Zinc in PDB 7v97: Arsenic-Bound P53 Dna-Binding Domain Mutant V272M

Protein crystallography data

The structure of Arsenic-Bound P53 Dna-Binding Domain Mutant V272M, PDB code: 7v97 was solved by M.Lu, Y.F.Xing, Z.Y.Wang, Y.Ni, H.X.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.80 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.839, 71.524, 84.684, 90, 90, 90
R / Rfree (%) 23.4 / 25.1

Other elements in 7v97:

The structure of Arsenic-Bound P53 Dna-Binding Domain Mutant V272M also contains other interesting chemical elements:

Arsenic (As) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Arsenic-Bound P53 Dna-Binding Domain Mutant V272M (pdb code 7v97). 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 V272M, PDB code: 7v97:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7v97

Go back to Zinc Binding Sites List in 7v97
Zinc binding site 1 out of 4 in the Arsenic-Bound P53 Dna-Binding Domain Mutant V272M


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 V272M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:20.7
occ:0.80
 ND1 A:HIS179 2.0 22.0 1.0
SG A:CYS242 2.3 26.1 1.0
SG A:CYS238 2.3 20.6 1.0
SG A:CYS176 2.3 23.4 1.0
CE1 A:HIS179 2.9 22.5 1.0
CG A:HIS179 3.0 22.6 1.0
CB A:CYS242 3.3 26.4 1.0
CB A:HIS179 3.4 22.5 1.0
CB A:CYS176 3.4 23.7 1.0
CB A:CYS238 3.5 19.9 1.0
CA A:CYS238 3.9 19.4 1.0
N A:CYS176 4.0 24.6 1.0
NE2 A:HIS179 4.0 22.4 1.0
CD2 A:HIS179 4.1 22.7 1.0
CA A:CYS176 4.3 24.4 1.0
N A:ASN239 4.3 20.6 1.0
N A:HIS179 4.5 23.9 1.0
CA A:HIS179 4.5 22.5 1.0
CA A:CYS242 4.6 27.5 1.0
C A:CYS238 4.6 19.8 1.0
O A:MET237 4.8 16.9 1.0
O A:ASN239 4.8 21.2 1.0
O A:CYS176 4.9 24.7 1.0
C A:CYS176 5.0 25.0 1.0

Zinc binding site 2 out of 4 in 7v97

Go back to Zinc Binding Sites List in 7v97
Zinc binding site 2 out of 4 in the Arsenic-Bound P53 Dna-Binding Domain Mutant V272M


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 V272M within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:22.7
occ:0.80
 ND1 B:HIS179 2.0 26.4 1.0
SG B:CYS242 2.3 28.9 1.0
SG B:CYS238 2.3 25.5 1.0
SG B:CYS176 2.3 29.8 1.0
CE1 B:HIS179 2.9 27.0 1.0
CG B:HIS179 3.0 27.0 1.0
CB B:CYS242 3.3 29.5 1.0
CB B:CYS176 3.4 27.7 1.0
CB B:HIS179 3.4 27.0 1.0
CB B:CYS238 3.6 25.5 1.0
CA B:CYS238 3.8 25.3 1.0
N B:CYS176 3.9 27.4 1.0
NE2 B:HIS179 4.1 27.3 1.0
CD2 B:HIS179 4.1 27.2 1.0
N B:ASN239 4.2 25.4 1.0
CA B:CYS176 4.3 28.1 1.0
C B:CYS238 4.5 25.7 1.0
N B:HIS179 4.5 27.6 1.0
CA B:CYS242 4.6 30.7 1.0
CA B:HIS179 4.6 26.6 1.0
O B:ASN239 4.8 25.4 1.0
O B:MET237 4.9 25.3 1.0
O B:CYS176 5.0 28.0 1.0
C B:CYS176 5.0 28.3 1.0

Zinc binding site 3 out of 4 in 7v97

Go back to Zinc Binding Sites List in 7v97
Zinc binding site 3 out of 4 in the Arsenic-Bound P53 Dna-Binding Domain Mutant V272M


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 V272M within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:22.3
occ:0.80
 ND1 C:HIS179 2.0 21.8 1.0
SG C:CYS242 2.3 29.1 1.0
SG C:CYS176 2.3 27.0 1.0
SG C:CYS238 2.4 25.7 1.0
CE1 C:HIS179 3.0 23.2 1.0
CG C:HIS179 3.1 23.2 1.0
CB C:CYS176 3.2 25.9 1.0
CB C:CYS242 3.3 30.8 1.0
CB C:HIS179 3.5 23.6 1.0
CB C:CYS238 3.6 26.2 1.0
N C:CYS176 3.8 25.9 1.0
CA C:CYS238 3.8 26.9 1.0
CA C:CYS176 4.1 26.3 1.0
NE2 C:HIS179 4.1 23.3 1.0
CD2 C:HIS179 4.2 23.2 1.0
N C:ASN239 4.2 29.7 1.0
C C:CYS238 4.4 28.2 1.0
N C:HIS179 4.5 23.9 1.0
CA C:HIS179 4.6 23.7 1.0
O C:ASN239 4.7 30.0 1.0
CA C:CYS242 4.7 32.3 1.0
OG A:SER106 4.7 23.4 0.7
C C:CYS176 4.9 26.2 1.0
O C:CYS176 4.9 26.7 1.0
O C:MET237 4.9 25.7 1.0
C C:ARG175 4.9 26.0 1.0

Zinc binding site 4 out of 4 in 7v97

Go back to Zinc Binding Sites List in 7v97
Zinc binding site 4 out of 4 in the Arsenic-Bound P53 Dna-Binding Domain Mutant V272M


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 V272M within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:21.2
occ:0.80
 ND1 D:HIS179 2.0 20.9 1.0
SG D:CYS176 2.3 23.8 1.0
SG D:CYS238 2.3 22.3 1.0
SG D:CYS242 2.3 27.1 1.0
CE1 D:HIS179 2.9 21.9 1.0
CG D:HIS179 3.0 21.8 1.0
CB D:CYS176 3.3 23.6 1.0
CB D:HIS179 3.3 22.1 1.0
CB D:CYS242 3.3 27.9 1.0
CB D:CYS238 3.5 22.6 1.0
N D:CYS176 3.8 24.9 1.0
CA D:CYS238 4.0 22.6 1.0
NE2 D:HIS179 4.0 22.1 1.0
CD2 D:HIS179 4.1 21.6 1.0
CA D:CYS176 4.1 24.7 1.0
N D:HIS179 4.4 22.6 1.0
N D:ASN239 4.5 23.8 1.0
CA D:HIS179 4.5 22.3 1.0
CA D:CYS242 4.7 29.6 1.0
C D:CYS238 4.7 22.9 1.0
O D:CYS176 4.8 24.9 1.0
C D:CYS176 4.8 24.3 1.0
O D:ASN239 4.9 23.4 1.0
O D:MET237 4.9 21.9 1.0
C D:ARG175 5.0 26.0 1.0

Reference:

H.X.Song, J.L.Wu, Y.G.Tang, M.Lu. Landscape of Arsenic-Rescuable P53 Mutations Potentializes Personalized P53-Targeted Therapy To Be Published.
Page generated: Wed Oct 30 12:35:01 2024

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