Zinc in PDB 1tup: Tumor Suppressor P53 Complexed with Dna
Protein crystallography data
The structure of Tumor Suppressor P53 Complexed with Dna, PDB code: 1tup
was solved by
Y.Cho,
S.Gorina,
P.D.Jeffrey,
N.P.Pavletich,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
6.00 /
2.20
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
117.500,
67.900,
108.800,
90.00,
105.50,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Tumor Suppressor P53 Complexed with Dna
(pdb code 1tup). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the
Tumor Suppressor P53 Complexed with Dna, PDB code: 1tup:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 1tup
Go back to
Zinc Binding Sites List in 1tup
Zinc binding site 1 out
of 3 in the Tumor Suppressor P53 Complexed with Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Tumor Suppressor P53 Complexed with Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn951
b:27.1
occ:1.00
|
ND1
|
A:HIS179
|
2.0
|
25.7
|
1.0
|
SG
|
A:CYS242
|
2.2
|
28.2
|
1.0
|
SG
|
A:CYS238
|
2.3
|
24.6
|
1.0
|
SG
|
A:CYS176
|
2.3
|
30.6
|
1.0
|
CE1
|
A:HIS179
|
2.9
|
26.8
|
1.0
|
CG
|
A:HIS179
|
3.1
|
23.7
|
1.0
|
CB
|
A:CYS242
|
3.1
|
25.9
|
1.0
|
CB
|
A:CYS176
|
3.4
|
19.2
|
1.0
|
CB
|
A:HIS179
|
3.5
|
28.0
|
1.0
|
CB
|
A:CYS238
|
3.6
|
20.2
|
1.0
|
CA
|
A:CYS238
|
3.9
|
15.1
|
1.0
|
N
|
A:CYS176
|
4.0
|
16.7
|
1.0
|
N
|
A:ASN239
|
4.0
|
17.5
|
1.0
|
NE2
|
A:HIS179
|
4.1
|
25.5
|
1.0
|
CD2
|
A:HIS179
|
4.2
|
24.2
|
1.0
|
CA
|
A:CYS176
|
4.3
|
13.1
|
1.0
|
N
|
A:HIS179
|
4.4
|
31.5
|
1.0
|
C
|
A:CYS238
|
4.4
|
13.8
|
1.0
|
O
|
A:HOH2139
|
4.5
|
48.8
|
1.0
|
CA
|
A:HIS179
|
4.5
|
30.1
|
1.0
|
CA
|
A:CYS242
|
4.6
|
28.9
|
1.0
|
O
|
A:HOH2123
|
4.8
|
36.0
|
1.0
|
O
|
A:ASN239
|
4.9
|
20.5
|
1.0
|
C
|
A:CYS176
|
4.9
|
17.6
|
1.0
|
O
|
A:MET237
|
5.0
|
19.0
|
1.0
|
|
Zinc binding site 2 out
of 3 in 1tup
Go back to
Zinc Binding Sites List in 1tup
Zinc binding site 2 out
of 3 in the Tumor Suppressor P53 Complexed with Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Tumor Suppressor P53 Complexed with Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn952
b:28.0
occ:1.00
|
ND1
|
B:HIS179
|
2.1
|
23.6
|
1.0
|
SG
|
B:CYS238
|
2.2
|
24.9
|
1.0
|
SG
|
B:CYS242
|
2.2
|
28.0
|
1.0
|
SG
|
B:CYS176
|
2.3
|
