Caesium in PDB 7eoj: Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak
Protein crystallography data
The structure of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak, PDB code: 7eoj
was solved by
K.Y.Huang,
A.M.Ren,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.85 /
1.77
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.277,
34.749,
58.124,
90,
127.93,
90
|
R / Rfree (%)
|
20.7 /
21.6
|
Other elements in 7eoj:
The structure of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak also contains other interesting chemical elements:
Caesium Binding Sites:
The binding sites of Caesium atom in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak
(pdb code 7eoj). This binding sites where shown within
5.0 Angstroms radius around Caesium atom.
In total 8 binding sites of Caesium where determined in the
Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak, PDB code: 7eoj:
Jump to Caesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Caesium binding site 1 out
of 8 in 7eoj
Go back to
Caesium Binding Sites List in 7eoj
Caesium binding site 1 out
of 8 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak
![](/pictures/CS/pdb/eo/7eoj-CS-sphere_01.jpg) Mono view
![](/pictures/CS/pdb/eo/7eoj-CS-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Caesium with other atoms in the Cs binding
site number 1 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cs111
b:35.4
occ:1.00
|
O6
|
A:G41
|
3.1
|
15.8
|
1.0
|
O
|
A:HOH225
|
3.2
|
22.0
|
1.0
|
N7
|
A:A6
|
3.2
|
15.9
|
1.0
|
OP2
|
A:C5
|
3.3
|
13.0
|
1.0
|
O
|
A:HOH268
|
3.3
|
19.2
|
1.0
|
N7
|
A:G41
|
3.5
|
15.4
|
1.0
|
C6
|
A:G41
|
3.7
|
16.1
|
1.0
|
C5
|
A:G41
|
3.8
|
16.3
|
1.0
|
O23
|
A:J8F101
|
3.8
|
29.4
|
1.0
|
OP1
|
A:C5
|
3.9
|
15.1
|
1.0
|
P
|
A:C5
|
4.0
|
15.6
|
1.0
|
C8
|
A:A6
|
4.1
|
14.9
|
1.0
|
O
|
A:HOH262
|
4.2
|
25.3
|
1.0
|
O
|
A:HOH243
|
4.2
|
26.4
|
1.0
|
N6
|
A:A6
|
4.2
|
12.3
|
1.0
|
C5
|
A:A6
|
4.2
|
14.2
|
1.0
|
OP2
|
A:A6
|
4.5
|
16.3
|
1.0
|
O5'
|
A:C5
|
4.5
|
16.4
|
1.0
|
C8
|
A:G41
|
4.6
|
17.1
|
1.0
|
C6
|
A:A6
|
4.7
|
15.1
|
1.0
|
C21
|
A:J8F101
|
4.7
|
20.6
|
1.0
|
N1
|
A:G41
|
4.8
|
14.2
|
1.0
|
|
Caesium binding site 2 out
of 8 in 7eoj
Go back to
Caesium Binding Sites List in 7eoj
Caesium binding site 2 out
of 8 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak
![](/pictures/CS/pdb/eo/7eoj-CS-sphere_02.jpg) Mono view
![](/pictures/CS/pdb/eo/7eoj-CS-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Caesium with other atoms in the Cs binding
site number 2 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cs112
