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Zinc 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:

Antimony (Sb) 4 atoms

Zinc Binding Sites:

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 7eax

Go back to Zinc Binding Sites List in 7eax
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 7eax

Go back to Zinc Binding Sites List in 7eax
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 7eax

Go back to Zinc Binding Sites List in 7eax
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 7eax

Go back to Zinc Binding Sites List in 7eax
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

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: Tue Oct 29 19:40:25 2024

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