Zinc in PDB 7xv8: Crystal Structure of the Human TR4 Dna-Binding Domain Homodimer Bound to DR1 Response Element
Protein crystallography data
The structure of Crystal Structure of the Human TR4 Dna-Binding Domain Homodimer Bound to DR1 Response Element, PDB code: 7xv8
was solved by
Y.Liu,
Z.Chen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.71 /
3.20
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
51.874,
51.874,
241.506,
90,
90,
90
|
R / Rfree (%)
|
21.3 /
24.9
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the Human TR4 Dna-Binding Domain Homodimer Bound to DR1 Response Element
(pdb code 7xv8). 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 Structure of the Human TR4 Dna-Binding Domain Homodimer Bound to DR1 Response Element, PDB code: 7xv8:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 7xv8
Go back to
Zinc Binding Sites List in 7xv8
Zinc binding site 1 out
of 4 in the Crystal Structure of the Human TR4 Dna-Binding Domain Homodimer Bound to DR1 Response Element
![](/pictures/ZN/pdb/xv/7xv8-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/xv/7xv8-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of the Human TR4 Dna-Binding Domain Homodimer Bound to DR1 Response Element within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn200
b:61.9
occ:1.00
|
SG
|
A:CYS120
|
2.0
|
53.0
|
1.0
|
SG
|
A:CYS134
|
2.1
|
56.4
|
1.0
|
SG
|
A:CYS137
|
2.2
|
58.5
|
1.0
|
SG
|
A:CYS117
|
2.3
|
67.9
|
1.0
|
CB
|
A:CYS117
|
3.2
|
63.5
|
1.0
|
CB
|
A:CYS120
|
3.2
|
50.3
|
1.0
|
CB
|
A:CYS137
|
3.2
|
63.0
|
1.0
|
CB
|
A:CYS134
|
3.3
|
55.6
|
1.0
|
N
|
A:CYS120
|
3.8
|
49.7
|
1.0
|
N
|
A:CYS134
|
3.8
|
61.9
|
1.0
|
CA
|
A:CYS120
|
4.0
|
49.0
|
1.0
|
NH1
|
A:ARG166
|
4.1
|
55.9
|
1.0
|
CA
|
A:CYS134
|
4.1
|
55.9
|
1.0
|
CB
|
A:VAL119
|
4.2
|
53.3
|
1.0
|
N
|
A:CYS137
|
4.2
|
52.2
|
1.0
|
CA
|
A:CYS137
|
4.3
|
61.6
|
1.0
|
CB
|
A:ASP122
|
4.6
|
60.4
|
1.0
|
CA
|
A:CYS117
|
4.7
|
61.1
|
1.0
|
C
|
A:CYS120
|
4.7
|
49.1
|
1.0
|
C
|
A:VAL119
|
4.7
|
58.0
|
1.0
|
O
|
A:CYS134
|
4.8
|
48.5
|
1.0
|
C
|
A:CYS134
|
4.8
|
51.7
|
1.0
|
N
|
A:GLY121
|
4.8
|
46.6
|
1.0
|
CA
|
A:VAL119
|
4.9
|
62.4
|
1.0
|
N
|
A:ASP122
|
4.9
|
54.0
|
1.0
|
C
|
A:SER133
|
5.0
|
63.8
|
1.0
|
|
Zinc binding site 2 out
of 4 in 7xv8
Go back to
Zinc Binding Sites List in 7xv8
Zinc binding site 2 out
of 4 in the Crystal Structure of the Human TR4 Dna-Binding Domain Homodimer Bound to DR1 Response Element
![](/pictures/ZN/pdb/xv/7xv8-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/xv/7xv8-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of the Human TR4 Dna-Binding Domain Homodimer Bound to DR1 Response Element within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn201
b:75.3
occ:1.00
|
SG
|
A:CYS153
|
2.1
|
57.2
|
1.0
|
SG
|
A:CYS172
|
2.1
|
63.1
|
1.0
|
SG
|
A:CYS169
|
2.1
|
53.2
|
1.0
|
SG
|
A:CYS159
|
2.2
|
61.8
|
1.0
|
CB
|
A:CYS159
|
3.0
|
64.8
|
1.0
|
CB
|
A:CYS169
|
3.0
|
56.2
|
1.0
|
CB
|
A:CYS172
|
3.2
|
62.4
|
1.0
|
CB
|
A:CYS153
|
3.2
|
51.7
|
1.0
|
N
|
A:CYS159
|
4.0
|
73.4
|
1.0
|
CA
|
A:CYS159
|
4.1
|
68.7
|
1.0
|
O
|
A:HOH302
|
4.1
|
47.3
|
1.0
|
CA
|
A:CYS153
|
4.2
|
55.4
|
1.0
|
N
|
A:CYS172
|
4.2
|
57.7
|
1.0
|
CA
|
A:GLN157
|
4.2
|
73.5
|
1.0
|
CA
|
A:CYS172
|
4.3
|
58.4
|
1.0
|
CA
|
A:CYS169
|
4.4
|
60.1
|
1.0
|
C
|
A:GLN157
