Zinc in PDB 8a32: P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769

The structure of P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769, PDB code: 8a32 was solved by D.I.Balourdas, J.R.Stephenson Clarke, M.G.J.Baud, S.Knapp, A.C.Joerger, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.01 / 1.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.119, 71.072, 105.315, 90, 90, 90
R / Rfree (%)	16.4 / 19.3

The structure of P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769 also contains other interesting chemical elements:

Iodine	(I)	4 atoms
Fluorine	(F)	4 atoms

The binding sites of Zinc atom in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769 (pdb code 8a32). 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 Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769, PDB code: 8a32:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769


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 Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:17.9 occ:1.00 ND1 A:HIS179 2.0 16.7 1.0 SG A:CYS238 2.2 19.1 0.5 SG A:CYS242 2.3 18.8 1.0 SG A:CYS176 2.3 17.1 1.0 SG A:CYS238 2.4 16.7 0.5 CE1 A:HIS179 3.0 16.8 1.0 CG A:HIS179 3.0 16.1 1.0 CB A:CYS242 3.1 19.3 1.0 CB A:CYS238 3.2 15.6 0.5 CB A:CYS176 3.3 17.4 1.0 CB A:HIS179 3.4 15.7 1.0 CB A:CYS238 3.5 17.8 0.5 CA A:CYS238 3.8 15.7 0.5 CA A:CYS238 3.9 16.9 0.5 N A:CYS176 4.0 16.2 1.0 NE2 A:HIS179 4.1 17.6 1.0 CD2 A:HIS179 4.1 18.3 1.0 CA A:CYS176 4.3 16.5 1.0 N A:HIS179 4.3 17.7 1.0 N A:TYR239 4.4 16.9 1.0 CA A:HIS179 4.5 16.4 1.0 CA A:CYS242 4.5 18.0 1.0 O A:HOH625 4.6 20.1 1.0 C A:CYS238 4.7 17.2 0.5 C A:CYS238 4.7 16.5 0.5 O A:MET237 4.7 15.9 1.0 C A:CYS176 5.0 17.2 1.0

Zinc binding site 2 out of 2 in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769


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 Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:18.2 occ:1.00 ND1 B:HIS179 2.0 18.3 1.0 SG B:CYS242 2.3 18.7 1.0 SG B:CYS176 2.3 18.0 1.0 SG B:CYS238 2.3 17.8 1.0 CE1 B:HIS179 3.0 18.8 1.0 CG B:HIS179 3.0 17.7 1.0 CB B:CYS242 3.1 19.3 1.0 CB B:CYS238 3.3 15.6 1.0 CB B:CYS176 3.4 17.3 1.0 CB B:HIS179 3.4 17.1 1.0 CA B:CYS238 3.8 14.9 1.0 N B:CYS176 4.0 16.4 1.0 NE2 B:HIS179 4.1 19.5 1.0 CD2 B:HIS179 4.2 18.6 1.0 CA B:CYS176 4.3 16.9 1.0 N B:HIS179 4.3 18.7 1.0 N B:TYR239 4.5 17.0 1.0 CA B:HIS179 4.5 16.8 1.0 CA B:CYS242 4.5 18.2 1.0 O B:HOH627 4.6 18.7 1.0 O B:MET237 4.6 16.1 1.0 C B:CYS238 4.7 16.1 1.0 N B:CYS238 5.0 14.5 1.0

J.R.Stephenson Clarke, L.R.Douglas, P.J.Duriez, D.I.Balourdas, A.C.Joerger, R.Khadiullina, E.Bulatov, M.G.J.Baud. Discovery of Nanomolar-Affinity Pharmacological Chaperones Stabilizing the Oncogenic P53 Mutant Y220C. Acs Pharmacol Transl Sci V. 5 1169 2022.
ISSN: ESSN 2575-910
PubMed: 36407959
DOI: 10.1021/ACSPTSCI.2C00164