Zinc 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:

Bromine	(Br)	3 atoms
Fluorine	(F)	9 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine, PDB code: 8a92:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn403 b:14.9 occ:1.00 ND1 A:HIS179 2.0 15.2 1.0 SG A:CYS242 2.3 16.0 1.0 SG A:CYS176 2.3 14.4 1.0 SG A:CYS238 2.3 14.7 1.0 CE1 A:HIS179 3.0 15.8 1.0 CB A:CYS242 3.1 15.3 1.0 CG A:HIS179 3.1 15.1 1.0 CB A:CYS238 3.3 12.7 1.0 CB A:CYS176 3.4 13.1 1.0 CB A:HIS179 3.4 14.8 1.0 CA A:CYS238 3.8 12.3 1.0 N A:CYS176 4.0 12.3 1.0 O A:HOH710 4.0 34.9 1.0 NE2 A:HIS179 4.1 17.3 1.0 CD2 A:HIS179 4.2 16.8 1.0 CA A:CYS176 4.3 13.2 1.0 N A:HIS179 4.3 15.0 1.0 N A:TYR239 4.5 15.0 1.0 CA A:CYS242 4.5 15.8 1.0 CA A:HIS179 4.5 15.3 1.0 O A:MET237 4.6 12.4 1.0 O A:HOH610 4.7 17.3 1.0 C A:CYS238 4.7 14.6 1.0 C A:CYS176 5.0 14.2 1.0 N A:CYS238 5.0 12.1 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 B:Zn402 b:15.8 occ:1.00 ND1 B:HIS179 2.0 14.8 1.0 SG B:CYS238 2.3 21.0 1.0 SG B:CYS242 2.3 17.4 1.0 SG B:CYS176 2.3 15.1 1.0 CE1 B:HIS179 2.9 16.2 1.0 CG B:HIS179 3.0 14.9 1.0 CB B:CYS242 3.0 18.2 1.0 CB B:CYS238 3.3 17.8 1.0 CB B:CYS176 3.4 13.8 1.0 CB B:HIS179 3.4 13.9 1.0 CA B:CYS238 3.8 14.7 1.0 O B:HOH700 4.0 34.4 1.0 N B:CYS176 4.0 13.5 1.0 NE2 B:HIS179 4.1 15.6 1.0 CD2 B:HIS179 4.1 15.8 1.0 N B:HIS179 4.3 13.7 1.0 CA B:CYS176 4.3 13.5 1.0 N B:TYR239 4.4 15.5 1.0 CA B:HIS179 4.5 14.1 1.0 CA B:CYS242 4.5 17.0 1.0 C B:CYS238 4.6 15.3 1.0 O B:HOH609 4.7 19.7 1.0 O B:MET237 4.7 12.5 1.0 C B:CYS176 5.0 14.6 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