Zinc in PDB 5g4n: Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083

The structure of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083, PDB code: 5g4n was solved by A.C.Joerger, M.Bauer, R.N.Jones, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.47 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.046, 71.139, 105.168, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 16.8

The structure of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 (pdb code 5g4n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083, PDB code: 5g4n:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1293 b:14.9 occ:1.00 ND1 A:HIS179 2.0 15.0 1.0 SG A:CYS242 2.3 16.6 1.0 SG A:CYS238 2.3 18.6 1.0 SG A:CYS176 2.3 14.3 1.0 CE1 A:HIS179 2.9 15.7 1.0 CG A:HIS179 3.0 14.1 1.0 CB A:CYS242 3.1 17.3 1.0 CB A:CYS176 3.4 14.4 1.0 CB A:CYS238 3.4 15.7 1.0 CB A:HIS179 3.4 13.5 1.0 CA A:CYS238 3.8 13.1 1.0 N A:CYS176 4.0 13.7 1.0 NE2 A:HIS179 4.1 16.9 1.0 O A:HOH2203 4.1 40.5 1.0 CD2 A:HIS179 4.1 16.3 1.0 CA A:CYS176 4.3 13.7 1.0 N A:HIS179 4.3 14.9 1.0 N A:TYR239 4.4 14.9 1.0 CA A:HIS179 4.5 14.0 1.0 CA A:CYS242 4.5 16.5 1.0 C A:CYS238 4.6 13.8 1.0 O A:HOH2136 4.7 19.1 1.0 O A:MET237 4.7 12.6 1.0 C A:CYS176 5.0 14.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1291 b:15.1 occ:1.00 ND1 B:HIS179 2.0 15.1 1.0 SG B:CYS242 2.3 16.1 1.0 SG B:CYS176 2.3 14.7 1.0 SG B:CYS238 2.3 15.3 1.0 CE1 B:HIS179 3.0 16.5 1.0 CG B:HIS179 3.1 14.7 1.0 CB B:CYS242 3.1 16.2 1.0 CB B:CYS238 3.3 13.7 1.0 CB B:CYS176 3.4 14.8 1.0 CB B:HIS179 3.4 13.9 1.0 CA B:CYS238 3.8 12.6 1.0 O B:HOH2175 4.0 44.2 1.0 N B:CYS176 4.0 12.6 1.0 NE2 B:HIS179 4.1 17.8 1.0 CD2 B:HIS179 4.2 17.2 1.0 CA B:CYS176 4.3 14.2 1.0 N B:HIS179 4.4 15.2 1.0 N B:TYR239 4.5 13.9 1.0 CA B:HIS179 4.5 14.2 1.0 CA B:CYS242 4.5 15.4 1.0 O B:MET237 4.6 13.5 1.0 O B:HOH2118 4.7 16.3 1.0 C B:CYS238 4.7 13.4 1.0 N B:CYS238 5.0 12.5 1.0 C B:CYS176 5.0 15.8 1.0

M.R.Bauer, R.N.Jones, M.G.J.Baud, R.Wilcken, F.M.Boeckler, A.R.Fersht, A.C.Joerger, J.Spencer. Harnessing Fluorine-Sulfur Contacts and Multipolar Interactions For the Design of P53 Mutant Y220C Rescue Drugs. Acs Chem.Biol. V. 11 2265 2016.
ISSN: ISSN 1554-8929
PubMed: 27267810
DOI: 10.1021/ACSCHEMBIO.6B00315