b:34.2
occ:1.00
|
O2
|
A:C48
|
2.7
|
17.1
|
1.0
|
O
|
A:HOH286
|
3.0
|
19.4
|
1.0
|
O2
|
A:C3
|
3.1
|
14.8
|
1.0
|
O2'
|
A:C48
|
3.8
|
23.0
|
1.0
|
N2
|
A:G47
|
3.8
|
16.6
|
1.0
|
C2
|
A:C48
|
3.8
|
18.4
|
1.0
|
C1'
|
A:C48
|
3.9
|
22.4
|
1.0
|
N2
|
A:G2
|
3.9
|
16.6
|
1.0
|
C2'
|
A:C48
|
4.3
|
21.1
|
1.0
|
C2
|
A:C3
|
4.3
|
15.2
|
1.0
|
N1
|
A:C48
|
4.4
|
17.4
|
1.0
|
O2'
|
A:C3
|
4.5
|
17.0
|
1.0
|
C1'
|
A:C3
|
4.5
|
14.4
|
1.0
|
O
|
A:HOH308
|
4.7
|
23.9
|
1.0
|
N3
|
A:C48
|
4.9
|
18.9
|
1.0
|
C2
|
A:G2
|
4.9
|
16.4
|
1.0
|
C2
|
A:G47
|
4.9
|
18.8
|
1.0
|
C2'
|
A:C3
|
4.9
|
12.5
|
1.0
|
N1
|
A:C3
|
5.0
|
12.4
|
1.0
|
O4'
|
A:C48
|
5.0
|
20.4
|
1.0
|
|
Caesium binding site 3 out
of 8 in 7eoj
Go back to
Caesium Binding Sites List in 7eoj
Caesium binding site 3 out
of 8 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak
![](/pictures/CS/pdb/eo/7eoj-CS-sphere_03.jpg) Mono view
![](/pictures/CS/pdb/eo/7eoj-CS-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Caesium with other atoms in the Cs binding
site number 3 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cs113
b:31.4
occ:1.00
|
O2
|
A:C5
|
3.1
|
15.7
|
1.0
|
O2
|
A:C46
|
3.1
|
17.9
|
1.0
|
O
|
A:HOH207
|
3.4
|
25.9
|
1.0
|
O
|
A:HOH331
|
3.4
|
18.8
|
1.0
|
O
|
A:HOH326
|
3.5
|
22.4
|
1.0
|
O
|
A:HOH253
|
3.8
|
23.9
|
1.0
|
N2
|
A:G45
|
3.9
|
17.3
|
1.0
|
O2'
|
A:C5
|
4.0
|
18.4
|
1.0
|
N2
|
A:G4
|
4.1
|
14.6
|
1.0
|
C2
|
A:C5
|
4.2
|
16.1
|
1.0
|
C2
|
A:C46
|
4.3
|
17.5
|
1.0
|
C1'
|
A:C5
|
4.3
|
14.9
|
1.0
|
O2'
|
A:C46
|
4.4
|
18.4
|
1.0
|
C1'
|
A:C46
|
4.4
|
18.3
|
1.0
|
C2'
|
A:C5
|
4.7
|
14.9
|
1.0
|
N1
|
A:C5
|
4.7
|
14.9
|
1.0
|
C2'
|
A:C46
|
4.8
|
18.7
|
1.0
|
C2
|
A:G45
|
4.9
|
15.9
|
1.0
|
N1
|
A:C46
|
4.9
|
18.0
|
1.0
|
|
Caesium binding site 4 out
of 8 in 7eoj
Go back to
Caesium Binding Sites List in 7eoj
Caesium binding site 4 out
of 8 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak
![](/pictures/CS/pdb/eo/7eoj-CS-sphere_04.jpg) Mono view
![](/pictures/CS/pdb/eo/7eoj-CS-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Caesium with other atoms in the Cs binding
site number 4 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cs114
b:40.5
occ:1.00
|
OP2
|
A:G9
|
3.0
|
14.4
|
1.0
|
OP1
|
A:U8
|
3.0
|
14.4
|
1.0
|
O
|
A:HOH223
|
3.6
|
17.2
|
1.0
|
P
|
A:U8
|
4.3
|
14.9
|
1.0
|
P
|
A:G9
|
4.3
|
19.0
|
1.0
|
C5'
|
A:U8
|
4.3
|
16.1
|
1.0
|
O5'
|
A:U8
|
4.5
|
14.5
|
1.0
|
OP1
|
A:G9
|
4.8
|
17.8
|
1.0
|
|
Caesium binding site 5 out
of 8 in 7eoj
Go back to
Caesium Binding Sites List in 7eoj
