Arsenic in PDB 7dhy: Arsenic-Bound P53 Dna-Binding Domain Mutant G245S

The structure of Arsenic-Bound P53 Dna-Binding Domain Mutant G245S, PDB code: 7dhy 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)	48.21 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.109, 68.243, 83.621, 90, 90.03, 90
R / Rfree (%)	18.7 / 21.9

The structure of Arsenic-Bound P53 Dna-Binding Domain Mutant G245S also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Arsenic atom in the Arsenic-Bound P53 Dna-Binding Domain Mutant G245S (pdb code 7dhy). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Arsenic-Bound P53 Dna-Binding Domain Mutant G245S, PDB code: 7dhy:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in the Arsenic-Bound P53 Dna-Binding Domain Mutant G245S


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Arsenic-Bound P53 Dna-Binding Domain Mutant G245S within 5.0Å range: probe atom residue distance (Å) B Occ A:As301 b:55.3 occ:1.00 SG A:CYS135 2.2 43.4 0.5 SG A:CYS135 2.2 40.5 0.5 SG A:CYS124 2.2 42.4 1.0 SG A:CYS141 2.2 49.0 1.0 CB A:CYS135 3.1 40.4 0.5 CB A:CYS135 3.1 39.4 0.5 CB A:CYS141 3.2 43.8 1.0 CB A:CYS124 3.3 38.0 1.0 CG A:MET133 3.3 35.1 1.0 SD A:MET133 3.4 37.1 1.0 CA A:CYS135 3.7 37.4 0.5 CA A:CYS135 3.7 38.1 0.5 CA A:CYS141 3.8 39.5 1.0 CA A:CYS124 3.9 34.3 1.0 O A:PHE134 3.9 35.1 1.0 C A:PHE134 4.2 34.3 1.0 N A:CYS135 4.2 36.0 0.5 N A:CYS135 4.2 36.2 0.5 CE A:MET133 4.3 38.0 1.0 O A:THR140 4.6 35.5 1.0 C A:CYS124 4.6 31.5 1.0 N A:THR125 4.6 29.0 1.0 C A:CYS141 4.7 38.2 1.0 CB A:MET133 4.8 32.7 1.0 N A:CYS141 4.8 39.6 1.0 O A:THR123 4.9 32.1 1.0 N A:PHE134 5.0 31.9 1.0

Arsenic binding site 2 out of 4 in the Arsenic-Bound P53 Dna-Binding Domain Mutant G245S


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Arsenic-Bound P53 Dna-Binding Domain Mutant G245S within 5.0Å range: probe atom residue distance (Å) B Occ B:As301 b:42.2 occ:1.00 SG B:CYS135 2.2 36.4 0.5 SG B:CYS141 2.2 35.3 1.0 SG B:CYS135 2.2 36.7 0.5 SG B:CYS124 2.2 32.1 1.0 CB B:CYS135 3.1 32.2 0.5 CB B:CYS135 3.1 32.6 0.5 CB B:CYS141 3.1 29.0 1.0 CB B:CYS124 3.2 30.0 1.0 CG B:MET133 3.4 29.0 1.0 SD B:MET133 3.5 32.4 1.0 CA B:CYS141 3.7 25.6 1.0 CA B:CYS135 3.7 30.1 0.5 CA B:CYS135 3.7 29.8 0.5 CA B:CYS124 3.8 27.9 1.0 O B:PHE134 3.9 25.1 1.0 N B:CYS135 4.3 28.0 0.5 N B:CYS135 4.3 27.6 0.5 C B:PHE134 4.3 27.0 1.0 CE B:MET133 4.4 29.4 1.0 O B:THR140 4.4 25.8 1.0 C B:CYS124 4.6 26.3 1.0 N B:THR125 4.6 24.7 1.0 C B:CYS141 4.7 23.9 1.0 N B:CYS141 4.7 24.8 1.0 O B:THR123 4.9 26.7 1.0 CB B:MET133 4.9 26.6 1.0 C B:THR140 5.0 25.5 1.0

Arsenic binding site 3 out of 4 in the Arsenic-Bound P53 Dna-Binding Domain Mutant G245S


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Arsenic-Bound P53 Dna-Binding Domain Mutant G245S within 5.0Å range: probe atom residue distance (Å) B Occ C:As301 b:45.9 occ:1.00 SG C:CYS135 2.2 42.8 0.5 SG C:CYS124 2.2 38.4 1.0 SG C:CYS135 2.2 41.3 0.5 SG C:CYS141 2.3 35.1 1.0 CB C:CYS135 3.0 40.7 0.5 CB C:CYS135 3.0 41.0 0.5 CB C:CYS141 3.1 35.1 1.0 CB C:CYS124 3.2 36.1 1.0 CG C:MET133 3.5 33.7 1.0 SD C:MET133 3.6 40.7 1.0 CA C:CYS135 3.6 38.7 0.5 CA C:CYS135 3.6 38.9 0.5 CA C:CYS141 3.7 33.4 1.0 CA C:CYS124 3.8 32.4 1.0 O C:PHE134 3.9 33.5 1.0 N C:CYS135 4.2 35.1 0.5 N C:CYS135 4.2 35.0 0.5 C C:PHE134 4.2 32.5 1.0 O C:THR140 4.4 36.5 1.0 CE C:MET133 4.5 38.8 1.0 C C:CYS124 4.5 29.3 1.0 N C:THR125 4.5 25.9 1.0 C C:CYS141 4.7 31.1 1.0 N C:CYS141 4.7 34.6 1.0 O C:THR123 4.8 34.4 1.0 C C:CYS135 4.9 39.6 0.5 C C:CYS135 4.9 39.7 0.5 CB C:MET133 5.0 30.6 1.0 N C:CYS124 5.0 34.5 1.0 C C:THR140 5.0 35.7 1.0

Arsenic binding site 4 out of 4 in the Arsenic-Bound P53 Dna-Binding Domain Mutant G245S


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Arsenic-Bound P53 Dna-Binding Domain Mutant G245S within 5.0Å range: probe atom residue distance (Å) B Occ D:As301 b:40.6 occ:1.00 SG D:CYS135 2.2 30.9 0.5 SG D:CYS124 2.2 33.2 1.0 SG D:CYS135 2.3 32.8 0.5 SG D:CYS141 2.3 33.3 1.0 CB D:CYS135 2.9 28.7 0.5 CB D:CYS135 3.2 29.7 0.5 CB D:CYS141 3.2 30.8 1.0 CB D:CYS124 3.3 28.4 1.0 CG D:MET133 3.3 28.5 1.0 SD D:MET133 3.4 31.8 1.0 CA D:CYS135 3.6 25.4 0.5 CA D:CYS141 3.7 27.9 1.0 CA D:CYS135 3.7 26.1 0.5 CA D:CYS124 3.8 26.6 1.0 O D:PHE134 3.9 22.9 1.0 N D:CYS135 4.1 24.4 0.5 C D:PHE134 4.2 23.2 1.0 N D:CYS135 4.2 24.9 0.5 CE D:MET133 4.3 31.6 1.0 N D:THR125 4.5 22.1 1.0 C D:CYS124 4.5 22.9 1.0 O D:THR140 4.5 27.7 1.0 C D:CYS141 4.7 26.6 1.0 N D:CYS141 4.8 26.9 1.0 CB D:MET133 4.8 25.1 1.0 O D:THR123 5.0 27.9 1.0 C D:CYS135 5.0 24.2 0.5 N D:PHE134 5.0 21.9 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