Zinc in PDB 4iqr: Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna
Protein crystallography data
The structure of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna, PDB code: 4iqr
was solved by
V.Chandra,
P.Huang,
Y.Kim,
F.Rastinejad,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.81 /
2.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
119.786,
57.596,
166.305,
90.00,
96.30,
90.00
|
R / Rfree (%)
|
23.9 /
27.8
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna
(pdb code 4iqr). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna, PDB code: 4iqr:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 4iqr
Go back to
Zinc Binding Sites List in 4iqr
Zinc binding site 1 out
of 8 in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:74.1
occ:1.00
|
SG
|
A:CYS54
|
2.1
|
78.5
|
1.0
|
SG
|
A:CYS71
|
2.4
|
61.9
|
1.0
|
SG
|
A:CYS68
|
2.5
|
87.0
|
1.0
|
SG
|
A:CYS51
|
2.5
|
79.0
|
1.0
|
CB
|
A:CYS54
|
3.1
|
68.5
|
1.0
|
N
|
A:CYS54
|
3.4
|
74.6
|
1.0
|
CB
|
A:CYS71
|
3.4
|
63.3
|
1.0
|
CB
|
A:CYS51
|
3.4
|
84.8
|
1.0
|
CB
|
A:CYS68
|
3.5
|
78.0
|
1.0
|
N
|
A:CYS68
|
3.7
|
83.7
|
1.0
|
CA
|
A:CYS54
|
3.7
|
74.7
|
1.0
|
CA
|
A:CYS68
|
4.2
|
77.7
|
1.0
|
CB
|
A:ILE53
|
4.3
|
68.4
|
1.0
|
N
|
A:CYS71
|
4.3
|
74.7
|
1.0
|
N
|
A:GLY55
|
4.4
|
78.5
|
1.0
|
C
|
A:CYS54
|
4.5
|
76.5
|
1.0
|
CA
|
A:CYS71
|
4.5
|
61.8
|
1.0
|
C
|
A:ILE53
|
4.5
|
74.0
|
1.0
|
CB
|
A:ASP56
|
4.7
|
91.2
|
1.0
|
CB
|
A:SER67
|
4.7
|
78.5
|
1.0
|
N
|
A:ASP56
|
4.7
|
85.3
|
1.0
|
C
|
A:SER67
|
4.7
|
84.6
|
1.0
|
NH1
|
A:ARG100
|
4.8
|
88.2
|
1.0
|
CA
|
A:SER67
|
4.8
|
78.0
|
1.0
|
CG2
|
A:ILE53
|
4.8
|
66.5
|
1.0
|
CA
|
A:CYS51
|
4.8
|
79.5
|
1.0
|
CA
|
A:ILE53
|
4.9
|
68.5
|
1.0
|
C
|
A:CYS68
|
4.9
|
76.7
|
1.0
|
O
|
A:CYS68
|
5.0
|
78.0
|
1.0
|
|
Zinc binding site 2 out
of 8 in 4iqr
Go back to
Zinc Binding Sites List in 4iqr
Zinc binding site 2 out
of 8 in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn403
b:77.4
occ:1.00
|
SG
|
A:CYS103
|
2.2
|
63.8
|
1.0
|
SG
|
A:CYS93
|
2.3
|
75.5
|
1.0
|
SG
|
A:CYS87
|
2.3
|
68.3
|
1.0
|
SG
|
A:CYS106
|
2.5
|
66.4
|
1.0
|
CB
|
A:CYS87
|
3.1
|
62.0
|
1.0
|
CB
|
A:CYS93
|
3.4
|
69.2
|
1.0
|
CB
|
A:CYS103
|
3.5
|
64.8
|
1.0
|
CB
|
A:CYS106
|
3.7
|
61.9
|
1.0
|
CA
|
A:CYS87
|
3.8
|
60.9
|
1.0
|
N
|
A:CYS106
|
4.0
|
56.9
|
1.0
|
N
|
A:CYS93
