Zinc in PDB 6si1: P53 Cancer Mutant Y220H

The structure of P53 Cancer Mutant Y220H, PDB code: 6si1 was solved by A.C.Joerger, A.Kraemer, S.Knapp, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.78 / 1.44
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.762, 70.771, 104.879, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 17.9

The binding sites of Zinc atom in the P53 Cancer Mutant Y220H (pdb code 6si1). 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 Y220H, PDB code: 6si1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the P53 Cancer Mutant Y220H


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 Y220H within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:13.6 occ:1.00 ND1 A:HIS179 2.0 13.3 1.0 SG A:CYS242 2.3 15.0 1.0 SG A:CYS238 2.3 17.9 1.0 SG A:CYS176 2.3 12.5 1.0 CE1 A:HIS179 2.9 13.8 1.0 CG A:HIS179 3.0 12.9 1.0 CB A:CYS242 3.1 15.8 1.0 CB A:CYS176 3.3 11.9 1.0 CB A:CYS238 3.3 14.9 1.0 CB A:HIS179 3.4 11.9 1.0 CA A:CYS238 3.8 11.6 1.0 O A:HOH740 4.0 36.2 1.0 N A:CYS176 4.0 11.1 1.0 NE2 A:HIS179 4.1 14.8 1.0 CD2 A:HIS179 4.1 13.6 1.0 CA A:CYS176 4.3 11.6 1.0 N A:HIS179 4.3 13.3 1.0 N A:TYR239 4.3 12.1 1.0 CA A:HIS179 4.5 12.2 1.0 CA A:CYS242 4.5 13.4 1.0 C A:CYS238 4.6 11.7 1.0 O A:HOH623 4.7 16.5 1.0 O A:MET237 4.7 11.0 1.0 C A:CYS176 5.0 11.8 1.0 N A:CYS238 5.0 10.6 1.0

Zinc binding site 2 out of 2 in the P53 Cancer Mutant Y220H


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 Y220H within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:12.9 occ:1.00 ND1 B:HIS179 2.0 14.1 1.0 SG B:CYS238 2.3 12.5 1.0 SG B:CYS242 2.3 13.3 1.0 SG B:CYS176 2.3 12.2 1.0 CE1 B:HIS179 3.0 14.5 1.0 CG B:HIS179 3.1 12.5 1.0 CB B:CYS242 3.1 13.7 1.0 CB B:CYS238 3.3 11.7 1.0 CB B:CYS176 3.3 11.8 1.0 CB B:HIS179 3.4 10.9 1.0 CA B:CYS238 3.8 11.0 1.0 N B:CYS176 4.0 10.9 1.0 NE2 B:HIS179 4.1 15.1 1.0 CD2 B:HIS179 4.2 14.5 1.0 CA B:CYS176 4.3 11.7 1.0 N B:HIS179 4.3 13.3 1.0 N B:TYR239 4.4 10.9 1.0 CA B:CYS242 4.5 13.4 1.0 CA B:HIS179 4.5 11.3 1.0 O B:MET237 4.6 11.3 1.0 O B:HOH617 4.7 14.6 1.0 C B:CYS238 4.7 10.4 1.0 N B:CYS238 4.9 10.5 1.0 C B:CYS176 5.0 13.1 1.0

M.R.Bauer, A.Kramer, G.Settanni, R.N.Jones, X.Ni, R.Khan Tareque, A.R.Fersht, J.Spencer, A.C.Joerger. Targeting Cavity-Creating P53 Cancer Mutations with Small-Molecule Stabilizers: the Y220X Paradigm. Acs Chem.Biol. 2020.
ISSN: ESSN 1554-8937
PubMed: 31990523
DOI: 10.1021/ACSCHEMBIO.9B00748