Phosphorus in PDB 1a6y: Reverba Orphan Nuclear Receptor/Dna Complex
Protein crystallography data
The structure of Reverba Orphan Nuclear Receptor/Dna Complex, PDB code: 1a6y
was solved by
Q.Zhao,
S.Khorasanizadeh,
F.Rastinejad,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
6.00 /
2.30
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
38.670,
45.690,
47.950,
75.16,
80.64,
85.58
|
R / Rfree (%)
|
19.2 /
28.8
|
Phosphorus Binding Sites:
Phosphorus binding site 1 out
of 38 in 1a6y
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Phosphorus Binding Sites List in 1a6y
Phosphorus binding site 1 out
of 38 in the Reverba Orphan Nuclear Receptor/Dna Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Reverba Orphan Nuclear Receptor/Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:P601
b:64.6
occ:1.00
|
P
|
C:DA601
|
0.0
|
64.6
|
1.0
|
OP2
|
C:DA601
|
1.5
|
62.8
|
1.0
|
OP1
|
C:DA601
|
1.5
|
53.7
|
1.0
|
O5'
|
C:DA601
|
1.6
|
61.9
|
1.0
|
O3'
|
C:DC600
|
1.6
|
60.9
|
1.0
|
C5'
|
C:DA601
|
2.6
|
57.1
|
1.0
|
C3'
|
C:DC600
|
2.6
|
55.1
|
1.0
|
C2'
|
C:DC600
|
3.2
|
49.4
|
1.0
|
O
|
C:HOH742
|
3.6
|
37.6
|
1.0
|
C4'
|
C:DA601
|
3.9
|
59.3
|
1.0
|
C4'
|
C:DC600
|
3.9
|
53.0
|
1.0
|
O
|
C:HOH929
|
4.0
|
48.5
|
1.0
|
C1'
|
C:DC600
|
4.2
|
52.3
|
1.0
|
O
|
C:HOH881
|
4.2
|
46.5
|
1.0
|
O4'
|
C:DA601
|
4.2
|
61.8
|
1.0
|
C8
|
C:DA601
|
4.3
|
51.4
|
1.0
|
O4'
|
C:DC600
|
4.6
|
54.0
|
1.0
|
C3'
|
C:DA601
|
4.6
|
64.6
|
1.0
|
C2'
|
C:DA601
|
4.7
|
60.0
|
1.0
|
O
|
C:HOH805
|
4.7
|
38.6
|
1.0
|
C1'
|
C:DA601
|
4.9
|
55.0
|
1.0
|
N9
|
C:DA601
|
4.9
|
49.0
|
1.0
|
|
Phosphorus binding site 2 out
of 38 in 1a6y
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Phosphorus Binding Sites List in 1a6y
Phosphorus binding site 2 out
of 38 in the Reverba Orphan Nuclear Receptor/Dna Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Reverba Orphan Nuclear Receptor/Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:P602
b:63.4
occ:1.00
|
P
|
C:DA602
|
0.0
|
63.4
|
1.0
|
OP1
|
C:DA602
|
1.5
|
58.6
|
1.0
|
OP2
|
C:DA602
|
1.5
|
64.0
|
1.0
|
O5'
|
C:DA602
|
1.6
|
60.6
|
1.0
|
O3'
|
C:DA601
|
1.6
|
64.8
|
1.0
|
C3'
|
C:DA601
|
2.6
|
64.6
|
1.0
|
C5'
|
C:DA602
|
2.6
|
51.2
|
1.0
|
C2'
|
C:DA601
|
3.3
|
60.0
|
1.0
|
O
|
C:HOH875
|
3.6
|
43.4
|
1.0
|
C4'
|
C:DA602
|
3.9
|
51.8
|
1.0
|
C4'
|
C:DA601
|
3.9
|
59.3
|
1.0
|
C1'
|
C:DA601
|
4.2
