Chlorine in PDB 7z7b: Crystal Structure of YTHDF2 with Compound YLI_DC1_003

The structure of Crystal Structure of YTHDF2 with Compound YLI_DC1_003, PDB code: 7z7b was solved by F.Nai, Y.Li, A.Dolbois, A.Caflisch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.97 / 1.80
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	80.38, 80.38, 113.44, 90, 90, 120
R / Rfree (%)	17.8 / 19.3

The binding sites of Chlorine atom in the Crystal Structure of YTHDF2 with Compound YLI_DC1_003 (pdb code 7z7b). 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 YTHDF2 with Compound YLI_DC1_003, PDB code: 7z7b:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of YTHDF2 with Compound YLI_DC1_003


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_003 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl605 b:31.1 occ:1.00 N A:ASP528 3.3 16.2 1.0 ND2 A:ASN462 3.9 21.5 1.0 CB A:ASP528 3.9 17.1 1.0 CA A:ARG527 4.0 20.3 1.0 CB A:LYS416 4.0 16.9 1.0 CB A:ARG527 4.0 22.3 1.0 CZ A:ARG527 4.0 33.6 1.0 C A:ARG527 4.2 18.1 1.0 CG A:LYS416 4.2 17.5 1.0 CA A:ASP528 4.2 17.8 1.0 CG A:ARG527 4.4 22.3 1.0 OH A:TYR418 4.4 31.8 1.0 C01 A:OYK607 4.4 16.2 1.0 NE A:ARG527 4.7 40.7 1.0 CE2 A:TYR418 4.9 22.6 1.0 CZ A:TYR418 4.9 25.5 1.0 O A:HOH776 4.9 29.5 1.0 CG A:ASN462 4.9 20.1 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of YTHDF2 with Compound YLI_DC1_003


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_003 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl606 b:25.7 occ:1.00 O A:HOH758 2.9 27.2 1.0 N A:LEU534 3.3 19.9 1.0 CB A:LEU534 3.8 19.1 1.0 CA A:PRO533 4.0 18.5 1.0 C A:PRO533 4.1 15.3 1.0 CA A:LEU534 4.2 18.8 1.0 CB A:PRO533 4.3 20.8 1.0 OE1 A:GLU535 4.7 24.0 1.0 O A:HOH712 4.8 26.4 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of YTHDF2 with Compound YLI_DC1_003


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_003 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl609 b:40.5 occ:1.00 O A:HOH737 3.0 26.5 1.0 O A:HOH776 3.7 29.5 1.0 NH2 A:ARG441 3.8 27.1 1.0 NE2 A:HIS437 3.9 25.2 1.0 NE A:ARG527 4.0 40.7 1.0 O A:HOH782 4.4 26.8 1.0 NH1 A:ARG441 4.5 32.2 1.0 CD A:ARG527 4.7 30.6 1.0 CZ A:ARG441 4.7 26.4 1.0 CD2 A:HIS437 4.7 26.4 1.0 CE1 A:HIS437 4.8 24.3 1.0 CZ A:ARG527 4.9 33.6 1.0 CB A:ARG527 4.9 22.3 1.0 O A:ASP528 5.0 18.6 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of YTHDF2 with Compound YLI_DC1_003


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 YTHDF2 with Compound YLI_DC1_003 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl604 b:30.7 occ:1.00 O B:HOH714 3.1 24.0 1.0 NH1 B:ARG494 3.4 32.8 1.0 O B:HOH715 3.5 23.2 1.0 CB B:CYS482 3.8 18.9 1.0 O B:HOH759 3.8 31.8 1.0 CG1 B:VAL485 4.2 21.3 1.0 N B:CYS482 4.4 22.3 1.0 CD B:ARG494 4.5 31.7 1.0 CZ B:ARG494 4.5 35.5 1.0 NH2 B:ARG425 4.6 21.9 1.0 CA B:CYS482 4.7 17.4 1.0 CG2 B:VAL485 4.7 20.6 1.0 O B:HOH716 4.7 27.8 1.0 O B:CYS482 4.8 24.2 1.0 CB B:THR481 4.8 22.5 1.0 CB B:VAL485 4.9 24.2 1.0 NE B:ARG494 4.9 35.2 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