Zinc in PDB 8qwm: Structure of P53 Cancer Mutant Y205C

The structure of Structure of P53 Cancer Mutant Y205C, PDB code: 8qwm was solved by D.I.Balourdas, S.Knapp, A.C.Joerger, Structural Genomics Consortium(Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.90 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.964, 70.896, 105.055, 90, 90, 90
R / Rfree (%)	18.4 / 22.1

The binding sites of Zinc atom in the Structure of P53 Cancer Mutant Y205C (pdb code 8qwm). 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 P53 Cancer Mutant Y205C, PDB code: 8qwm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of P53 Cancer Mutant Y205C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of P53 Cancer Mutant Y205C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:22.6 occ:1.00 ND1 A:HIS179 2.0 21.5 1.0 SG A:CYS176 2.3 22.5 1.0 SG A:CYS242 2.3 23.3 1.0 SG A:CYS238 2.4 21.5 0.9 SG A:CYS238 2.4 21.9 0.1 CE1 A:HIS179 3.0 23.4 1.0 CG A:HIS179 3.0 21.7 1.0 CB A:CYS242 3.1 25.2 1.0 CB A:CYS238 3.3 20.9 0.1 CB A:CYS238 3.3 18.7 0.9 CB A:CYS176 3.4 23.0 1.0 CB A:HIS179 3.4 20.9 1.0 CA A:CYS238 3.8 20.1 0.1 CA A:CYS238 3.8 17.4 0.9 N A:CYS176 4.0 20.6 1.0 NE2 A:HIS179 4.1 22.8 1.0 CD2 A:HIS179 4.1 23.1 1.0 CA A:CYS176 4.3 22.0 1.0 N A:HIS179 4.3 22.8 1.0 N A:TYR239 4.4 19.6 1.0 CA A:HIS179 4.5 22.3 1.0 CA A:CYS242 4.5 24.1 1.0 O A:HOH616 4.6 23.8 1.0 C A:CYS238 4.6 19.9 0.1 O A:MET237 4.7 19.9 1.0 C A:CYS238 4.7 19.1 0.9 C A:CYS176 5.0 23.1 1.0 N A:CYS238 5.0 17.7 0.9

Zinc binding site 2 out of 2 in the Structure of P53 Cancer Mutant Y205C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of P53 Cancer Mutant Y205C within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:23.4 occ:1.00 ND1 B:HIS179 2.1 25.2 1.0 SG B:CYS176 2.3 22.1 1.0 SG B:CYS242 2.3 24.8 1.0 SG B:CYS238 2.3 21.1 1.0 CE1 B:HIS179 3.0 26.1 1.0 CB B:CYS242 3.1 24.0 1.0 CG B:HIS179 3.1 24.2 1.0 CB B:CYS238 3.3 18.6 1.0 CB B:CYS176 3.3 21.9 1.0 CB B:HIS179 3.5 22.4 1.0 CA B:CYS238 3.8 17.9 1.0 N B:CYS176 4.0 22.2 1.0 NE2 B:HIS179 4.1 25.3 1.0 CD2 B:HIS179 4.2 25.9 1.0 CA B:CYS176 4.3 20.6 1.0 N B:HIS179 4.3 24.1 1.0 CA B:CYS242 4.5 24.7 1.0 N B:TYR239 4.5 20.0 1.0 O B:HOH626 4.5 23.8 1.0 CA B:HIS179 4.5 21.4 1.0 O B:MET237 4.6 20.8 1.0 C B:CYS238 4.7 20.1 1.0 C B:CYS176 5.0 22.4 1.0 N B:CYS238 5.0 19.2 1.0

D.I.Balourdas, A.M.Markl, A.Kramer, G.Settanni, A.C.Joerger. Structural Basis of P53 Inactivation By Cavity-Creating Cancer Mutations and Its Implications For the Development of Mutant P53 Reactivators. Cell Death Dis V. 15 408 2024.
ISSN: ISSN 2041-4889
PubMed: 38862470
DOI: 10.1038/S41419-024-06739-X