 C04 A:J9B601 4.1 39.0 1.0 C08 A:J9B601 4.2 44.6 1.0 CB A:ASN364 4.3 45.3 1.0 CA A:ASN364 4.3 42.2 1.0 C A:SER362 4.4 36.5 1.0 CB A:ASN367 4.4 36.4 1.0 O A:ASN364 4.6 36.9 1.0 CA A:SER362 4.7 32.1 1.0 C07 A:J9B601 4.7 42.7 1.0 CB A:SER362 4.7 37.3 1.0 CG A:ASN363 4.7 51.7 1.0 CB A:PRO431 4.7 65.3 1.0 OD1 A:ASN367 4.9 42.7 1.0 N A:PRO431 4.9 66.2 1.0 C A:ASN364 4.9 39.5 1.0 O A:ASN363 4.9 42.5 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of YTHDC1 in Complex with Compound 25 (ZA_349)


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 25 (ZA_349) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:72.8 occ:1.00 CL14 A:J9B601 0.0 72.8 1.0 C13 A:J9B601 1.8 61.2 1.0 C12 A:J9B601 2.9 53.8 1.0 C15 A:J9B601 2.9 60.5 1.0 CB A:PRO431 3.4 65.3 1.0 ND2 A:ASN363 3.7 53.5 1.0 CG A:PRO431 4.0 63.9 1.0 N A:GLY433 4.2 72.7 1.0 C11 A:J9B601 4.3 51.6 1.0 C16 A:J9B601 4.3 57.8 1.0 N A:ALA432 4.3 70.8 1.0 CB A:MET434 4.4 70.6 1.0 C A:GLY433 4.5 73.0 1.0 C A:PRO431 4.5 69.5 1.0 O A:GLY433 4.5 74.5 1.0 CG A:ASN363 4.6 51.7 1.0 CA A:PRO431 4.6 68.0 1.0 CD A:PRO431 4.7 63.8 1.0 CA A:GLY433 4.7 70.7 1.0 N A:MET434 4.8 71.9 1.0 C17 A:J9B601 4.8 56.3 1.0 C A:ALA432 4.9 74.0 1.0 CA A:ALA432 5.0 68.2 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of YTHDC1 in Complex with Compound 25 (ZA_349)


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 25 (ZA_349) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:56.6 occ:1.00 CL01 B:J9B601 0.0 56.6 1.0 C02 B:J9B601 1.8 36.6 1.0 N20 B:J9B601 2.8 35.9 1.0 N03 B:J9B601 2.8 39.2 1.0 ND2 B:ASN364 2.9 40.8 1.0 CG B:ASN364 3.1 40.9 1.0 OD1 B:ASN364 3.2 39.2 1.0 N B:ASN364 3.2 35.4 1.0 N B:ASN363 3.4 36.1 1.0 ND2 B:ASN367 3.4 35.6 1.0 CG B:PRO431 3.5 47.5 1.0 OG B:SER362 3.5 33.3 1.0 C B:ASN363 3.8 35.9 1.0 CA B:ASN363 3.8 38.9 1.0 CB B:ASN363 3.9 42.6 1.0 CD B:PRO431 4.0 50.5 1.0 CB B:ASN364 4.0 36.9 1.0 CA B:ASN364 4.1 39.0 1.0 C04 B:J9B601 4.1 34.7 1.0 C08 B:J9B601 4.2 40.1 1.0 CG B:ASN367 4.2 33.5 1.0 O B:VAL429 4.3 41.8 1.0 CB B:ASN367 4.4 29.9 1.0 O B:ASN364 4.4 36.3 1.0 C B:SER362 4.4 29.3 1.0 CB B:SER362 4.6 32.5 1.0 CA B:SER362 4.7 32.3 1.0 C07 B:J9B601 4.7 37.4 1.0 C B:ASN364 4.7 35.5 1.0 O B:ASN363 4.9 39.0 1.0 CB B:PRO431 4.9 55.1 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of YTHDC1 in Complex with Compound 25 (ZA_349)


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 25 (ZA_349) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:67.0 occ:1.00 CL14 B:J9B601 0.0 67.0 1.0 C13 B:J9B601 1.8 57.8 1.0 C12 B:J9B601 2.9 50.0 1.0 C15 B:J9B601 2.9 56.9 1.0 CG B:MET434 3.2 63.4 1.0 CB B:PRO431 3.8 55.1 1.0 C B:GLY433 3.9 69.9 1.0 CA B:GLY433 4.0 67.7 1.0 N B:GLY433 4.0 63.2 1.0 O B:GLY433 4.0 72.1 1.0 SD B:MET434 4.0 65.2 1.0 ND2 B:ASN363 4.1 52.0 1.0 C11 B:J9B601 4.3 50.5 1.0 C16 B:J9B601 4.3 53.0 1.0 CG B:PRO431 4.4 47.5 1.0 N B:MET434 4.5 66.5 1.0 CB B:MET434 4.5 62.1 1.0 C B:PRO431 4.8 59.2 1.0 C17 B:J9B601 4.8 50.9 1.0 O B:PRO431 4.9 59.6 1.0 CA B:PRO431 4.9 56.1 1.0

R.K.Bedi, F.Zalesak, A.Caflisch. Crystal Structure of YTHDC1 in Complex with Compound 25 (ZA_349) To Be Published.