Chlorine in PDB 7z5m: Crystal Structure of YTHDF2 with Compound YLI_DC1_008

The structure of Crystal Structure of YTHDF2 with Compound YLI_DC1_008, PDB code: 7z5m 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)	44.10 / 1.70
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	80.33, 80.33, 114.03, 90, 90, 120
R / Rfree (%)	20.9 / 23.3

The binding sites of Chlorine atom in the Crystal Structure of YTHDF2 with Compound YLI_DC1_008 (pdb code 7z5m). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of YTHDF2 with Compound YLI_DC1_008, PDB code: 7z5m:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of YTHDF2 with Compound YLI_DC1_008


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_DC1_008 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl604 b:39.3 occ:1.00 N A:ASP528 3.4 18.6 1.0 O A:HOH780 3.5 33.9 1.0 ND2 A:ASN462 3.6 28.9 1.0 CB A:ASP528 3.9 19.1 1.0 CA A:ARG527 4.0 17.7 1.0 CB A:LYS416 4.0 15.3 1.0 CG A:LYS416 4.1 15.0 1.0 CB A:ARG527 4.1 21.9 1.0 C A:ARG527 4.2 18.6 1.0 CA A:ASP528 4.2 16.6 1.0 OH A:TYR418 4.4 36.4 1.0 C08 A:5ZK606 4.4 18.0 1.0 CG A:ARG527 4.6 27.9 1.0 CG A:ASN462 4.7 22.3 1.0 CZ A:TYR418 4.8 29.2 1.0 CE2 A:TYR418 4.8 24.4 1.0 OD1 A:ASN462 4.9 24.5 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of YTHDF2 with Compound YLI_DC1_008


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_DC1_008 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl605 b:49.4 occ:1.00 O A:HOH709 3.5 31.3 1.0 NH2 A:ARG511 3.7 39.4 1.0 ND2 A:ASN507 3.8 24.0 1.0 CB A:ASN507 4.0 25.5 1.0 O A:HOH714 4.1 28.7 1.0 NE A:ARG511 4.1 45.7 1.0 CZ A:ARG511 4.4 47.2 1.0 CG A:ASN507 4.4 21.8 1.0 OD1 A:ASN525 5.0 28.8 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of YTHDF2 with Compound YLI_DC1_008


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 YTHDF2 with Compound YLI_DC1_008 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:52.9 occ:1.00 ND1 B:HIS437 2.8 44.2 1.0 N B:HIS437 3.0 31.4 1.0 N B:GLU436 3.4 27.6 1.0 CB B:GLU436 3.6 29.8 1.0 CG B:HIS437 3.6 42.4 1.0 CB B:HIS437 3.7 31.9 1.0 CB B:THR435 3.7 27.5 1.0 CA B:GLU436 3.8 32.6 1.0 CE1 B:HIS437 3.8 42.8 1.0 C B:GLU436 3.9 30.2 1.0 CA B:HIS437 3.9 27.7 1.0 OG1 B:THR435 3.9 24.6 1.0 C B:THR435 4.3 24.1 1.0 CG B:GLU436 4.4 43.3 1.0 CA B:THR435 4.5 22.6 1.0 CG2 B:THR435 4.6 30.7 1.0 CD2 B:HIS437 4.8 43.9 1.0 NE2 B:HIS437 4.9 45.6 1.0 N B:GLY438 5.0 21.7 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