|
4.2
|
78.3
|
1.0
|
CA
|
A:ARG91
|
4.3
|
72.7
|
1.0
|
CB
|
A:TYR105
|
4.4
|
66.4
|
1.0
|
CD2
|
A:TYR105
|
4.4
|
69.3
|
1.0
|
CA
|
A:CYS93
|
4.4
|
74.2
|
1.0
|
CA
|
A:CYS106
|
4.4
|
62.7
|
1.0
|
N
|
A:ARG91
|
4.6
|
73.7
|
1.0
|
N
|
A:ARG88
|
4.7
|
69.5
|
1.0
|
N
|
A:GLN92
|
4.7
|
76.9
|
1.0
|
C
|
A:ARG91
|
4.8
|
78.3
|
1.0
|
C
|
A:CYS87
|
4.8
|
68.2
|
1.0
|
CG
|
A:TYR105
|
4.9
|
65.9
|
1.0
|
N
|
A:CYS87
|
4.9
|
60.8
|
1.0
|
CA
|
A:CYS103
|
4.9
|
67.2
|
1.0
|
|
Zinc binding site 3 out
of 8 in 4iqr
Go back to
Zinc Binding Sites List in 4iqr
Zinc binding site 3 out
of 8 in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:98.4
occ:1.00
|
SG
|
B:CYS54
|
2.3
|
98.6
|
1.0
|
SG
|
B:CYS71
|
2.3
|
82.1
|
1.0
|
SG
|
B:CYS51
|
2.5
|
89.5
|
1.0
|
SG
|
B:CYS68
|
2.5
|
81.3
|
1.0
|
CB
|
B:CYS71
|
3.2
|
89.6
|
1.0
|
CB
|
B:CYS51
|
3.6
|
92.9
|
1.0
|
CB
|
B:CYS54
|
3.8
|
94.4
|
1.0
|
CB
|
B:CYS68
|
3.9
|
93.5
|
1.0
|
N
|
B:CYS68
|
3.9
|
88.3
|
1.0
|
N
|
B:CYS71
|
4.1
|
83.5
|
1.0
|
NH1
|
B:ARG100
|
4.1
|
87.5
|
1.0
|
N
|
B:CYS54
|
4.1
|
92.3
|
1.0
|
CA
|
B:CYS71
|
4.3
|
88.4
|
1.0
|
CA
|
B:CYS68
|
4.4
|
91.2
|
1.0
|
CB
|
B:ASP56
|
4.5
|
90.7
|
1.0
|
CA
|
B:CYS54
|
4.5
|
92.5
|
1.0
|
CB
|
B:SER67
|
4.6
|
86.4
|
1.0
|
O
|
B:CYS68
|
4.6
|
87.1
|
1.0
|
CB
|
B:ILE53
|
4.6
|
94.7
|
1.0
|
N
|
B:ASP56
|
4.7
|
96.1
|
1.0
|
C
|
B:CYS68
|
4.9
|
89.7
|
1.0
|
CD
|
B:ARG100
|
4.9
|
80.4
|
1.0
|
C
|
B:SER67
|
4.9
|
86.8
|
1.0
|
N
|
B:GLY55
|
4.9
|
94.3
|
1.0
|
CA
|
B:SER67
|
5.0
|
87.7
|
1.0
|
CA
|
B:CYS51
|
5.0
|
92.7
|
1.0
|
|
Zinc binding site 4 out
of 8 in 4iqr
Go back to
Zinc Binding Sites List in 4iqr
Zinc binding site 4 out
of 8 in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn403
b:98.7
occ:1.00
|
SG
|
B:CYS87
|
2.2
|
0.9
|
1.0
|
SG
|
B:CYS93
|
2.3
|
0.3
|
1.0
|
SG
|
B:CYS106
|
2.4
|
93.2
|
1.0
|
SG
|
B:CYS103
|
2.6
|
0.7
|
1.0
|
CB
|
B:CYS93
|
3.0
|
0.8
|
1.0
|
CB
|
B:CYS103
|
3.1
|
94.8
|
1.0
|
CB
|
B:CYS106
|
3.4
|
0.8
|
1.0
|
CB
|
B:CYS87
|
3.5
|
0.3
|
1.0
|
N
|
B:CYS93
|
4.0
|
0.2
|
1.0
|
CA
|
B:CYS93
|
4.2
|
0.3
|
1.0
|
CA
|
B:CYS87
|
4.2
|
0.9
|
1.0
|
N
|
B:CYS106
|
4.2
|
93.6
|
1.0
|
CA
|
B:CYS106
|
4.4
|
0.5
|
1.0
|
CA
|
B:ARG91
|
4.6
|
0.1
|
1.0
|
CA
|
B:CYS103
|
4.6
|
97.4
|
1.0
|
N
|
B:GLN92
|
4.8
|
0.1
|
1.0
|
CD2
|
B:PHE89
|
4.8
|
0.1
|
1.0
|
CD2
|
B:TYR105
|
4.9
