Chlorine in PDB 7r5w: Crystal Structure of YTHDF2 with Compound YLI_DF_029

The structure of Crystal Structure of YTHDF2 with Compound YLI_DF_029, PDB code: 7r5w 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 / 1.75
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	81.06, 81.06, 113.36, 90, 90, 120
R / Rfree (%)	19.8 / 22.6

The binding sites of Chlorine atom in the Crystal Structure of YTHDF2 with Compound YLI_DF_029 (pdb code 7r5w). 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_029, PDB code: 7r5w:
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_029


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_029 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl605 b:34.1 occ:1.00 N A:LEU534 3.3 23.9 1.0 CA A:PRO533 3.9 22.0 1.0 CB A:LEU534 3.9 28.0 1.0 C A:PRO533 4.1 17.6 1.0 CA A:LEU534 4.2 21.6 1.0 CB A:PRO533 4.2 19.9 1.0 OE1 A:GLU535 4.4 38.7 1.0 O A:HOH727 5.0 34.9 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of YTHDF2 with Compound YLI_DF_029


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_029 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl604 b:39.5 occ:1.00 O B:HOH723 3.3 27.3 1.0 NH1 B:ARG494 3.4 36.0 1.0 O B:HOH770 3.4 28.3 1.0 CB B:CYS482 3.9 20.5 1.0 CD B:ARG494 4.3 32.9 1.0 N B:CYS482 4.4 26.2 1.0 CG1 B:VAL485 4.4 22.4 1.0 CZ B:ARG494 4.4 44.3 1.0 O B:CYS482 4.7 26.9 1.0 CA B:CYS482 4.7 22.1 1.0 CB B:THR481 4.7 27.8 1.0 NE B:ARG494 4.8 30.2 1.0 NH2 B:ARG425 4.8 21.0 0.6 CG2 B:VAL485 5.0 22.5 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