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

Protein crystallography data

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

Other elements in 7eax:

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

Zinc (Zn) 4 atoms

Antimony Binding Sites:

The binding sites of Antimony 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 Antimony atom.
In total 4 binding sites of Antimony where determined in the Crystal Complex of P53-V272M and Antimony Ion, PDB code: 7eax:
Jump to Antimony binding site number: 1; 2; 3; 4;

Antimony binding site 1 out of 4 in 7eax

Go back to Antimony Binding Sites List in 7eax
Antimony 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 Antimony with other atoms in the Sb 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:Sb402

b:56.4
occ:1.00
CB A:CYS135 2.8 44.8 1.0
SG A:CYS135 3.0 48.4 1.0
SG A:CYS141 3.0 48.7 1.0
SG A:CYS124 3.0 43.5 1.0
CG A:MET133 3.0 46.5 1.0
CA A:CYS135 3.4 44.1 1.0
O A:PHE134 3.4 36.2 1.0
CB A:CYS124 3.4 40.4 1.0
SD A:MET133 3.5 52.3 1.0
CB A:CYS141 3.6 42.4 1.0
N A:CYS135 3.6 42.4 1.0
C A:PHE134 3.6 38.9 1.0
CA A:CYS124 3.9 38.1 1.0
CA A:CYS141 4.1 40.8 1.0
N A:PHE134 4.3 39.8 1.0
CE A:MET133 4.4 51.9 1.0
CB A:MET133 4.4 44.0 1.0
N A:THR125 4.5 37.8 1.0
C A:CYS124 4.6 38.2 1.0
CA A:PHE134 4.6 38.0 1.0
SD A:MET272 4.7 46.3 1.0
C A:MET133 4.8 39.6 1.0
O A:THR125 4.8 35.4 1.0
C A:CYS135 4.9 43.4 1.0

Antimony binding site 2 out of 4 in 7eax

Go back to Antimony Binding Sites List in 7eax
Antimony 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 Antimony with other atoms in the Sb 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:Sb402

b:57.1
occ:1.00
CB B:CYS135 2.8 47.6 1.0
SG B:CYS135 3.0 50.4 1.0
SG B:CYS141 3.0 51.4 1.0
SG B:CYS124 3.0 48.3 1.0
CG B:MET133 3.0 53.8 1.0
SD B:MET133 3.4 56.1 1.0
O B:PHE134 3.4 44.2 1.0
CB B:CYS124 3.5 44.2 1.0
CA B:CYS135 3.5 48.2 1.0
CB B:CYS141 3.5 45.4 1.0
C B:PHE134 3.7 45.0 1.0
N B:CYS135 3.7 45.9 1.0
CA B:CYS124 3.9 43.1 1.0
CA B:CYS141 4.1 42.6 1.0
CE B:MET133 4.3 57.2 1.0
N B:PHE134 4.3 43.7 1.0
CB B:MET133 4.4 50.8 1.0
N B:THR125 4.5 39.7 1.0
C B:CYS124 4.6 41.7 1.0
CA B:PHE134 4.6 43.2 1.0
SD B:MET272 4.7 48.0 1.0
C B:MET133 4.8 43.8 1.0
O B:THR125 4.8 35.6 1.0
C B:CYS135 5.0 48.7 1.0
O B:THR140 5.0 38.3 1.0

Antimony binding site 3 out of 4 in 7eax

Go back to Antimony Binding Sites List in 7eax
Antimony 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 Antimony with other atoms in the Sb 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:Sb402

b:50.5
occ:1.00
CB C:CYS135 2.9 47.0 1.0
SG C:CYS124 3.0 48.6 1.0
SG C:CYS141 3.0 43.7 1.0
SG C:CYS135 3.0 50.9 1.0
CG C:MET133 3.0 50.6 1.0
CB C:CYS124 3.4 43.6 1.0
SD C:MET133 3.4 53.8 1.0
O C:PHE134 3.5 41.4 1.0
CA C:CYS135 3.5 46.4 1.0
CB C:CYS141 3.5 39.7 1.0
C C:PHE134 3.7 41.8 1.0
N C:CYS135 3.7 43.1 1.0
CA C:CYS124 3.9 41.7 1.0
CA C:CYS141 4.0 37.5 1.0
CE C:MET133 4.3 53.1 1.0
N C:PHE134 4.4 42.3 1.0
CB C:MET133 4.4 48.5 1.0
N C:THR125 4.5 36.0 1.0
C C:CYS124 4.6 38.4 1.0
CA C:PHE134 4.7 41.7 1.0
SD C:MET272 4.8 47.1 1.0
O C:THR125 4.8 38.7 1.0
C C:MET133 4.8 43.7 1.0
O C:THR140 4.9 35.7 1.0
C C:CYS141 5.0 37.8 1.0
C C:CYS135 5.0 47.2 1.0

Antimony binding site 4 out of 4 in 7eax

Go back to Antimony Binding Sites List in 7eax
Antimony 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 Antimony with other atoms in the Sb 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:Sb402

b:46.8
occ:1.00
CB D:CYS135 2.9 47.2 1.0
SG D:CYS124 2.9 41.0 1.0
SG D:CYS141 3.0 39.4 1.0
SG D:CYS135 3.0 51.8 1.0
CG D:MET133 3.1 40.6 1.0
CB D:CYS124 3.3 36.0 1.0
SD D:MET133 3.4 36.9 1.0
CB D:CYS141 3.5 34.8 1.0
O D:PHE134 3.5 41.6 1.0
CA D:CYS135 3.5 45.6 1.0
C D:PHE134 3.8 41.5 1.0
N D:CYS135 3.8 44.2 1.0
CA D:CYS124 3.9 35.4 1.0
CA D:CYS141 3.9 32.7 1.0
CE D:MET133 4.3 37.3 1.0
N D:THR125 4.5 31.6 1.0
N D:PHE134 4.5 41.2 1.0
CB D:MET133 4.5 39.8 1.0
C D:CYS124 4.5 33.2 1.0
CA D:PHE134 4.8 40.2 1.0
O D:THR125 4.9 36.8 1.0
O D:THR140 4.9 29.6 1.0
SD D:MET272 4.9 48.2 1.0
C D:CYS141 4.9 32.3 1.0
C D:MET133 4.9 40.4 1.0

Reference:

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
Page generated: Thu Oct 10 13:18:37 2024

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