|
0.3
|
1.0
|
C
|
B:ARG91
|
4.9
|
1.0
|
1.0
|
N
|
B:ARG91
|
5.0
|
0.4
|
1.0
|
C
|
B:CYS87
|
5.0
|
1.0
|
1.0
|
O
|
B:CYS103
|
5.0
|
86.0
|
1.0
|
|
Zinc binding site 5 out
of 8 in 4iqr
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Zinc Binding Sites List in 4iqr
Zinc binding site 5 out
of 8 in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn402
b:88.0
occ:1.00
|
SG
|
E:CYS54
|
2.2
|
88.5
|
1.0
|
SG
|
E:CYS71
|
2.2
|
63.4
|
1.0
|
SG
|
E:CYS51
|
2.3
|
86.0
|
1.0
|
SG
|
E:CYS68
|
2.3
|
86.9
|
1.0
|
CB
|
E:CYS54
|
3.3
|
85.5
|
1.0
|
CB
|
E:CYS71
|
3.3
|
74.3
|
1.0
|
CB
|
E:CYS51
|
3.3
|
88.3
|
1.0
|
N
|
E:CYS54
|
3.5
|
90.8
|
1.0
|
CB
|
E:CYS68
|
3.7
|
86.8
|
1.0
|
CA
|
E:CYS54
|
4.0
|
86.2
|
1.0
|
N
|
E:CYS68
|
4.0
|
95.2
|
1.0
|
CB
|
E:ILE53
|
4.2
|
87.9
|
1.0
|
N
|
E:CYS71
|
4.4
|
74.9
|
1.0
|
CA
|
E:CYS68
|
4.4
|
84.4
|
1.0
|
CA
|
E:CYS71
|
4.4
|
67.6
|
1.0
|
NH1
|
E:ARG100
|
4.5
|
80.7
|
1.0
|
N
|
E:GLY55
|
4.5
|
87.0
|
1.0
|
C
|
E:ILE53
|
4.6
|
92.5
|
1.0
|
CA
|
E:CYS51
|
4.8
|
89.1
|
1.0
|
C
|
E:CYS54
|
4.8
|
87.0
|
1.0
|
CG2
|
E:ILE53
|
4.8
|
84.7
|
1.0
|
CA
|
E:ILE53
|
4.8
|
85.4
|
1.0
|
N
|
E:ILE53
|
4.9
|
92.4
|
1.0
|
CB
|
E:ASP56
|
4.9
|
99.5
|
1.0
|
N
|
E:ASP56
|
4.9
|
95.8
|
1.0
|
|
Zinc binding site 6 out
of 8 in 4iqr
Go back to
Zinc Binding Sites List in 4iqr
Zinc binding site 6 out
of 8 in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn403
b:95.4
occ:1.00
|
SG
|
E:CYS93
|
2.2
|
0.4
|
1.0
|
SG
|
E:CYS106
|
2.2
|
85.0
|
1.0
|
SG
|
E:CYS87
|
2.2
|
88.4
|
1.0
|
SG
|
E:CYS103
|
2.3
|
75.8
|
1.0
|
CB
|
E:CYS93
|
3.0
|
90.6
|
1.0
|
CB
|
E:CYS103
|
3.3
|
75.4
|
1.0
|
CB
|
E:CYS106
|
3.4
|
77.6
|
1.0
|
CB
|
E:CYS87
|
3.5
|
83.9
|
1.0
|
N
|
E:CYS93
|
3.8
|
0.3
|
1.0
|
CA
|
E:CYS93
|
4.0
|
90.4
|
1.0
|
N
|
E:CYS106
|
4.1
|
73.3
|
1.0
|
CA
|
E:CYS106
|
4.4
|
77.4
|
1.0
|
CA
|
E:CYS87
|
4.4
|
86.4
|
1.0
|
CA
|
E:ARG91
|
4.5
|
0.4
|
1.0
|
N
|
E:GLN92
|
4.5
|
99.3
|
1.0
|
N
|
E:ARG91
|
4.7
|
0.4
|
1.0
|
CA
|
E:CYS103
|
4.7
|
74.4
|
1.0
|
CD2
|
E:TYR105
|
4.8
|
79.1
|
1.0
|
C
|
E:ARG91
|
4.8
|
0.2
|
1.0
|
CB
|
E:TYR105
|
4.8
|
72.8
|
1.0
|
|
Zinc binding site 7 out
of 8 in 4iqr
Go back to
Zinc Binding Sites List in 4iqr
Zinc binding site 7 out
of 8 in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn402
b:0.2
occ:1.00
|
SG
|
F:CYS54
|
2.3
|
99.5
|
