Chlorine in PDB 7r5f: Crystal Structure of YTHDF2 with Compound YLI_DF_012

The structure of Crystal Structure of YTHDF2 with Compound YLI_DF_012, PDB code: 7r5f 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)	43.98 / 2.00
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	79.95, 79.95, 113.88, 90, 90, 120
R / Rfree (%)	20.5 / 24.9

The binding sites of Chlorine atom in the Crystal Structure of YTHDF2 with Compound YLI_DF_012 (pdb code 7r5f). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Crystal Structure of YTHDF2 with Compound YLI_DF_012, PDB code: 7r5f:

Chlorine binding site 1 out of 1 in the Crystal Structure of YTHDF2 with Compound YLI_DF_012


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_012 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl605 b:57.2 occ:1.00 O A:HOH806 3.4 51.5 1.0 CD2 A:HIS437 3.7 49.7 1.0 N A:GLU436 3.7 35.2 1.0 CB A:GLU436 3.8 38.1 1.0 N A:HIS437 3.8 31.6 1.0 CB A:THR435 4.0 33.2 1.0 CA A:GLU436 4.2 33.3 1.0 OG1 A:THR435 4.3 36.5 1.0 CG A:HIS437 4.5 47.2 1.0 C A:GLU436 4.5 30.8 1.0 CB A:HIS437 4.5 43.9 1.0 C A:THR435 4.7 34.4 1.0 NE2 A:HIS437 4.8 54.5 1.0 CA A:HIS437 4.8 41.8 1.0 CA A:THR435 4.9 32.0 1.0 CG A:GLU436 4.9 38.0 1.0 CG2 A:THR435 4.9 35.9 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