Zinc 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:

Arsenic

(As)

4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Arsenic-Bound P53 Dna-Binding Domain Mutant G245S, PDB code: 7dhy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc 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 Zinc with other atoms in the Zn 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:Zn302 b:92.5 occ:1.00 ND1 A:HIS179 2.0 107.6 1.0 SG A:CYS242 2.3 100.4 1.0 SG A:CYS238 2.3 81.8 1.0 SG A:CYS176 2.3 111.9 1.0 CE1 A:HIS179 2.9 106.0 1.0 CG A:HIS179 3.1 109.7 1.0 CB A:CYS242 3.1 99.0 1.0 CB A:CYS176 3.4 105.3 1.0 CB A:CYS238 3.5 70.9 1.0 CB A:HIS179 3.5 114.2 1.0 CA A:CYS238 3.7 62.0 1.0 N A:ASN239 3.8 70.6 1.0 N A:CYS176 4.0 89.7 1.0 NE2 A:HIS179 4.1 107.2 1.0 CD2 A:HIS179 4.1 108.2 1.0 CA A:CYS176 4.3 99.2 1.0 C A:CYS238 4.3 64.5 1.0 OG A:SER245 4.4 100.7 1.0 N A:HIS179 4.4 122.5 1.0 CA A:HIS179 4.6 121.0 1.0 CA A:CYS242 4.6 98.8 1.0 O A:ASN239 4.7 74.6 1.0 CA A:ASN239 5.0 73.0 1.0 C A:CYS176 5.0 102.4 1.0 O A:CYS176 5.0 98.0 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn302 b:30.7 occ:1.00 ND1 B:HIS179 2.0 24.0 1.0 SG B:CYS242 2.3 33.4 1.0 SG B:CYS238 2.3 38.6 1.0 SG B:CYS176 2.4 31.4 1.0 CE1 B:HIS179 2.9 24.9 1.0 CG B:HIS179 3.0 26.7 1.0 CB B:CYS242 3.1 35.7 1.0 CB B:CYS238 3.4 34.6 1.0 CB B:CYS176 3.4 30.3 1.0 CB B:HIS179 3.5 28.5 1.0 CA B:CYS238 3.7 32.5 1.0 N B:ASN239 3.8 34.9 1.0 N B:CYS176 4.0 27.2 1.0 NE2 B:HIS179 4.0 25.0 1.0 CD2 B:HIS179 4.1 25.5 1.0 C B:CYS238 4.3 33.7 1.0 CA B:CYS176 4.3 29.5 1.0 N B:HIS179 4.4 32.9 1.0 OG B:SER245 4.4 43.9 1.0 CA B:CYS242 4.6 36.5 1.0 CA B:HIS179 4.6 31.1 1.0 OG A:SER106 4.6 58.3 1.0 O B:ASN239 4.7 33.6 1.0 CA B:ASN239 4.9 34.2 1.0 O B:MET237 5.0 28.5 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn302 b:66.1 occ:1.00 ND1 C:HIS179 1.9 69.7 1.0 SG C:CYS242 2.3 74.0 1.0 SG C:CYS238 2.4 64.9 1.0 SG C:CYS176 2.4 78.2 1.0 CE1 C:HIS179 2.8 69.4 1.0 CG C:HIS179 2.9 71.3 1.0 CB C:CYS242 3.2 73.9 1.0 CB C:HIS179 3.4 75.2 1.0 CB C:CYS238 3.4 60.3 1.0 CB C:CYS176 3.5 78.0 1.0 CA C:CYS238 3.7 55.6 1.0 N C:ASN239 3.8 54.9 1.0 NE2 C:HIS179 3.9 69.9 1.0 CD2 C:HIS179 4.0 70.4 1.0 N C:CYS176 4.1 73.4 1.0 C C:CYS238 4.2 56.2 1.0 CA C:CYS176 4.4 78.5 1.0 N C:HIS179 4.4 84.5 1.0 CA C:HIS179 4.5 80.3 1.0 OG C:SER245 4.6 80.2 1.0 CA C:CYS242 4.6 71.6 1.0 O C:ASN239 4.8 51.7 1.0 O C:MET237 4.9 51.7 1.0 CA C:ASN239 4.9 55.4 1.0 N C:CYS238 5.0 51.9 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn302 b:25.1 occ:1.00 ND1 D:HIS179 2.1 21.4 1.0 SG D:CYS176 2.3 25.2 1.0 SG D:CYS238 2.3 25.7 1.0 SG D:CYS242 2.3 25.9 1.0 CE1 D:HIS179 3.0 22.4 1.0 CG D:HIS179 3.1 22.7 1.0 CB D:CYS242 3.1 28.0 1.0 CB D:CYS176 3.3 25.2 1.0 CB D:CYS238 3.5 25.5 1.0 CB D:HIS179 3.5 23.7 1.0 CA D:CYS238 3.8 24.8 1.0 N D:ASN239 3.9 27.2 1.0 N D:CYS176 3.9 24.1 1.0 NE2 D:HIS179 4.1 22.5 1.0 CD2 D:HIS179 4.2 22.5 1.0 CA D:CYS176 4.2 24.4 1.0 C D:CYS238 4.3 25.3 1.0 OG D:SER245 4.4 35.7 1.0 N D:HIS179 4.4 23.6 1.0 CA D:HIS179 4.6 24.7 1.0 CA D:CYS242 4.6 29.3 1.0 O D:ASN239 4.7 26.6 1.0 C D:CYS176 4.9 24.4 1.0 O D:CYS176 4.9 24.8 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