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

The structure of P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 5 Mm, PDB code: 8rba 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)	47.82 / 1.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.913, 70.705, 105.33, 90, 90, 90
R / Rfree (%)	15 / 18.3

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

Fluorine

(F)

4 atoms

The binding sites of Zinc atom in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 5 Mm (pdb code 8rba). 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 5 Mm, PDB code: 8rba:
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 5 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 5 Mm within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn412 b:24.5 occ:1.00 ND1 A:HIS179 2.0 25.1 1.0 SG A:CYS242 2.3 26.4 1.0 SG A:CYS238 2.3 26.2 1.0 SG A:CYS176 2.3 22.7 1.0 CE1 A:HIS179 3.0 27.0 1.0 CG A:HIS179 3.1 25.1 1.0 CB A:CYS242 3.1 24.1 1.0 CB A:CYS176 3.3 21.5 1.0 CB A:CYS238 3.4 23.6 1.0 CB A:HIS179 3.4 22.9 1.0 CA A:CYS238 3.8 21.1 1.0 N A:CYS176 4.0 20.1 1.0 O A:HOH698 4.0 45.3 1.0 NE2 A:HIS179 4.1 29.1 1.0 CD2 A:HIS179 4.2 28.0 1.0 N A:HIS179 4.3 25.1 1.0 CA A:CYS176 4.3 19.7 1.0 N A:TYR239 4.4 22.8 1.0 CA A:HIS179 4.5 20.8 1.0 CA A:CYS242 4.5 23.8 1.0 C A:CYS238 4.7 23.0 1.0 O A:MET237 4.7 20.1 1.0 O A:HOH598 4.7 26.8 1.0 C A:CYS176 5.0 22.0 1.0 O A:TYR239 5.0 23.9 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 5 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 5 Mm within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn412 b:22.6 occ:1.00 ND1 B:HIS179 1.9 19.5 1.0 SG B:CYS238 2.3 27.6 1.0 SG B:CYS242 2.3 23.5 1.0 SG B:CYS176 2.3 20.4 1.0 CE1 B:HIS179 2.9 22.6 1.0 CG B:HIS179 3.0 20.4 1.0 CB B:CYS242 3.1 24.4 1.0 CB B:CYS176 3.3 21.4 1.0 CB B:HIS179 3.4 19.8 1.0 CB B:CYS238 3.5 23.5 1.0 CA B:CYS238 3.8 17.9 1.0 NE2 B:HIS179 4.0 22.5 1.0 N B:CYS176 4.0 18.6 1.0 CD2 B:HIS179 4.1 22.8 1.0 O B:HOH693 4.2 48.3 1.0 N B:TYR239 4.2 21.7 1.0 CA B:CYS176 4.3 19.2 1.0 N B:HIS179 4.3 20.2 1.0 CA B:HIS179 4.5 18.1 1.0 CA B:CYS242 4.5 22.9 1.0 C B:CYS238 4.6 21.2 1.0 O B:HOH581 4.7 26.7 1.0 O B:MET237 4.8 18.5 1.0 C B:CYS176 5.0 21.5 1.0 O B:TYR239 5.0 21.1 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