|
55.0
|
1.0
|
O4'
|
C:DA602
|
4.2
|
46.1
|
1.0
|
C8
|
C:DA602
|
4.4
|
27.1
|
1.0
|
C3'
|
C:DA602
|
4.5
|
56.2
|
1.0
|
C2'
|
C:DA602
|
4.5
|
50.6
|
1.0
|
O4'
|
C:DA601
|
4.6
|
61.8
|
1.0
|
C1'
|
C:DA602
|
4.9
|
43.9
|
1.0
|
|
Phosphorus binding site 3 out
of 38 in 1a6y
Go back to
Phosphorus Binding Sites List in 1a6y
Phosphorus binding site 3 out
of 38 in the Reverba Orphan Nuclear Receptor/Dna Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Reverba Orphan Nuclear Receptor/Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:P603
b:55.1
occ:1.00
|
P
|
C:DC603
|
0.0
|
55.1
|
1.0
|
OP1
|
C:DC603
|
1.5
|
54.1
|
1.0
|
OP2
|
C:DC603
|
1.5
|
46.1
|
1.0
|
O5'
|
C:DC603
|
1.6
|
41.2
|
1.0
|
O3'
|
C:DA602
|
1.6
|
57.1
|
1.0
|
C5'
|
C:DC603
|
2.6
|
51.9
|
1.0
|
C3'
|
C:DA602
|
2.6
|
56.2
|
1.0
|
C2'
|
C:DA602
|
3.3
|
50.6
|
1.0
|
CD
|
A:ARG175
|
3.7
|
60.6
|
1.0
|
CG
|
A:ARG175
|
3.8
|
61.2
|
1.0
|
C4'
|
C:DC603
|
3.9
|
44.6
|
1.0
|
C4'
|
C:DA602
|
4.0
|
51.8
|
1.0
|
CB
|
A:ARG175
|
4.0
|
59.8
|
1.0
|
C1'
|
C:DA602
|
4.1
|
43.9
|
1.0
|
C3'
|
C:DC603
|
4.2
|
40.9
|
1.0
|
O4'
|
C:DA602
|
4.6
|
46.1
|
1.0
|
C2'
|
C:DC603
|
4.7
|
47.6
|
1.0
|
NE
|
A:ARG175
|
4.7
|
61.3
|
1.0
|
O4'
|
C:DC603
|
4.7
|
46.1
|
1.0
|
CA
|
A:ARG175
|
4.7
|
53.5
|
1.0
|
O
|
C:HOH926
|
5.0
|
54.5
|
1.0
|
|
Phosphorus binding site 4 out
of 38 in 1a6y
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Phosphorus Binding Sites List in 1a6y
Phosphorus binding site 4 out
of 38 in the Reverba Orphan Nuclear Receptor/Dna Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Reverba Orphan Nuclear Receptor/Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:P604
b:28.6
occ:1.00
|
P
|
C:DT604
|
0.0
|
28.6
|
1.0
|
OP1
|
C:DT604
|
1.5
|
30.0
|
1.0
|
OP2
|
C:DT604
|
1.5
|
8.8
|
1.0
|
O5'
|
C:DT604
|
1.6
|
11.9
|
1.0
|
O3'
|
C:DC603
|
1.6
|
38.9
|
1.0
|
C5'
|
C:DT604
|
2.6
|
11.8
|
1.0
|
C3'
|
C:DC603
|
2.6
|
40.9
|
1.0
|
C2'
|
C:DC603
|
3.3
|
47.6
|
1.0
|
C4'
|
C:DT604
|
3.8
|
14.1
|
1.0
|
C4'
|
C:DC603
|
3.9
|
44.6
|
1.0
|
O4'
|
C:DT604
|
3.9
|
17.7
|
1.0
|
O
|
C:HOH872
|
4.0
|
49.2
|
1.0
|
N
|
A:PHE111
|
4.0
|
19.9
|
1.0
|
C1'
|
C:DC603
|
4.1
|
42.1
|
1.0
|
C6
|
C:DT604
|
4.2
|
18.3
|
1.0
|
O
|
A:HOH883
|
4.3
|
42.9
|
1.0
|
O
|
A:PHE111
|
4.5
|
31.5
|
1.0
|
CA
|
A:GLY110
|
4.5
|
25.4
|
1.0
|
C3'
|
C:DT604
|
4.6
|
12.2
|
1.0
|
CB
|
A:PHE111
|
4.6
|
26.5
|
1.0
|
