Zinc in PDB 4agp: Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5176

The structure of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5176, PDB code: 4agp was solved by A.C.Joerger, R.Wilcken, A.R.Fersht, F.M.Boeckler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.62 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.080, 71.170, 104.980, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 18.7

The structure of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5176 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 PHIKAN5176 (pdb code 4agp). 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 PHIKAN5176, PDB code: 4agp:
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 PHIKAN5176


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 PHIKAN5176 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1300 b:8.4 occ:1.00 ND1 A:HIS179 2.0 7.7 1.0 SG A:CYS242 2.3 10.1 1.0 SG A:CYS238 2.3 10.4 1.0 SG A:CYS176 2.3 7.8 1.0 CE1 A:HIS179 3.0 10.0 1.0 CG A:HIS179 3.1 6.5 1.0 CB A:CYS242 3.1 10.7 1.0 CB A:CYS238 3.4 6.0 1.0 CB A:CYS176 3.4 8.3 1.0 CB A:HIS179 3.4 6.0 1.0 CA A:CYS238 3.8 6.0 1.0 O A:HOH2261 3.9 23.9 1.0 N A:CYS176 4.0 6.7 1.0 NE2 A:HIS179 4.1 9.2 1.0 CD2 A:HIS179 4.2 8.8 1.0 CA A:CYS176 4.3 7.5 1.0 N A:HIS179 4.3 8.3 1.0 N A:TYR239 4.4 7.8 1.0 CA A:HIS179 4.5 7.3 1.0 CA A:CYS242 4.5 9.8 1.0 O A:HOH2164 4.6 10.6 1.0 C A:CYS238 4.7 8.1 1.0 O A:MET237 4.7 6.7 1.0 C A:CYS176 5.0 5.7 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 PHIKAN5176


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 PHIKAN5176 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1300 b:8.3 occ:1.00 ND1 B:HIS179 2.1 9.5 1.0 SG B:CYS238 2.3 8.1 1.0 SG B:CYS176 2.3 7.7 1.0 SG B:CYS242 2.4 9.4 1.0 CE1 B:HIS179 3.0 10.2 1.0 CB B:CYS242 3.1 6.6 1.0 CG B:HIS179 3.1 7.8 1.0 CB B:CYS238 3.3 5.4 1.0 CB B:CYS176 3.4 7.7 1.0 CB B:HIS179 3.4 8.6 1.0 CA B:CYS238 3.8 5.9 1.0 O B:HOH2164 4.0 23.6 1.0 N B:CYS176 4.0 6.5 1.0 NE2 B:HIS179 4.2 10.3 1.0 CD2 B:HIS179 4.2 10.1 1.0 CA B:CYS176 4.3 7.3 1.0 N B:HIS179 4.3 10.8 1.0 N B:TYR239 4.4 7.9 1.0 CA B:CYS242 4.5 6.8 1.0 CA B:HIS179 4.5 9.4 1.0 O B:MET237 4.6 6.9 1.0 C B:CYS238 4.7 7.1 1.0 O B:HOH2155 4.8 8.3 1.0 N B:CYS238 5.0 5.4 1.0 C B:CYS176 5.0 7.7 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