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:
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
|