O4'
|
C:DC603
|
4.6
|
46.1
|
1.0
|
C2'
|
C:DT604
|
4.6
|
12.1
|
1.0
|
C1'
|
C:DT604
|
4.8
|
14.5
|
1.0
|
C
|
A:GLY110
|
4.8
|
25.8
|
1.0
|
CA
|
A:PHE111
|
4.9
|
18.9
|
1.0
|
C7
|
C:DT604
|
4.9
|
12.4
|
1.0
|
N1
|
C:DT604
|
5.0
|
16.2
|
1.0
|
|
Phosphorus binding site 5 out
of 38 in 1a6y
Go back to
Phosphorus Binding Sites List in 1a6y
Phosphorus binding site 5 out
of 38 in the Reverba Orphan Nuclear Receptor/Dna Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of Reverba Orphan Nuclear Receptor/Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:P605
b:23.7
occ:1.00
|
P
|
C:DA605
|
0.0
|
23.7
|
1.0
|
OP2
|
C:DA605
|
1.5
|
37.5
|
1.0
|
OP1
|
C:DA605
|
1.5
|
28.5
|
1.0
|
O5'
|
C:DA605
|
1.6
|
32.7
|
1.0
|
O3'
|
C:DT604
|
1.6
|
14.3
|
1.0
|
C3'
|
C:DT604
|
2.6
|
12.2
|
1.0
|
C5'
|
C:DA605
|
2.6
|
23.4
|
1.0
|
C2'
|
C:DT604
|
3.5
|
12.1
|
1.0
|
C8
|
C:DA605
|
3.5
|
24.0
|
1.0
|
C4'
|
C:DT604
|
3.8
|
14.1
|
1.0
|
CD2
|
A:HIS112
|
3.9
|
26.8
|
1.0
|
C4'
|
C:DA605
|
3.9
|
13.5
|
1.0
|
O
|
A:HOH709
|
3.9
|
17.9
|
1.0
|
N
|
A:TYR113
|
4.0
|
12.0
|
1.0
|
CG1
|
A:VAL171
|
4.1
|
18.0
|
1.0
|
CA
|
A:HIS112
|
4.1
|
17.7
|
1.0
|
O
|
A:PHE111
|
4.1
|
31.5
|
1.0
|
N7
|
C:DA605
|
4.2
|
28.8
|
1.0
|
O4'
|
C:DA605
|
4.3
|
16.1
|
1.0
|
N9
|
C:DA605
|
4.4
|
16.7
|
1.0
|
C1'
|
C:DT604
|
4.4
|
14.5
|
1.0
|
C2'
|
C:DA605
|
4.5
|
16.1
|
1.0
|
C3'
|
C:DA605
|
4.5
|
18.6
|
1.0
|
CG
|
A:HIS112
|
4.5
|
23.0
|
1.0
|
CB
|
A:HIS112
|
4.6
|
24.1
|
1.0
|
C1'
|
C:DA605
|
4.6
|
21.7
|
1.0
|
C
|
A:HIS112
|
4.6
|
20.5
|
1.0
|
O4'
|
C:DT604
|
4.7
|
17.7
|
1.0
|
C5'
|
C:DT604
|
4.8
|
11.8
|
1.0
|
CG2
|
A:VAL171
|
4.8
|
24.5
|
1.0
|
NE2
|
A:HIS112
|
4.9
|
15.2
|
1.0
|
CD2
|
A:TYR113
|
5.0
|
30.5
|
1.0
|
|
Phosphorus binding site 6 out
of 38 in 1a6y
Go back to
Phosphorus Binding Sites List in 1a6y
Phosphorus binding site 6 out
of 38 in the Reverba Orphan Nuclear Receptor/Dna Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of Reverba Orphan Nuclear Receptor/Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:P606
b:41.0
occ:1.00
|
P
|
C:DG606
|
0.0
|
41.0
|
1.0
|
OP1
|
C:DG606
|
1.5
|
30.9
|
1.0
|
OP2
|
C:DG606
|
1.5
|
36.8
|
1.0
|
O5'
|
C:DG606
|
1.6
|
42.2
|
1.0
|
O3'
|
C:DA605
|
1.6
|
18.0
|
1.0
|
C5'
|
C:DG606
|
2.6
|
42.1
|
1.0
|
C3'
|
C:DA605
|
2.6
|
18.6
|
1.0
|
C2'
|
C:DA605
|
3.2
|
16.1
|
1.0
|
O
|
C:HOH792
|
3.6
|
39.7
|
1.0
|
NH1
|
A:ARG168
|
3.7
