Zinc in PDB 6si3: P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301

The structure of P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301, PDB code: 6si3 was solved by A.C.Joerger, M.R.Bauer, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.57 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.982, 71.298, 105.417, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 17.6

The structure of P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301 also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Bromine	(Br)	2 atoms

The binding sites of Zinc atom in the P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301 (pdb code 6si3). 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 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301, PDB code: 6si3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:15.5 occ:1.00 ND1 A:HIS179 2.0 14.6 1.0 SG A:CYS242 2.3 16.3 1.0 SG A:CYS238 2.3 16.1 1.0 SG A:CYS176 2.3 15.2 1.0 CE1 A:HIS179 3.0 15.9 1.0 CG A:HIS179 3.0 14.4 1.0 CB A:CYS242 3.1 17.2 1.0 CB A:CYS238 3.3 14.6 1.0 CB A:CYS176 3.4 14.4 1.0 CB A:HIS179 3.4 13.3 1.0 CA A:CYS238 3.8 13.2 1.0 N A:CYS176 4.0 13.8 1.0 NE2 A:HIS179 4.1 17.4 1.0 CD2 A:HIS179 4.2 16.4 1.0 CA A:CYS176 4.3 14.0 1.0 N A:HIS179 4.3 15.1 1.0 N A:TYR239 4.4 14.0 1.0 CA A:HIS179 4.5 14.6 1.0 CA A:CYS242 4.5 16.5 1.0 C A:CYS238 4.7 13.8 1.0 O A:HOH600 4.7 18.1 1.0 O A:MET237 4.7 13.3 1.0 N A:CYS238 5.0 12.3 1.0 C A:CYS176 5.0 14.6 1.0

Zinc binding site 2 out of 2 in the P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:16.8 occ:1.00 ND1 B:HIS179 2.0 17.0 1.0 SG B:CYS242 2.3 17.2 1.0 SG B:CYS238 2.3 15.4 1.0 SG B:CYS176 2.3 16.0 1.0 CE1 B:HIS179 3.0 18.4 1.0 CG B:HIS179 3.1 16.4 1.0 CB B:CYS242 3.1 17.3 1.0 CB B:CYS238 3.3 14.5 1.0 CB B:CYS176 3.4 14.8 1.0 CB B:HIS179 3.4 15.7 1.0 CA B:CYS238 3.8 14.3 1.0 N B:CYS176 4.0 14.5 1.0 NE2 B:HIS179 4.1 19.8 1.0 CD2 B:HIS179 4.2 18.1 1.0 CA B:CYS176 4.3 13.9 1.0 N B:HIS179 4.4 17.6 1.0 N B:TYR239 4.5 15.0 1.0 CA B:CYS242 4.5 16.6 1.0 CA B:HIS179 4.5 16.7 1.0 O B:HOH612 4.6 16.9 1.0 O B:MET237 4.6 15.0 1.0 C B:CYS238 4.7 14.9 1.0 N B:CYS238 5.0 13.8 1.0

M.R.Bauer, A.Kramer, G.Settanni, R.N.Jones, X.Ni, R.Khan Tareque, A.R.Fersht, J.Spencer, A.C.Joerger. Targeting Cavity-Creating P53 Cancer Mutations with Small-Molecule Stabilizers: the Y220X Paradigm. Acs Chem.Biol. 2020.
ISSN: ESSN 1554-8937
PubMed: 31990523
DOI: 10.1021/ACSCHEMBIO.9B00748