29.7
|
1.0
|
CE1
|
B:HIS179
|
3.0
|
20.4
|
1.0
|
CG
|
B:HIS179
|
3.1
|
18.3
|
1.0
|
CB
|
B:CYS238
|
3.2
|
21.8
|
1.0
|
CB
|
B:CYS242
|
3.2
|
27.4
|
1.0
|
CB
|
B:CYS176
|
3.4
|
22.6
|
1.0
|
CB
|
B:HIS179
|
3.5
|
23.2
|
1.0
|
CA
|
B:CYS238
|
3.8
|
19.0
|
1.0
|
N
|
B:CYS176
|
4.0
|
26.1
|
1.0
|
NE2
|
B:HIS179
|
4.1
|
21.4
|
1.0
|
CD2
|
B:HIS179
|
4.2
|
19.2
|
1.0
|
CA
|
B:CYS176
|
4.3
|
24.2
|
1.0
|
O
|
B:HOH2153
|
4.3
|
54.3
|
1.0
|
N
|
B:ASN239
|
4.5
|
15.2
|
1.0
|
CA
|
B:CYS242
|
4.5
|
31.0
|
1.0
|
N
|
B:HIS179
|
4.6
|
24.1
|
1.0
|
CA
|
B:HIS179
|
4.6
|
22.5
|
1.0
|
C
|
B:CYS238
|
4.7
|
15.1
|
1.0
|
O
|
B:MET237
|
4.7
|
21.8
|
1.0
|
O
|
B:HOH2037
|
4.7
|
18.3
|
1.0
|
O
|
B:CYS176
|
4.9
|
31.2
|
1.0
|
C
|
B:CYS176
|
4.9
|
29.5
|
1.0
|
N
|
B:CYS238
|
5.0
|
18.9
|
1.0
|
|
Zinc binding site 3 out
of 3 in 1tup
Go back to
Zinc Binding Sites List in 1tup
Zinc binding site 3 out
of 3 in the Tumor Suppressor P53 Complexed with Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Tumor Suppressor P53 Complexed with Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn953
b:41.3
occ:1.00
|
ND1
|
C:HIS179
|
2.1
|
43.1
|
1.0
|
SG
|
C:CYS242
|
2.1
|
36.9
|
1.0
|
SG
|
C:CYS238
|
2.3
|
41.1
|
1.0
|
SG
|
C:CYS176
|
2.4
|
46.3
|
1.0
|
CG
|
C:HIS179
|
3.0
|
41.6
|
1.0
|
CB
|
C:CYS242
|
3.1
|
36.9
|
1.0
|
CB
|
C:HIS179
|
3.2
|
42.8
|
1.0
|
CE1
|
C:HIS179
|
3.2
|
43.5
|
1.0
|
CB
|
C:CYS238
|
3.4
|
34.6
|
1.0
|
CB
|
C:CYS176
|
3.4
|
40.3
|
1.0
|
N
|
C:CYS176
|
3.8
|
31.9
|
1.0
|
CA
|
C:CYS238
|
3.9
|
35.0
|
1.0
|
CD2
|
C:HIS179
|
4.2
|
41.0
|
1.0
|
CA
|
C:CYS176
|
4.3
|
36.9
|
1.0
|
NE2
|
C:HIS179
|
4.3
|
41.5
|
1.0
|
CA
|
C:HIS179
|
4.4
|
42.2
|
1.0
|
N
|
C:ASN239
|
4.4
|
29.3
|
1.0
|
N
|
C:HIS179
|
4.4
|
46.4
|
1.0
|
CA
|
C:CYS242
|
4.5
|
38.6
|
1.0
|
C
|
C:CYS238
|
4.7
|
33.7
|
1.0
|
O
|
C:HOH2060
|
4.7
|
31.6
|
1.0
|
O
|
C:HOH2220
|
4.9
|
31.0
|
1.0
|
O
|
C:CYS176
|
4.9
|
32.3
|
1.0
|
C
|
C:ARG175
|
4.9
|
35.2
|
1.0
|
O
|
C:MET237
|
4.9
|
42.5
|
1.0
|
C
|
C:CYS176
|
5.0
|
38.2
|
1.0
|
|
Reference:
Y.Cho,
S.Gorina,
P.D.Jeffrey,
N.P.Pavletich.
Crystal Structure of A P53 Tumor Suppressor-Dna Complex: Understanding Tumorigenic Mutations. Science V. 265 346 1994.
ISSN: ISSN 0036-8075
PubMed: 8023157
Page generated: Wed Oct 16 19:17:53 2024
|