Zinc in PDB 2vuk: Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small-Molecule Drug PHIKAN083

The structure of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small-Molecule Drug PHIKAN083, PDB code: 2vuk was solved by A.C.Joerger, 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)	65.10 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.093, 71.234, 105.207, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 20.8

The binding sites of Zinc atom in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small-Molecule Drug PHIKAN083 (pdb code 2vuk). 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 Drug PHIKAN083, PDB code: 2vuk:
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 Drug PHIKAN083


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 Drug PHIKAN083 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1300 b:10.1 occ:1.00 ND1 A:HIS179 2.0 8.9 1.0 SG A:CYS242 2.3 11.6 1.0 SG A:CYS176 2.3 8.7 1.0 SG A:CYS238 2.3 12.7 1.0 CE1 A:HIS179 3.0 10.0 1.0 CG A:HIS179 3.0 9.5 1.0 CB A:CYS242 3.1 10.2 1.0 CB A:CYS176 3.4 10.1 1.0 CB A:HIS179 3.4 7.7 1.0 CB A:CYS238 3.4 8.5 1.0 CA A:CYS238 3.8 8.8 1.0 O A:HOH2118 3.9 34.8 1.0 N A:CYS176 4.0 8.9 1.0 NE2 A:HIS179 4.1 10.9 1.0 CD2 A:HIS179 4.2 9.0 1.0 N A:HIS179 4.3 9.4 1.0 CA A:CYS176 4.3 7.6 1.0 N A:TYR239 4.4 9.3 1.0 CA A:HIS179 4.5 8.3 1.0 CA A:CYS242 4.5 9.7 1.0 C A:CYS238 4.6 9.5 1.0 O A:HOH2104 4.7 13.1 1.0 O A:MET237 4.8 8.3 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 Drug PHIKAN083


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 Drug PHIKAN083 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1300 b:9.8 occ:1.00 ND1 B:HIS179 2.0 9.5 1.0 SG B:CYS176 2.3 8.8 1.0 SG B:CYS242 2.3 10.4 1.0 SG B:CYS238 2.3 9.4 1.0 CE1 B:HIS179 2.9 11.5 1.0 CG B:HIS179 3.0 9.3 1.0 CB B:CYS242 3.1 9.2 1.0 CB B:CYS238 3.3 8.1 1.0 CB B:CYS176 3.4 10.2 1.0 CB B:HIS179 3.4 9.8 1.0 CA B:CYS238 3.8 6.2 1.0 O B:HOH2102 3.9 33.7 1.0 N B:CYS176 4.0 9.4 1.0 NE2 B:HIS179 4.1 12.3 1.0 CD2 B:HIS179 4.1 9.8 1.0 CA B:CYS176 4.3 10.2 1.0 N B:HIS179 4.4 10.1 1.0 N B:TYR239 4.5 9.1 1.0 CA B:CYS242 4.5 10.3 1.0 CA B:HIS179 4.5 9.9 1.0 O B:HOH2091 4.6 12.2 1.0 O B:MET237 4.6 8.8 1.0 C B:CYS238 4.7 7.9 1.0 N B:CYS238 5.0 8.4 1.0

F.M.Boeckler, A.C.Joerger, G.Jaggi, T.J.Rutherford, D.B.Veprintsev, A.R.Fersht. Targeted Rescue of A Destabilized Mutant of P53 By An in Silico Screened Drug. Proc.Natl.Acad.Sci.Usa V. 105 10360 2008.
ISSN: ISSN 0027-8424
PubMed: 18650397
DOI: 10.1073/PNAS.0805326105