Bromine in PDB 7z8p: Crystal Structure of YTHDF2 with Compound ZA_166

The structure of Crystal Structure of YTHDF2 with Compound ZA_166, PDB code: 7z8p was solved by F.Nai, F.Zalesak, 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 / 1.97
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	80.08, 80.08, 114.29, 90, 90, 120
R / Rfree (%)	20.8 / 24.2

The binding sites of Bromine atom in the Crystal Structure of YTHDF2 with Compound ZA_166 (pdb code 7z8p). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of YTHDF2 with Compound ZA_166, PDB code: 7z8p:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of YTHDF2 with Compound ZA_166


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of YTHDF2 with Compound ZA_166 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br604 b:47.4 occ:1.00 BR07 A:IFZ604 0.0 47.4 1.0 C06 A:IFZ604 1.9 38.3 1.0 O2 A:SO4603 2.9 49.9 1.0 C05 A:IFZ604 2.9 32.5 1.0 N08 A:IFZ604 3.0 31.7 1.0 O A:LYS416 3.0 30.3 1.0 N10 A:IFZ604 3.4 32.0 1.0 C A:LYS416 3.8 26.3 1.0 CD2 A:TYR418 3.9 28.1 1.0 CE2 A:TYR418 4.0 32.6 1.0 CB A:ASP528 4.0 29.4 1.0 ND2 A:ASN462 4.1 32.2 1.0 N09 A:IFZ604 4.1 34.9 1.0 C04 A:IFZ604 4.1 37.6 1.0 CG A:ASP528 4.1 25.5 1.0 OD2 A:ASP528 4.2 25.4 1.0 S A:SO4603 4.3 42.2 1.0 CA A:SER417 4.3 20.8 1.0 CB A:LYS416 4.4 26.3 1.0 N A:SER417 4.4 21.0 1.0 N A:TYR418 4.4 20.0 1.0 OD1 A:ASP528 4.7 20.3 1.0 C A:SER417 4.7 21.8 1.0 O3 A:SO4603 4.7 46.1 1.0 CA A:LYS416 4.7 24.3 1.0 C11 A:IFZ604 4.8 36.0 1.0 CG A:TYR418 4.8 25.1 1.0 CH2 A:TRP491 4.9 34.5 1.0 CZ A:TYR418 5.0 34.3 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of YTHDF2 with Compound ZA_166


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of YTHDF2 with Compound ZA_166 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br602 b:29.8 occ:1.00 BR07 B:IFZ602 0.0 29.8 1.0 C06 B:IFZ602 1.9 23.1 1.0 O B:HOH742 2.9 27.5 1.0 N08 B:IFZ602 2.9 24.5 1.0 C05 B:IFZ602 3.0 24.3 1.0 N10 B:IFZ602 3.5 23.8 1.0 O B:LYS416 3.6 20.2 1.0 CD2 B:TYR418 3.8 33.6 1.0 CE2 B:TYR418 3.8 39.3 1.0 C B:LYS416 3.8 22.9 1.0 OD2 B:ASP528 4.0 22.8 1.0 N09 B:IFZ602 4.0 24.1 1.0 CA B:SER417 4.0 23.1 1.0 C04 B:IFZ602 4.1 29.2 1.0 CG B:ASP528 4.1 24.4 1.0 N B:SER417 4.1 21.6 1.0 CH2 B:TRP491 4.2 27.5 1.0 CB B:ASP528 4.2 24.9 1.0 CB B:LYS416 4.3 22.8 1.0 N B:TYR418 4.3 19.1 1.0 ND2 B:ASN462 4.3 24.8 1.0 O B:HOH741 4.5 26.2 1.0 C B:SER417 4.5 21.4 1.0 OD1 B:ASP528 4.6 22.0 1.0 CA B:LYS416 4.6 21.1 1.0 CG B:TYR418 4.7 30.9 1.0 CZ B:TYR418 4.7 37.5 1.0 CZ2 B:TRP491 4.7 27.8 1.0 CZ3 B:TRP491 4.9 28.2 1.0 C11 B:IFZ602 4.9 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