|
29.3
|
1.0
|
C4'
|
C:DA605
|
3.9
|
13.5
|
1.0
|
C4'
|
C:DG606
|
3.9
|
27.1
|
1.0
|
NH2
|
A:ARG168
|
4.0
|
20.8
|
1.0
|
OH
|
A:TYR113
|
4.1
|
30.2
|
1.0
|
C1'
|
C:DA605
|
4.2
|
21.7
|
1.0
|
CZ
|
A:ARG168
|
4.4
|
19.2
|
1.0
|
C3'
|
C:DG606
|
4.4
|
31.4
|
1.0
|
O4'
|
C:DA605
|
4.5
|
16.1
|
1.0
|
CE1
|
A:TYR113
|
4.9
|
30.5
|
1.0
|
CZ
|
A:TYR113
|
4.9
|
29.7
|
1.0
|
O4'
|
C:DG606
|
5.0
|
21.4
|
1.0
|
|
Phosphorus binding site 7 out
of 38 in 1a6y
Go back to
Phosphorus Binding Sites List in 1a6y
Phosphorus binding site 7 out
of 38 in the Reverba Orphan Nuclear Receptor/Dna Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 7 of Reverba Orphan Nuclear Receptor/Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:P607
b:35.3
occ:1.00
|
P
|
C:DG607
|
0.0
|
35.3
|
1.0
|
OP1
|
C:DG607
|
1.5
|
33.5
|
1.0
|
OP2
|
C:DG607
|
1.5
|
42.3
|
1.0
|
O5'
|
C:DG607
|
1.6
|
28.4
|
1.0
|
O3'
|
C:DG606
|
1.6
|
41.0
|
1.0
|
C5'
|
C:DG607
|
2.6
|
35.5
|
1.0
|
C3'
|
C:DG606
|
2.6
|
31.4
|
1.0
|
C2'
|
C:DG606
|
3.1
|
23.4
|
1.0
|
C4'
|
C:DG607
|
3.9
|
33.2
|
1.0
|
C4'
|
C:DG606
|
4.0
|
27.1
|
1.0
|
O
|
C:HOH777
|
4.0
|
67.2
|
1.0
|
C1'
|
C:DG606
|
4.1
|
28.4
|
1.0
|
C3'
|
C:DG607
|
4.4
|
36.4
|
1.0
|
O4'
|
C:DG607
|
4.5
|
40.0
|
1.0
|
O4'
|
C:DG606
|
4.5
|
21.4
|
1.0
|
C8
|
C:DG607
|
4.7
|
20.2
|
1.0
|
C2'
|
C:DG607
|
4.7
|
34.9
|
1.0
|
NE2
|
A:GLN130
|
4.9
|
66.5
|
1.0
|
|
Phosphorus binding site 8 out
of 38 in 1a6y
Go back to
Phosphorus Binding Sites List in 1a6y
Phosphorus binding site 8 out
of 38 in the Reverba Orphan Nuclear Receptor/Dna Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 8 of Reverba Orphan Nuclear Receptor/Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:P608
b:30.2
occ:1.00
|
P
|
C:DT608
|
0.0
|
30.2
|
1.0
|
OP1
|
C:DT608
|
1.5
|
35.1
|
1.0
|
OP2
|
C:DT608
|
1.5
|
23.8
|
1.0
|
O5'
|
C:DT608
|
1.6
|
19.9
|
1.0
|
O3'
|
C:DG607
|
1.6
|
26.9
|
1.0
|
C5'
|
C:DT608
|
2.6
|
28.5
|
1.0
|
C3'
|
C:DG607
|
2.6
|
36.4
|
1.0
|
C2'
|
C:DG607
|
3.2
|
34.9
|
1.0
|
O
|
C:HOH868
|
3.3
|
50.2
|
1.0
|
O
|
C:HOH818
|
3.8
|
26.4
|
1.0
|
C4'
|
C:DT608
|
3.9
|
27.5
|
1.0
|
C4'
|
C:DG607
|
3.9
|
33.2
|
1.0
|
C1'
|
C:DG607
|
4.1
|
29.4
|
1.0
|
C3'
|
C:DT608
|
4.2
|
27.4
|
1.0
|
O4'
|
C:DG607
|
4.5
|
40.0
|
1.0
|
C2'
|
C:DT608
|
4.5
|
34.7
|
1.0
|
O4'
|
C:DT608
|
4.5
|
28.7
|
1.0
|
O
|
C:HOH743
|
4.6
|
48.8
|
1.0
|
|
Phosphorus binding site 9 out
