Bromine in PDB 8a92: P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine

The structure of P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine, PDB code: 8a92 was solved by J.Stahlecker, M.B.Braun, T.Stehle, F.M.Boeckler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.68 / 1.37
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.077, 71.109, 105.226, 90, 90, 90
R / Rfree (%)	15.3 / 18.3

The structure of P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine also contains other interesting chemical elements:

Fluorine	(F)	9 atoms
Zinc	(Zn)	2 atoms

The binding sites of Bromine atom in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine (pdb code 8a92). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine, PDB code: 8a92:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br401 b:39.9 occ:0.40 BR1 A:LE9401 0.0 39.9 0.4 C1 A:LE9401 1.9 36.3 0.4 N2 A:LE9401 2.2 39.8 0.4 C3 A:LE9401 2.9 33.5 0.4 F2 A:LE9401 3.0 42.9 0.4 C2 A:LE9401 3.0 35.7 0.4 N1 A:LE9401 3.0 39.5 0.4 C3 A:LE9401 3.2 40.4 0.4 F2 A:LE9401 3.2 32.2 0.4 C4 A:LE9401 3.4 29.8 0.4 N3 A:LE9401 3.5 36.0 0.4 C4 A:LE9401 3.6 41.6 0.4 F3 A:LE9401 3.7 27.5 0.4 CB A:CYS220 3.9 21.8 0.8 C A:GLU221 3.9 28.4 1.0 O A:GLU221 3.9 27.0 1.0 N2 A:LE9401 4.0 33.5 0.4 O A:CYS220 4.1 26.6 1.0 N1 A:LE9401 4.1 34.8 0.4 C A:CYS220 4.1 24.4 1.0 C2 A:LE9401 4.1 39.9 0.4 N A:PRO222 4.1 31.3 1.0 CG A:PRO151 4.1 20.6 1.0 CD A:PRO151 4.2 18.2 1.0 C1 A:LE9401 4.2 39.8 0.4 N A:GLU221 4.3 25.1 1.0 CA A:GLU221 4.4 28.0 1.0 CA A:PRO222 4.4 32.9 1.0 F1 A:LE9401 4.5 41.2 0.4 CG2 A:THR150 4.5 26.1 1.0 O A:PRO151 4.5 18.6 1.0 F3 A:LE9401 4.6 42.0 0.4 CA A:CYS220 4.6 20.9 1.0 F1 A:LE9401 4.7 25.8 0.4 CD A:PRO222 4.7 32.9 1.0

Bromine binding site 2 out of 3 in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br401 b:40.0 occ:0.40 BR1 A:LE9401 0.0 40.0 0.4 C1 A:LE9401 1.9 39.8 0.4 N2 A:LE9401 2.1 33.5 0.4 C3 A:LE9401 2.9 40.4 0.4 F1 A:LE9401 2.9 25.8 0.4 C2 A:LE9401 3.0 39.9 0.4 O A:LEU145 3.0 17.0 1.0 N1 A:LE9401 3.0 34.8 0.4 C3 A:LE9401 3.1 33.5 0.4 O A:HOH674 3.1 18.1 1.0 F3 A:LE9401 3.1 42.0 0.4 C4 A:LE9401 3.4 41.6 0.4 C4 A:LE9401 3.4 29.8 0.4 N3 A:LE9401 3.5 40.4 0.4 N A:THR230 3.5 20.0 1.0 OG1 A:THR230 3.7 24.2 1.0 F1 A:LE9401 3.9 41.2 0.4 C A:LEU145 3.9 13.7 1.0 F3 A:LE9401 4.0 27.5 0.4 N2 A:LE9401 4.0 39.8 0.4 CA A:CYS229 4.0 21.6 1.0 N1 A:LE9401 4.1 39.5 0.4 CG2 A:VAL147 4.1 17.4 1.0 CB A:THR230 4.1 21.0 1.0 C2 A:LE9401 4.1 35.7 0.4 C1 A:LE9401 4.2 36.3 0.4 C A:CYS229 4.3 22.6 1.0 CG A:PRO223 4.4 33.8 1.0 N A:VAL147 4.4 14.5 1.0 CA A:THR230 4.4 18.8 1.0 CA A:TRP146 4.4 13.2 1.0 CB A:CYS229 4.5 20.7 1.0 CB A:LEU145 4.6 15.5 1.0 N A:TRP146 4.6 12.4 1.0 F2 A:LE9401 4.6 32.2 0.4 CD A:PRO223 4.6 33.7 1.0 F2 A:LE9401 4.7 42.9 0.4 C A:TRP146 4.7 13.7 1.0 O A:ASP228 4.8 28.2 1.0 CA A:LEU145 4.9 13.1 1.0

Bromine binding site 3 out of 3 in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:Br403 b:50.0 occ:0.60 BR1 B:LE9403 0.0 50.0 0.6 C1 B:LE9403 1.9 49.8 0.6 C3 B:LE9403 2.9 50.1 0.6 C2 B:LE9403 3.0 49.9 0.6 O B:LEU145 3.0 16.7 1.0 O B:HOH582 3.1 23.1 1.0 F1 B:LE9403 3.1 52.1 0.6 C4 B:LE9403 3.4 51.0 0.6 N3 B:LE9403 3.5 50.1 0.6 OG1 B:THR230 3.7 22.7 0.5 N B:THR230 3.7 18.2 1.0 OG1 B:THR230 3.8 21.9 0.5 CG2 B:VAL147 3.9 16.2 1.0 C B:LEU145 3.9 13.7 1.0 F2 B:LE9403 3.9 50.1 0.6 CA B:CYS229 3.9 19.5 1.0 N2 B:LE9403 4.0 49.7 0.6 CG B:PRO223 4.0 38.5 1.0 N1 B:LE9403 4.1 49.3 0.6 N B:VAL147 4.2 14.3 1.0 C B:CYS229 4.2 19.1 1.0 CG2 B:THR230 4.2 21.5 0.5 CD B:PRO223 4.2 37.9 1.0 CB B:THR230 4.3 20.6 0.5 CA B:TRP146 4.3 14.4 1.0 O B:HOH503 4.3 40.6 1.0 CB B:THR230 4.4 20.9 0.5 N B:TRP146 4.4 13.7 1.0 C B:TRP146 4.5 14.2 1.0 CB B:CYS229 4.6 19.8 1.0 CA B:THR230 4.6 18.3 0.5 F3 B:LE9403 4.7 52.4 0.6 CA B:THR230 4.7 18.6 0.5 CB B:LEU145 4.7 16.4 1.0 O B:ASP228 4.7 26.4 1.0 CB B:VAL147 4.8 15.0 1.0 CG1 B:VAL147 4.8 16.2 1.0 CA B:LEU145 4.9 14.2 1.0 N B:CYS229 5.0 21.7 1.0

J.Stahlecker, T.Klett, M.Schwer, S.Jaag, M.Dammann, L.N.Ernst, M.B.Braun, M.O.Zimmermann, M.Kramer, M.Laemmerhofer, T.Stehle, M.Coles, F.M.Boeckler. Revisiting A Challenging P53 Binding Site: A Diversity-Optimized Heflib Reveals Diverse Binding Modes in T-P53C-Y220C Rsc Med Chem 2022.
ISSN: ESSN 2632-8682
DOI: 10.1039/D2MD00246A