Zinc in PDB 8rbb: P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm

The structure of P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm, PDB code: 8rbb was solved by J.Stahlecker, T.Klett, T.Stehle, F.M.Boeckler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.97 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.083, 70.989, 105.94, 90, 90, 90
R / Rfree (%)	16.4 / 20.7

The structure of P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm also contains other interesting chemical elements:

Fluorine

(F)

18 atoms

The binding sites of Zinc atom in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm (pdb code 8rbb). 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 Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm, PDB code: 8rbb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm


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 Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn413 b:35.8 occ:1.00 ND1 A:HIS179 2.0 33.7 1.0 SG A:CYS238 2.3 40.5 1.0 SG A:CYS242 2.3 39.4 1.0 SG A:CYS176 2.3 34.1 1.0 CE1 A:HIS179 2.9 36.5 1.0 CG A:HIS179 3.1 32.8 1.0 CB A:CYS242 3.1 38.7 1.0 CB A:CYS176 3.3 34.3 1.0 CB A:HIS179 3.5 31.1 1.0 CB A:CYS238 3.6 37.9 1.0 CA A:CYS238 3.9 32.5 1.0 N A:CYS176 4.1 30.1 1.0 NE2 A:HIS179 4.1 36.7 1.0 CD2 A:HIS179 4.2 35.4 1.0 O A:HOH627 4.2 54.3 1.0 N A:HIS179 4.3 31.5 1.0 CA A:CYS176 4.3 31.2 1.0 N A:TYR239 4.3 30.2 1.0 CA A:HIS179 4.5 30.1 1.0 CA A:CYS242 4.5 38.5 1.0 C A:CYS238 4.6 32.1 1.0 O A:HOH561 4.8 40.1 1.0 O A:MET237 4.8 31.9 1.0 C A:CYS176 4.9 32.4 1.0 O A:TYR239 5.0 35.6 1.0

Zinc binding site 2 out of 2 in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm


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 Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn410 b:37.6 occ:1.00 ND1 B:HIS179 2.0 38.9 1.0 SG B:CYS242 2.3 40.7 1.0 SG B:CYS176 2.3 35.8 1.0 SG B:CYS238 2.3 40.7 1.0 CE1 B:HIS179 2.9 42.1 1.0 CG B:HIS179 3.1 36.9 1.0 CB B:CYS242 3.1 40.5 1.0 CB B:CYS176 3.3 31.6 1.0 CB B:HIS179 3.5 33.5 1.0 CB B:CYS238 3.5 37.8 1.0 CA B:CYS238 3.9 34.0 1.0 N B:CYS176 4.1 28.5 1.0 NE2 B:HIS179 4.1 43.4 1.0 CD2 B:HIS179 4.1 40.7 1.0 CA B:CYS176 4.2 29.1 1.0 N B:HIS179 4.3 31.8 1.0 N B:TYR239 4.3 31.0 1.0 CA B:HIS179 4.5 30.6 1.0 CA B:CYS242 4.5 42.0 1.0 C B:CYS238 4.7 32.8 1.0 O B:HOH585 4.7 44.5 1.0 O B:MET237 4.9 31.5 1.0 C B:CYS176 4.9 32.5 1.0 O B:HOH508 5.0 58.4 1.0 O B:TYR239 5.0 35.3 1.0

T.Klett, J.Stahlecker, S.Jaag, B.Masberg, C.Knappe, M.Lammerhofer, M.Coles, T.Stehle, F.M.Boeckler. Covalent Fragments Acting As Tyrosine Mimics For Mutant P53-Y220C Rescue By Nucleophilic Aromatic Substitution Acs Pharmacol Transl Sci 2024.
ISSN: ESSN 2575-910
DOI: 10.1021/ACSPTSCI.4C00414