Zinc in PDB 7eax: Crystal Complex of P53-V272M and Antimony Ion

The structure of Crystal Complex of P53-V272M and Antimony Ion, PDB code: 7eax was solved by M.Lu, Y.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.53 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.876, 72.551, 85.067, 90, 90, 90
R / Rfree (%)	20.6 / 23.5

The structure of Crystal Complex of P53-V272M and Antimony Ion also contains other interesting chemical elements:

Antimony

(Sb)

4 atoms

The binding sites of Zinc atom in the Crystal Complex of P53-V272M and Antimony Ion (pdb code 7eax). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Complex of P53-V272M and Antimony Ion, PDB code: 7eax:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Complex of P53-V272M and Antimony Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Complex of P53-V272M and Antimony Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:48.7 occ:0.80 ND1 A:HIS179 2.0 48.7 1.0 SG A:CYS242 2.3 53.5 1.0 SG A:CYS238 2.3 48.3 1.0 SG A:CYS176 2.3 49.2 1.0 CE1 A:HIS179 2.9 48.8 1.0 CG A:HIS179 3.0 48.7 1.0 CB A:CYS242 3.3 55.9 1.0 CB A:CYS176 3.4 50.8 1.0 CB A:HIS179 3.5 49.2 1.0 CB A:CYS238 3.6 44.7 1.0 CA A:CYS238 3.7 43.5 1.0 N A:CYS176 4.0 52.7 1.0 NE2 A:HIS179 4.0 47.5 1.0 N A:ASN239 4.1 46.9 1.0 CD2 A:HIS179 4.1 48.4 1.0 CA A:CYS176 4.3 53.0 1.0 C A:CYS238 4.4 43.4 1.0 N A:HIS179 4.6 51.3 1.0 CA A:HIS179 4.6 50.7 1.0 CA A:CYS242 4.7 58.8 1.0 O A:ASN239 4.7 52.1 1.0 O A:MET237 4.8 31.4 1.0 O A:CYS176 4.9 55.5 1.0 N A:CYS238 5.0 38.6 1.0

Zinc binding site 2 out of 4 in the Crystal Complex of P53-V272M and Antimony Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Complex of P53-V272M and Antimony Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:46.4 occ:0.80 ND1 B:HIS179 2.0 46.4 1.0 SG B:CYS242 2.3 48.9 1.0 SG B:CYS176 2.3 47.4 1.0 SG B:CYS238 2.3 45.9 1.0 CE1 B:HIS179 3.0 46.0 1.0 CG B:HIS179 3.1 45.7 1.0 CB B:CYS242 3.2 52.0 1.0 CB B:CYS176 3.4 48.0 1.0 CB B:HIS179 3.4 46.9 1.0 CB B:CYS238 3.6 44.6 1.0 CA B:CYS238 3.7 43.6 1.0 N B:CYS176 4.0 49.9 1.0 N B:ASN239 4.1 44.4 1.0 NE2 B:HIS179 4.1 44.6 1.0 CD2 B:HIS179 4.2 45.1 1.0 CA B:CYS176 4.3 50.0 1.0 C B:CYS238 4.4 44.2 1.0 N B:HIS179 4.6 48.7 1.0 CA B:HIS179 4.6 48.3 1.0 CA B:CYS242 4.6 52.5 1.0 O B:ASN239 4.7 49.6 1.0 O B:MET237 4.8 35.8 1.0 O B:CYS176 4.9 54.3 1.0 C B:CYS176 5.0 51.1 1.0 N B:CYS238 5.0 40.2 1.0

Zinc binding site 3 out of 4 in the Crystal Complex of P53-V272M and Antimony Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Complex of P53-V272M and Antimony Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:41.2 occ:0.80 ND1 C:HIS179 1.9 35.4 1.0 SG C:CYS242 2.3 47.5 1.0 SG C:CYS176 2.4 37.3 1.0 SG C:CYS238 2.4 45.9 1.0 CE1 C:HIS179 2.9 36.3 1.0 CG C:HIS179 3.0 38.2 1.0 CB C:CYS242 3.3 50.9 1.0 CB C:HIS179 3.4 40.2 1.0 CB C:CYS176 3.4 39.5 1.0 CB C:CYS238 3.6 41.6 1.0 CA C:CYS238 3.8 41.0 1.0 N C:CYS176 4.0 37.9 1.0 NE2 C:HIS179 4.0 36.5 1.0 CD2 C:HIS179 4.1 37.4 1.0 N C:ASN239 4.1 41.7 1.0 CA C:CYS176 4.3 38.9 1.0 OG A:SER106 4.4 39.9 0.7 C C:CYS238 4.5 41.1 1.0 N C:HIS179 4.5 40.1 1.0 CA C:HIS179 4.6 41.1 1.0 CA C:CYS242 4.7 53.5 1.0 O C:ASN239 4.8 45.8 1.0 O C:MET237 4.8 37.0 1.0 O C:CYS176 4.9 42.2 1.0 C C:CYS176 5.0 39.0 1.0

Zinc binding site 4 out of 4 in the Crystal Complex of P53-V272M and Antimony Ion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Complex of P53-V272M and Antimony Ion within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:44.2 occ:1.00 ND1 D:HIS179 2.0 40.5 1.0 SG D:CYS242 2.3 47.9 1.0 SG D:CYS176 2.3 41.8 1.0 SG D:CYS238 2.3 45.1 1.0 CE1 D:HIS179 2.9 41.0 1.0 CG D:HIS179 3.0 42.4 1.0 CB D:CYS242 3.3 53.0 1.0 CB D:HIS179 3.4 45.1 1.0 CB D:CYS176 3.4 42.7 1.0 CB D:CYS238 3.6 44.7 1.0 CA D:CYS238 3.8 42.9 1.0 N D:CYS176 4.0 44.6 1.0 NE2 D:HIS179 4.0 40.0 1.0 CD2 D:HIS179 4.1 42.2 1.0 N D:ASN239 4.1 46.4 1.0 CA D:CYS176 4.3 44.2 1.0 C D:CYS238 4.5 45.2 1.0 N D:HIS179 4.5 45.8 1.0 CA D:HIS179 4.6 46.0 1.0 CA D:CYS242 4.7 57.3 1.0 O D:MET237 4.8 36.1 1.0 O D:ASN239 4.8 49.0 1.0 O D:CYS176 4.9 43.7 1.0 C D:CYS176 5.0 43.7 1.0

Y.Tang, H.Song, Z.Wang, S.Xiao, X.Xiang, H.Zhan, L.Wu, J.Wu, Y.Xing, Y.Tan, Y.Liang, N.Yan, Y.Li, J.Li, J.Wu, D.Zheng, Y.Jia, Z.Chen, Y.Li, Q.Zhang, J.Zhang, H.Zeng, W.Tao, F.Liu, Y.Wu, M.Lu. Repurposing Antiparasitic Antimonials to Noncovalently Rescue Temperature-Sensitive P53 Mutations. Cell Rep V. 39 10622 2022.
ISSN: ESSN 2211-1247
PubMed: 35417717
DOI: 10.1016/J.CELREP.2022.110622