Zinc in PDB 8a31: P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694

The structure of P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694, PDB code: 8a31 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)	47.98 / 1.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.981, 71.063, 105.089, 90, 90, 90
R / Rfree (%)	15.7 / 19.1

The structure of P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694 also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Iodine	(I)	6 atoms

The binding sites of Zinc atom in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694 (pdb code 8a31). 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 JC694, PDB code: 8a31:
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 JC694


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 JC694 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:16.1 occ:1.00 ND1 A:HIS179 2.0 16.3 1.0 SG A:CYS238 2.3 18.8 0.8 SG A:CYS242 2.3 17.4 1.0 SG A:CYS176 2.3 15.6 1.0 SG A:CYS238 2.5 13.6 0.2 CE1 A:HIS179 2.9 16.4 1.0 CG A:HIS179 3.1 15.5 1.0 CB A:CYS242 3.1 18.1 1.0 CB A:CYS238 3.3 13.7 0.2 CB A:CYS176 3.3 15.5 1.0 CB A:CYS238 3.4 16.9 0.8 CB A:HIS179 3.4 14.5 1.0 CA A:CYS238 3.8 15.0 0.8 CA A:CYS238 3.8 13.7 0.2 O A:HOH707 4.0 35.7 1.0 N A:CYS176 4.0 14.1 1.0 NE2 A:HIS179 4.1 16.9 1.0 CD2 A:HIS179 4.2 17.2 1.0 CA A:CYS176 4.3 14.5 1.0 N A:HIS179 4.3 15.6 1.0 N A:TYR239 4.4 14.8 1.0 CA A:HIS179 4.5 15.1 1.0 CA A:CYS242 4.5 16.7 1.0 C A:CYS238 4.6 14.2 0.2 C A:CYS238 4.7 15.2 0.8 O A:HOH606 4.7 18.8 1.0 O A:MET237 4.7 14.0 1.0 C A:CYS176 5.0 15.2 1.0

Zinc binding site 2 out of 2 in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694


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 JC694 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:16.5 occ:1.00 ND1 B:HIS179 2.0 16.9 1.0 SG B:CYS176 2.3 15.7 1.0 SG B:CYS242 2.3 17.4 1.0 SG B:CYS238 2.3 16.7 1.0 CE1 B:HIS179 3.0 17.1 1.0 CG B:HIS179 3.1 16.1 1.0 CB B:CYS242 3.1 16.7 1.0 CB B:CYS238 3.3 14.8 1.0 CB B:CYS176 3.4 15.1 1.0 CB B:HIS179 3.4 15.0 1.0 CA B:CYS238 3.8 13.8 1.0 N B:CYS176 4.0 14.2 1.0 NE2 B:HIS179 4.1 18.1 1.0 CD2 B:HIS179 4.2 17.8 1.0 CA B:CYS176 4.3 15.1 1.0 N B:HIS179 4.3 16.4 1.0 N B:TYR239 4.4 15.8 1.0 CA B:HIS179 4.5 15.0 1.0 CA B:CYS242 4.5 15.7 1.0 O B:MET237 4.6 14.8 1.0 C B:CYS238 4.7 15.3 1.0 O B:HOH619 4.7 16.1 1.0 N B:CYS238 5.0 13.1 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