Zinc in PDB 5o1d: P53 Cancer Mutant Y220C in Complex with Compound MB481

The structure of P53 Cancer Mutant Y220C in Complex with Compound MB481, PDB code: 5o1d was solved by A.C.Joerger, M.R.Bauer, M.G.J.Baud, A.R.Fersht, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.60 / 1.36
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.176, 71.185, 105.321, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 16.4

The structure of P53 Cancer Mutant Y220C in Complex with Compound MB481 also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Zinc atom in the P53 Cancer Mutant Y220C in Complex with Compound MB481 (pdb code 5o1d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the P53 Cancer Mutant Y220C in Complex with Compound MB481, PDB code: 5o1d:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the P53 Cancer Mutant Y220C in Complex with Compound MB481


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of P53 Cancer Mutant Y220C in Complex with Compound MB481 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:14.0 occ:1.00 ND1 A:HIS179 2.0 13.9 1.0 SG A:CYS242 2.3 16.1 1.0 SG A:CYS238 2.3 18.4 1.0 SG A:CYS176 2.3 13.3 1.0 CE1 A:HIS179 2.9 13.4 1.0 CG A:HIS179 3.0 14.1 1.0 CB A:CYS242 3.1 15.8 1.0 CB A:CYS238 3.4 15.3 1.0 CB A:CYS176 3.4 12.6 1.0 CB A:HIS179 3.4 12.6 1.0 CA A:CYS238 3.8 12.6 1.0 N A:CYS176 4.0 11.8 1.0 NE2 A:HIS179 4.1 16.0 1.0 CD2 A:HIS179 4.1 15.5 1.0 N A:HIS179 4.3 14.0 1.0 CA A:CYS176 4.3 12.2 1.0 N A:TYR239 4.4 13.8 1.0 CA A:HIS179 4.5 13.4 1.0 CA A:CYS242 4.5 14.8 1.0 C A:CYS238 4.6 13.8 1.0 O A:HOH608 4.7 16.8 1.0 O A:MET237 4.8 12.2 1.0 C A:CYS176 5.0 12.6 1.0

Zinc binding site 2 out of 2 in the P53 Cancer Mutant Y220C in Complex with Compound MB481


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of P53 Cancer Mutant Y220C in Complex with Compound MB481 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:14.1 occ:1.00 ND1 B:HIS179 2.1 14.9 1.0 SG B:CYS242 2.3 15.2 1.0 SG B:CYS176 2.3 14.1 1.0 SG B:CYS238 2.3 14.0 1.0 CE1 B:HIS179 3.0 15.9 1.0 CG B:HIS179 3.1 14.5 1.0 CB B:CYS242 3.1 15.1 1.0 CB B:CYS238 3.3 13.0 1.0 CB B:CYS176 3.4 13.9 1.0 CB B:HIS179 3.4 13.3 1.0 CA B:CYS238 3.8 11.2 1.0 N B:CYS176 4.0 11.9 1.0 NE2 B:HIS179 4.1 16.9 1.0 CD2 B:HIS179 4.2 16.4 1.0 CA B:CYS176 4.3 12.7 1.0 N B:HIS179 4.3 15.1 1.0 N B:TYR239 4.5 12.9 1.0 CA B:HIS179 4.5 14.2 1.0 CA B:CYS242 4.5 14.5 1.0 O B:MET237 4.6 12.8 1.0 O B:HOH612 4.7 16.2 1.0 C B:CYS238 4.7 12.6 1.0 N B:CYS238 5.0 11.0 1.0 C B:CYS176 5.0 14.2 1.0

M.G.J.Baud, M.R.Bauer, L.Verduci, F.A.Dingler, K.J.Patel, D.Horil Roy, A.C.Joerger, A.R.Fersht. Aminobenzothiazole Derivatives Stabilize the Thermolabile P53 Cancer Mutant Y220C and Show Anticancer Activity in P53-Y220C Cell Lines. Eur J Med Chem V. 152 101 2018.
ISSN: ISSN 1768-3254
PubMed: 29702446
DOI: 10.1016/J.EJMECH.2018.04.035