Iodine 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:

Zinc	(Zn)	2 atoms
Fluorine	(F)	4 atoms

The binding sites of Iodine 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 Iodine atom.
In total 4 binding sites of Iodine where determined in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769, PDB code: 8a32:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 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 Iodine with other atoms in the I 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:I401 b:52.6 occ:1.00 I A:KVA401 0.0 52.6 1.0 C3 A:KVA401 2.1 39.3 1.0 C2 A:KVA401 3.0 37.5 1.0 C4 A:KVA401 3.1 31.6 1.0 N A:KVA401 3.4 26.4 1.0 C5 A:KVA401 3.8 23.4 1.0 CB A:CYS220 3.9 21.9 1.0 CG A:PRO151 4.0 22.5 1.0 CD A:PRO151 4.0 21.1 1.0 C A:GLU221 4.0 25.8 1.0 N A:PRO222 4.0 26.5 1.0 CG2 A:THR150 4.2 25.9 1.0 C A:CYS220 4.3 22.6 1.0 O A:GLU221 4.3 24.4 1.0 C8 A:KVA401 4.3 25.1 1.0 N A:GLU221 4.3 22.6 1.0 CA A:PRO222 4.3 26.8 1.0 C1 A:KVA401 4.4 34.4 1.0 O A:CYS220 4.4 25.9 1.0 CD A:PRO222 4.4 28.3 1.0 O A:HOH528 4.4 46.2 1.0 CA A:GLU221 4.5 25.9 1.0 C9 A:KVA401 4.5 27.4 1.0 O A:PRO151 4.5 21.0 1.0 C6 A:KVA401 4.7 24.0 1.0 CA A:CYS220 4.7 20.7 1.0 CB A:PRO222 4.8 29.2 1.0 N A:PRO151 4.9 20.8 1.0 C10 A:KVA401 5.0 30.7 1.0 C7 A:KVA401 5.0 25.0 1.0

Iodine binding site 2 out of 4 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 Iodine with other atoms in the I 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 A:I401 b:21.3 occ:1.00 I1 A:KVA401 0.0 21.3 1.0 C9 A:KVA401 2.1 27.4 1.0 O A:LEU145 3.0 16.6 1.0 C10 A:KVA401 3.1 30.7 1.0 C4 A:KVA401 3.2 31.6 1.0 O2 A:KVA401 3.2 30.6 1.0 N A:KVA401 3.2 26.4 1.0 C8 A:KVA401 3.5 25.1 1.0 O A:HOH617 3.5 21.6 1.0 C A:LEU145 3.7 15.7 1.0 N A:THR230 3.8 18.2 1.0 C5 A:KVA401 3.9 23.4 1.0 OG1 A:THR230 4.0 21.6 1.0 CG2 A:VAL147 4.0 17.0 1.0 CA A:TRP146 4.1 15.7 1.0 C7 A:KVA401 4.1 25.0 1.0 N A:TRP146 4.2 15.3 1.0 CA A:CYS229 4.2 18.7 1.0 CB A:THR230 4.2 20.3 1.0 N A:VAL147 4.2 17.5 1.0 CB A:LEU145 4.3 16.4 1.0 C6 A:KVA401 4.3 24.0 1.0 C A:TRP146 4.3 16.9 1.0 C A:CYS229 4.4 18.5 1.0 C1 A:KVA401 4.4 34.4 1.0 C3 A:KVA401 4.5 39.3 1.0 CG A:PRO223 4.5 28.1 1.0 CA A:THR230 4.6 18.6 1.0 CA A:LEU145 4.6 15.6 1.0 CG1 A:VAL147 4.7 16.6 1.0 CD A:PRO223 4.7 27.0 1.0 CB A:CYS229 4.7 19.7 1.0 CB A:VAL147 4.8 15.5 1.0 O A:ASP228 4.9 24.1 1.0 C2 A:KVA401 5.0 37.5 1.0 F1 A:KVA401 5.0 26.1 1.0

Iodine binding site 3 out of 4 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 Iodine with other atoms in the I binding site number 3 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:I401 b:51.3 occ:1.00 I B:KVA401 0.0 51.3 1.0 C3 B:KVA401 2.1 39.6 1.0 C2 B:KVA401 3.0 38.8 1.0 C4 B:KVA401 3.1 33.2 1.0 N B:KVA401 3.4 27.7 1.0 C5 B:KVA401 3.7 26.3 1.0 C B:GLU221 4.0 24.0 1.0 N B:PRO222 4.0 26.0 1.0 CB B:CYS220 4.1 19.7 1.0 CD B:PRO151 4.1 20.4 1.0 CG2 B:THR150 4.1 30.7 1.0 CG B:PRO151 4.1 21.6 1.0 O B:GLU221 4.1 21.7 1.0 C8 B:KVA401 4.3 27.2 1.0 CD B:PRO222 4.3 28.2 1.0 CA B:PRO222 4.3 26.8 1.0 N B:GLU221 4.4 22.0 1.0 C1 B:KVA401 4.4 36.1 1.0 C B:CYS220 4.4 22.0 1.0 CA B:GLU221 4.5 24.8 1.0 O B:PRO151 4.5 21.3 1.0 C9 B:KVA401 4.5 29.6 1.0 C6 B:KVA401 4.6 27.4 1.0 O B:CYS220 4.6 24.4 1.0 CB B:PRO222 4.8 28.8 1.0 CA B:CYS220 4.9 18.5 1.0 N B:PRO151 4.9 20.2 1.0 C7 B:KVA401 4.9 27.3 1.0 C10 B:KVA401 5.0 32.4 1.0

Iodine binding site 4 out of 4 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 Iodine with other atoms in the I binding site number 4 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:I401 b:23.5 occ:1.00 I1 B:KVA401 0.0 23.5 1.0 C9 B:KVA401 2.1 29.6 1.0 O B:LEU145 3.0 21.0 1.0 C10 B:KVA401 3.1 32.4 1.0 C4 B:KVA401 3.2 33.2 1.0 O2 B:KVA401 3.2 31.9 1.0 N B:KVA401 3.2 27.7 1.0 O B:HOH662 3.4 22.7 1.0 C8 B:KVA401 3.4 27.2 1.0 C B:LEU145 3.7 18.1 1.0 N B:THR230 3.7 18.8 1.0 C5 B:KVA401 3.9 26.3 1.0 CG2 B:VAL147 4.0 19.2 1.0 OG1 B:THR230 4.1 21.6 1.0 CA B:TRP146 4.1 16.4 1.0 C7 B:KVA401 4.1 27.3 1.0 CA B:CYS229 4.2 21.1 1.0 CB B:THR230 4.2 19.7 1.0 N B:TRP146 4.2 16.4 1.0 N B:VAL147 4.2 18.4 1.0 CB B:LEU145 4.3 19.1 1.0 C6 B:KVA401 4.4 27.4 1.0 C B:TRP146 4.4 17.5 1.0 C B:CYS229 4.4 21.3 1.0 C1 B:KVA401 4.4 36.1 1.0 C3 B:KVA401 4.5 39.6 1.0 CA B:THR230 4.6 19.2 1.0 CA B:LEU145 4.6 17.3 1.0 CG B:PRO223 4.7 29.2 1.0 CB B:CYS229 4.7 21.8 1.0 CG1 B:VAL147 4.7 19.3 1.0 CB B:VAL147 4.8 19.1 1.0 O B:ASP228 4.9 26.7 1.0 CD B:PRO223 4.9 28.6 1.0 F1 B:KVA401 4.9 27.4 1.0 C2 B:KVA401 5.0 38.8 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