Chlorine in PDB 7z93: Crystal Structure of YTHDF2 with Compound YLI_DF_022

The structure of Crystal Structure of YTHDF2 with Compound YLI_DF_022, PDB code: 7z93 was solved by F.Nai, Y.Li, A.Caflisch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.09 / 1.97
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	80.64, 80.64, 113.71, 90, 90, 120
R / Rfree (%)	21.2 / 24.1

The binding sites of Chlorine atom in the Crystal Structure of YTHDF2 with Compound YLI_DF_022 (pdb code 7z93). 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 YTHDF2 with Compound YLI_DF_022, PDB code: 7z93:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of YTHDF2 with Compound YLI_DF_022


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 YTHDF2 with Compound YLI_DF_022 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:70.5 occ:1.00 N A:VAL502 3.4 29.5 1.0 CA A:PHE501 3.9 36.1 1.0 C A:PHE501 4.1 38.6 1.0 CD1 A:PHE501 4.2 54.6 1.0 O A:VAL502 4.2 36.8 1.0 CA A:VAL502 4.3 38.3 1.0 CB A:VAL502 4.4 33.8 1.0 O A:ILE500 4.5 47.7 1.0 N A:PHE501 4.6 39.4 1.0 C A:VAL502 4.6 35.4 1.0 CG2 A:VAL502 4.7 27.6 1.0 CE1 A:PHE501 4.7 56.7 1.0 C A:ILE500 4.8 40.4 1.0 CG A:PHE501 4.9 47.8 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of YTHDF2 with Compound YLI_DF_022


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 YTHDF2 with Compound YLI_DF_022 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl604 b:74.7 occ:1.00 ND2 A:ASN507 3.9 33.2 1.0 NH1 A:ARG511 3.9 56.0 1.0 CB A:ASN507 4.0 31.3 1.0 CG A:ASN507 4.5 34.4 1.0 OD1 A:ASN525 5.0 41.7 1.0

F.Nai, R.Nachawati, F.Zalesak, X.Wang, Y.Li, A.Caflisch. Fragment Ligands of the M 6 A-Rna Reader YTHDF2. Acs Med.Chem.Lett. V. 13 1500 2022.
ISSN: ISSN 1948-5875
PubMed: 36110386
DOI: 10.1021/ACSMEDCHEMLETT.2C00303