|
4.6
|
77.8
|
1.0
|
N
|
A:GLN157
|
4.7
|
74.9
|
1.0
|
N
|
A:ASP158
|
4.7
|
84.1
|
1.0
|
CD2
|
A:PHE171
|
4.8
|
65.9
|
1.0
|
N
|
A:ARG154
|
4.9
|
71.4
|
1.0
|
C
|
A:CYS153
|
4.9
|
65.5
|
1.0
|
|
Zinc binding site 3 out
of 4 in 7xv8
Go back to
Zinc Binding Sites List in 7xv8
Zinc binding site 3 out
of 4 in the Crystal Structure of the Human TR4 Dna-Binding Domain Homodimer Bound to DR1 Response Element
![](/pictures/ZN/pdb/xv/7xv8-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/xv/7xv8-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of the Human TR4 Dna-Binding Domain Homodimer Bound to DR1 Response Element within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn200
b:63.0
occ:1.00
|
SG
|
B:CYS120
|
2.0
|
45.7
|
1.0
|
SG
|
B:CYS137
|
2.1
|
56.1
|
1.0
|
SG
|
B:CYS117
|
2.3
|
54.9
|
1.0
|
SG
|
B:CYS134
|
2.4
|
55.0
|
1.0
|
CB
|
B:CYS120
|
3.0
|
48.0
|
1.0
|
CB
|
B:CYS137
|
3.4
|
52.3
|
1.0
|
CB
|
B:CYS117
|
3.4
|
51.1
|
1.0
|
N
|
B:CYS120
|
3.5
|
55.8
|
1.0
|
CB
|
B:CYS134
|
3.5
|
53.5
|
1.0
|
CA
|
B:CYS120
|
3.8
|
54.3
|
1.0
|
N
|
B:CYS134
|
4.0
|
63.9
|
1.0
|
CB
|
B:VAL119
|
4.1
|
52.4
|
1.0
|
N
|
B:CYS137
|
4.3
|
53.0
|
1.0
|
CA
|
B:CYS134
|
4.3
|
55.6
|
1.0
|
CA
|
B:CYS137
|
4.4
|
52.9
|
1.0
|
C
|
B:VAL119
|
4.6
|
59.9
|
1.0
|
N
|
B:GLY121
|
4.7
|
60.2
|
1.0
|
C
|
B:CYS120
|
4.7
|
60.7
|
1.0
|
CA
|
B:VAL119
|
4.8
|
56.6
|
1.0
|
CA
|
B:CYS117
|
4.8
|
53.7
|
1.0
|
N
|
B:VAL119
|
4.9
|
57.0
|
1.0
|
CB
|
B:ASP122
|
4.9
|
69.7
|
1.0
|
NH2
|
B:ARG173
|
4.9
|
56.1
|
1.0
|
C
|
B:CYS134
|
5.0
|
48.6
|
1.0
|
O
|
B:CYS134
|
5.0
|
39.3
|
1.0
|
|
Zinc binding site 4 out
of 4 in 7xv8
Go back to
Zinc Binding Sites List in 7xv8
Zinc binding site 4 out
of 4 in the Crystal Structure of the Human TR4 Dna-Binding Domain Homodimer Bound to DR1 Response Element
![](/pictures/ZN/pdb/xv/7xv8-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/xv/7xv8-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of the Human TR4 Dna-Binding Domain Homodimer Bound to DR1 Response Element within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn201
b:77.5
occ:1.00
|
SG
|
B:CYS153
|
1.8
|
63.6
|
1.0
|
SG
|
B:CYS159
|
2.1
|
61.9
|
1.0
|
SG
|
B:CYS169
|
2.2
|
57.4
|
1.0
|
SG
|
B:CYS172
|
2.3
|
53.3
|
1.0
|
CB
|
B:CYS169
|
3.0
|
55.3
|
1.0
|
O
|
B:HOH303
|
3.1
|
57.9
|
1.0
|
CB
|
B:CYS159
|
3.2
|
59.8
|
1.0
|
CB
|
B:CYS153
|
3.3
|
71.6
|
1.0
|
CB
|
B:CYS172
|
3.4
|
58.4
|
1.0
|
CA
|
B:CYS153
|
4.1
|
75.4
|
1.0
|
N
|
B:CYS172
|
4.2
|
59.3
|
1.0
|
N
|
B:CYS159
|
4.2
|
65.0
|
1.0
|
CA
|
B:GLN157
|
4.2
|
63.8
|
1.0
|
N
|
B:GLN157
|
4.3
|
76.4
|
1.0
|
CA
|
B:CYS159
|
4.3
|
59.9
|
1.0
|
CA
|
B:CYS172
|
4.3
|
62.4
|
1.0
|
CA
|
B:CYS169
|
4.4
|
57.2
|
1.0
|
CD2
|
B:PHE171
|
4.7
|
77.2
|
1.0
|
O
|
B:SER155
|
4.7
|
83.8
|
1.0
|
N
|
B:ASP158
|
4.8
|
58.3
|
1.0
|
N
|
B:ARG154
|
4.8
|
81.0
|
1.0
|
C
|
B:GLN157
|
4.8
|
59.6
|
1.0
|
N
|
B:SER155
|
4.9
|
70.8
|
1.0
|
C
|
B:CYS153
|
4.9
|
80.7
|
1.0
|
C
|
B:SER155
|
4.9
|
78.4
|
1.0
|
|
Reference:
Y.Liu,
L.Ma,
M.Li,
Z.Tian,
M.Yang,
X.Wu,
X.Wang,
G.Shang,
M.Xie,
Y.Chen,
X.Liu,
L.Jiang,
W.Wu,
C.Xu,
L.Xia,
G.Li,
S.Dai,
Z.Chen.
Structures of Human TR4LBD-JAZF1 and TR4DBD-Dna Complexes Reveal the Molecular Basis of Transcriptional Regulation Nucleic Acids Res. 2022.
ISSN: ESSN 1362-4962
Page generated: Sat Apr 8 06:05:34 2023
|