1.0
|
SG
|
F:CYS71
|
2.4
|
90.4
|
1.0
|
SG
|
F:CYS51
|
2.4
|
95.0
|
1.0
|
SG
|
F:CYS68
|
2.8
|
86.2
|
1.0
|
CB
|
F:CYS51
|
3.3
|
97.3
|
1.0
|
CB
|
F:CYS54
|
3.4
|
0.7
|
1.0
|
CB
|
F:CYS71
|
3.5
|
87.1
|
1.0
|
N
|
F:CYS54
|
3.9
|
0.7
|
1.0
|
CB
|
F:CYS68
|
3.9
|
87.9
|
1.0
|
N
|
F:CYS71
|
4.0
|
84.8
|
1.0
|
N
|
F:CYS68
|
4.1
|
88.8
|
1.0
|
CA
|
F:CYS54
|
4.2
|
0.5
|
1.0
|
CA
|
F:CYS71
|
4.4
|
86.1
|
1.0
|
CB
|
F:ILE53
|
4.4
|
95.3
|
1.0
|
NH2
|
F:ARG100
|
4.4
|
0.4
|
1.0
|
CZ
|
F:ARG100
|
4.5
|
99.6
|
1.0
|
CA
|
F:CYS68
|
4.6
|
89.5
|
1.0
|
CB
|
F:ASP56
|
4.7
|
0.8
|
1.0
|
C
|
F:ILE53
|
4.8
|
0.3
|
1.0
|
CA
|
F:CYS51
|
4.8
|
96.9
|
1.0
|
NH1
|
F:ARG107
|
4.8
|
71.3
|
1.0
|
NE
|
F:ARG100
|
4.8
|
95.6
|
1.0
|
N
|
F:GLY55
|
4.8
|
0.1
|
1.0
|
CB
|
F:SER67
|
4.9
|
93.2
|
1.0
|
O
|
F:CYS68
|
4.9
|
80.9
|
1.0
|
N
|
F:ASP56
|
4.9
|
0.0
|
1.0
|
NH1
|
F:ARG100
|
5.0
|
93.7
|
1.0
|
C
|
F:CYS54
|
5.0
|
0.4
|
1.0
|
|
Zinc binding site 8 out
of 8 in 4iqr
Go back to
Zinc Binding Sites List in 4iqr
Zinc binding site 8 out
of 8 in the Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Multi-Domain Organization of the HNF4ALPHA Nuclear Receptor Complex on Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn403
b:0.3
occ:1.00
|
SG
|
F:CYS87
|
2.2
|
0.8
|
1.0
|
SG
|
F:CYS93
|
2.4
|
86.8
|
1.0
|
SG
|
F:CYS106
|
2.4
|
90.9
|
1.0
|
SG
|
F:CYS103
|
2.5
|
0.1
|
1.0
|
CB
|
F:CYS87
|
3.3
|
0.9
|
1.0
|
CB
|
F:CYS93
|
3.4
|
97.6
|
1.0
|
CB
|
F:CYS106
|
3.5
|
96.8
|
1.0
|
CB
|
F:CYS103
|
3.5
|
0.4
|
1.0
|
N
|
F:CYS106
|
4.0
|
99.1
|
1.0
|
CA
|
F:CYS87
|
4.1
|
0.2
|
1.0
|
CA
|
F:ARG91
|
4.2
|
0.7
|
1.0
|
CA
|
F:CYS106
|
4.3
|
98.2
|
1.0
|
N
|
F:CYS93
|
4.3
|
0.8
|
1.0
|
CD2
|
F:TYR105
|
4.5
|
0.6
|
1.0
|
CA
|
F:CYS93
|
4.5
|
96.2
|
1.0
|
N
|
F:ARG91
|
4.5
|
0.9
|
1.0
|
CB
|
F:TYR105
|
4.6
|
0.4
|
1.0
|
C
|
F:ARG91
|
4.7
|
0.8
|
1.0
|
N
|
F:GLN92
|
4.8
|
0.5
|
1.0
|
N
|
F:ARG88
|
4.9
|
0.3
|
1.0
|
CA
|
F:CYS103
|
4.9
|
0.1
|
1.0
|
C
|
F:TYR105
|
5.0
|
0.1
|
1.0
|
|
Reference:
V.Chandra,
P.Huang,
N.Potluri,
D.Wu,
Y.Kim,
F.Rastinejad.
Multidomain Integration in the Structure of the Hnf-4 Alpha Nuclear Receptor Complex. Nature V. 495 394 2013.
ISSN: ISSN 0028-0836
PubMed: 23485969
DOI: 10.1038/NATURE11966
Page generated: Sun Oct 27 00:50:55 2024
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