of 38 in 1a6y
Go back to
Phosphorus Binding Sites List in 1a6y
Phosphorus binding site 9 out
of 38 in the Reverba Orphan Nuclear Receptor/Dna Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 9 of Reverba Orphan Nuclear Receptor/Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:P609
b:28.2
occ:1.00
|
P
|
C:DC609
|
0.0
|
28.2
|
1.0
|
OP2
|
C:DC609
|
1.5
|
14.2
|
1.0
|
OP1
|
C:DC609
|
1.5
|
33.9
|
1.0
|
O5'
|
C:DC609
|
1.6
|
23.1
|
1.0
|
O3'
|
C:DT608
|
1.6
|
31.1
|
1.0
|
C3'
|
C:DT608
|
2.6
|
27.4
|
1.0
|
C5'
|
C:DC609
|
2.6
|
30.2
|
1.0
|
C2'
|
C:DT608
|
3.4
|
34.7
|
1.0
|
O
|
C:HOH825
|
3.8
|
56.1
|
1.0
|
C4'
|
C:DT608
|
3.9
|
27.5
|
1.0
|
C4'
|
C:DC609
|
3.9
|
28.0
|
1.0
|
C1'
|
C:DT608
|
4.2
|
34.9
|
1.0
|
C3'
|
C:DC609
|
4.3
|
14.1
|
1.0
|
O4'
|
C:DC609
|
4.4
|
27.4
|
1.0
|
C2'
|
C:DC609
|
4.5
|
10.9
|
1.0
|
O4'
|
C:DT608
|
4.6
|
28.7
|
1.0
|
O
|
C:HOH917
|
4.9
|
40.4
|
1.0
|
C5'
|
C:DT608
|
4.9
|
28.5
|
1.0
|
|
Phosphorus binding site 10 out
of 38 in 1a6y
Go back to
Phosphorus Binding Sites List in 1a6y
Phosphorus binding site 10 out
of 38 in the Reverba Orphan Nuclear Receptor/Dna Complex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 10 of Reverba Orphan Nuclear Receptor/Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:P610
b:34.0
occ:1.00
|
P
|
C:DA610
|
0.0
|
34.0
|
1.0
|
OP2
|
C:DA610
|
1.5
|
17.7
|
1.0
|
OP1
|
C:DA610
|
1.5
|
25.3
|
1.0
|
O5'
|
C:DA610
|
1.6
|
31.7
|
1.0
|
O3'
|
C:DC609
|
1.6
|
20.2
|
1.0
|
C3'
|
C:DC609
|
2.6
|
14.1
|
1.0
|
C5'
|
C:DA610
|
2.6
|
32.3
|
1.0
|
C4'
|
C:DC609
|
3.4
|
28.0
|
1.0
|
O
|
C:HOH749
|
3.7
|
58.6
|
1.0
|
C8
|
C:DA610
|
3.8
|
6.8
|
1.0
|
C4'
|
C:DA610
|
3.8
|
24.0
|
1.0
|
C2'
|
C:DC609
|
3.8
|
10.9
|
1.0
|
O4'
|
C:DA610
|
4.0
|
20.4
|
1.0
|
O
|
C:HOH719
|
4.1
|
46.4
|
1.0
|
C2'
|
C:DA610
|
4.3
|
9.2
|
1.0
|
C5'
|
C:DC609
|
4.4
|
30.2
|
1.0
|
C1'
|
C:DC609
|
4.4
|
18.3
|
1.0
|
N9
|
C:DA610
|
4.4
|
6.5
|
1.0
|
O4'
|
C:DC609
|
4.4
|
27.4
|
1.0
|
C1'
|
C:DA610
|
4.5
|
12.7
|
1.0
|
C3'
|
C:DA610
|
4.5
|
15.9
|
1.0
|
N7
|
C:DA610
|
4.7
|
3.5
|
1.0
|
O5'
|
C:DC609
|
4.9
|
23.1
|
1.0
|
|
Reference:
Q.Zhao,
S.Khorasanizadeh,
Y.Miyoshi,
M.A.Lazar,
F.Rastinejad.
Structural Elements of An Orphan Nuclear Receptor-Dna Complex. Mol.Cell V. 1 849 1998.
ISSN: ISSN 1097-2765
PubMed: 9660968
DOI: 10.1016/S1097-2765(00)80084-2
Page generated: Fri Sep 25 12:20:01 2020
|