Zinc in PDB 7dhz: Arsenic-Bound P53 Dna-Binding Domain Mutant R249S

The structure of Arsenic-Bound P53 Dna-Binding Domain Mutant R249S, PDB code: 7dhz was solved by S.Chen, M.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.52 / 1.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.551, 68.768, 66.784, 90, 93.22, 90
R / Rfree (%)	19.7 / 25.7

The structure of Arsenic-Bound P53 Dna-Binding Domain Mutant R249S also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Arsenic-Bound P53 Dna-Binding Domain Mutant R249S (pdb code 7dhz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Arsenic-Bound P53 Dna-Binding Domain Mutant R249S, PDB code: 7dhz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Arsenic-Bound P53 Dna-Binding Domain Mutant R249S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Arsenic-Bound P53 Dna-Binding Domain Mutant R249S within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:14.8 occ:1.00 ND1 A:HIS179 2.0 12.1 1.0 SG A:CYS176 2.3 15.2 1.0 SG A:CYS238 2.3 12.1 1.0 SG A:CYS242 2.3 18.2 1.0 CE1 A:HIS179 2.9 13.0 1.0 CG A:HIS179 3.1 13.0 1.0 CB A:CYS242 3.2 17.4 1.0 CB A:CYS176 3.3 14.2 1.0 CB A:CYS238 3.4 12.5 1.0 CB A:HIS179 3.6 13.2 1.0 CA A:CYS238 3.8 13.0 1.0 N A:CYS176 4.0 14.0 1.0 NE2 A:HIS179 4.0 12.1 1.0 N A:ASN239 4.1 15.0 1.0 CD2 A:HIS179 4.2 12.1 1.0 CA A:CYS176 4.2 13.6 1.0 N A:HIS179 4.3 13.1 1.0 N A:SER240 4.4 16.2 1.0 C A:CYS238 4.5 13.5 1.0 CA A:CYS242 4.5 19.1 1.0 N A:CYS242 4.5 18.3 1.0 CA A:HIS179 4.6 13.2 1.0 O A:SER240 4.8 19.3 1.0 CA A:SER240 4.8 16.7 1.0 O A:HOH611 4.9 21.1 1.0 C A:SER240 4.9 17.8 1.0 C A:CYS176 4.9 13.6 1.0 O A:MET237 5.0 12.8 1.0 O A:CYS176 5.0 12.5 1.0

Zinc binding site 2 out of 2 in the Arsenic-Bound P53 Dna-Binding Domain Mutant R249S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Arsenic-Bound P53 Dna-Binding Domain Mutant R249S within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:28.0 occ:1.00 ND1 B:HIS179 2.0 43.9 1.0 SG B:CYS238 2.3 21.6 0.5 SG B:CYS242 2.3 31.0 1.0 SG B:CYS238 2.3 22.9 0.5 SG B:CYS176 2.4 28.8 1.0 CE1 B:HIS179 2.9 44.8 1.0 CG B:HIS179 2.9 44.3 1.0 CB B:CYS242 3.2 33.1 1.0 CB B:HIS179 3.4 44.1 1.0 CB B:CYS176 3.4 27.6 1.0 CB B:CYS238 3.4 21.8 0.5 CB B:CYS238 3.4 22.7 0.5 CA B:CYS238 3.9 21.6 0.5 NE2 B:HIS179 3.9 43.7 1.0 CA B:CYS238 3.9 21.1 0.5 N B:CYS176 4.0 23.6 1.0 CD2 B:HIS179 4.0 43.7 1.0 CA B:CYS176 4.2 25.9 1.0 N B:HIS179 4.2 42.3 1.0 N B:ASN239 4.3 21.9 1.0 CA B:HIS179 4.4 45.2 1.0 C B:CYS238 4.6 21.9 0.5 CA B:CYS242 4.6 34.5 1.0 C B:CYS238 4.6 21.6 0.5 O B:CYS176 4.9 28.3 1.0 C B:CYS176 4.9 26.9 1.0 O B:MET237 4.9 20.2 1.0

S.Chen, J.L.Wu, Y.Liang, Y.G.Tang, H.X.Song, L.L.Wu, Y.F.Xing, N.Yan, Y.T.Li, Z.Y.Wang, S.J.Xiao, X.Lu, S.J.Chen, M.Lu. Arsenic Trioxide Rescues Structural P53 Mutations Through A Cryptic Allosteric Site. Cancer Cell V. 39 225 2021.
ISSN: ISSN 1535-6108
PubMed: 33357454
DOI: 10.1016/J.CCELL.2020.11.013