Zinc in PDB 4agn: Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5116

The structure of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5116, PDB code: 4agn was solved by A.C.Joerger, R.Wilcken, F.M.Boeckler, A.R.Fersht, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.61 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.040, 71.260, 104.880, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 19.4

The structure of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5116 also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Zinc atom in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5116 (pdb code 4agn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5116, PDB code: 4agn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5116


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5116 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1293 b:10.3 occ:1.00 ND1 A:HIS179 2.0 8.7 1.0 SG A:CYS238 2.3 11.8 1.0 SG A:CYS242 2.3 11.4 1.0 SG A:CYS176 2.3 9.0 1.0 CE1 A:HIS179 3.0 9.4 1.0 CG A:HIS179 3.0 8.8 1.0 CB A:CYS242 3.1 12.9 1.0 CB A:HIS179 3.4 9.5 1.0 CB A:CYS238 3.4 9.3 1.0 CB A:CYS176 3.4 9.6 1.0 CA A:CYS238 3.9 8.9 1.0 O A:HOH2262 4.0 28.6 1.0 N A:CYS176 4.0 8.8 1.0 NE2 A:HIS179 4.1 9.9 1.0 CD2 A:HIS179 4.1 11.4 1.0 N A:HIS179 4.3 11.1 1.0 CA A:CYS176 4.3 11.0 1.0 N A:TYR239 4.4 8.2 1.0 CA A:HIS179 4.5 10.2 1.0 CA A:CYS242 4.5 15.2 1.0 O A:HOH2174 4.6 12.8 1.0 C A:CYS238 4.7 10.2 1.0 O A:MET237 4.7 9.8 1.0 C A:CYS176 5.0 9.3 1.0

Zinc binding site 2 out of 2 in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5116


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5116 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1291 b:10.3 occ:1.00 ND1 B:HIS179 2.1 10.8 1.0 SG B:CYS238 2.3 9.2 1.0 SG B:CYS176 2.3 9.0 1.0 SG B:CYS242 2.4 12.2 1.0 CB B:CYS242 3.1 10.5 1.0 CG B:HIS179 3.1 9.4 1.0 CE1 B:HIS179 3.1 12.6 1.0 CB B:CYS238 3.4 11.4 1.0 CB B:HIS179 3.4 9.3 1.0 CB B:CYS176 3.4 8.3 1.0 CA B:CYS238 3.8 8.8 1.0 N B:CYS176 4.0 6.9 1.0 O B:HOH2273 4.1 27.6 1.0 NE2 B:HIS179 4.2 15.2 1.0 CD2 B:HIS179 4.2 13.8 1.0 CA B:CYS176 4.3 8.1 1.0 N B:HIS179 4.3 11.7 1.0 CA B:CYS242 4.5 9.7 1.0 N B:TYR239 4.5 11.0 1.0 CA B:HIS179 4.5 9.7 1.0 O B:MET237 4.6 9.9 1.0 O B:HOH2175 4.7 10.2 1.0 C B:CYS238 4.7 13.3 1.0 C B:CYS176 5.0 9.0 1.0 N B:CYS238 5.0 8.0 1.0

R.Wilcken, X.Liu, M.O.Zimmermann, T.J.Rutherford, A.R.Fersht, A.C.Joerger, F.M.Boeckler. Halogen-Enriched Fragment Libraries As Leads For Drug Rescue of Mutant P53. J.Am.Chem.Soc. V. 134 6810 2012.
ISSN: ISSN 0002-7863
PubMed: 22439615
DOI: 10.1021/JA301056A