Caesium binding site 5 out
of 8 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak
![](/pictures/CS/pdb/eo/7eoj-CS-sphere_05.jpg) Mono view
![](/pictures/CS/pdb/eo/7eoj-CS-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Caesium with other atoms in the Cs binding
site number 5 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cs115
b:66.0
occ:1.00
|
O2
|
A:C13
|
3.0
|
26.7
|
1.0
|
O
|
A:HOH235
|
3.1
|
34.5
|
1.0
|
O2
|
A:C38
|
3.2
|
22.1
|
1.0
|
O
|
A:HOH334
|
3.5
|
28.3
|
1.0
|
O2'
|
A:C13
|
3.7
|
31.7
|
1.0
|
N2
|
A:G12
|
3.9
|
20.8
|
1.0
|
C1'
|
A:C13
|
4.1
|
25.4
|
1.0
|
C2
|
A:C13
|
4.2
|
23.1
|
1.0
|
N2
|
A:G37
|
4.2
|
26.2
|
1.0
|
C2'
|
A:C13
|
4.3
|
29.3
|
1.0
|
C2
|
A:C38
|
4.3
|
22.3
|
1.0
|
C1'
|
A:C38
|
4.5
|
21.5
|
1.0
|
N1
|
A:C13
|
4.7
|
24.1
|
1.0
|
O4'
|
A:U14
|
4.7
|
40.2
|
1.0
|
O2'
|
A:C38
|
4.7
|
20.6
|
1.0
|
N1
|
A:C38
|
4.9
|
20.8
|
1.0
|
C2
|
A:G12
|
5.0
|
22.7
|
1.0
|
|
Caesium binding site 6 out
of 8 in 7eoj
Go back to
Caesium Binding Sites List in 7eoj
Caesium binding site 6 out
of 8 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak
![](/pictures/CS/pdb/eo/7eoj-CS-sphere_06.jpg) Mono view
![](/pictures/CS/pdb/eo/7eoj-CS-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Caesium with other atoms in the Cs binding
site number 6 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cs116
b:50.9
occ:1.00
|
O2
|
A:C28
|
3.0
|
23.1
|
1.0
|
O2
|
A:C16
|
3.4
|
35.7
|
1.0
|
O2'
|
A:C28
|
3.4
|
21.7
|
1.0
|
O
|
A:HOH337
|
3.6
|
37.6
|
1.0
|
N2
|
A:G15
|
3.7
|
29.0
|
1.0
|
C1'
|
A:C28
|
4.0
|
24.4
|
1.0
|
C2
|
A:C28
|
4.1
|
26.1
|
1.0
|
C2'
|
A:C28
|
4.1
|
21.5
|
1.0
|
O2'
|
A:C16
|
4.1
|
51.6
|
1.0
|
N2
|
A:G27
|
4.2
|
31.6
|
1.0
|
C2
|
A:C16
|
4.4
|
37.1
|
1.0
|
C1'
|
A:C16
|
4.5
|
44.0
|
1.0
|
C2'
|
A:C16
|
4.6
|
48.6
|
1.0
|
N1
|
A:C28
|
4.6
|
21.9
|
1.0
|
N1
|
A:C16
|
4.9
|
36.6
|
1.0
|
C2
|
A:G15
|
4.9
|
28.9
|
1.0
|
|
Caesium binding site 7 out
of 8 in 7eoj
Go back to
Caesium Binding Sites List in 7eoj
Caesium binding site 7 out
of 8 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak
![](/pictures/CS/pdb/eo/7eoj-CS-sphere_07.jpg) Mono view
![](/pictures/CS/pdb/eo/7eoj-CS-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Caesium with other atoms in the Cs binding
site number 7 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cs117
b:31.1
occ:1.00
|
O6
|
A:G34
|
3.1
|
15.7
|
1.0
|
O2
|
A:U32
|
3.1
|
18.4
|
1.0
|
OP2
|
A:C38
|
3.1
|
19.5
|
1.0
|
OP1
|
A:C38
|
3.2
|
21.4
|
1.0
|
O4
|
A:U35
|
3.3
|
18.7
|
1.0
|
O
|
A:HOH259
|
3.3
|
20.5
|
1.0
|
O
|
A:HOH233
|
3.3
|
16.1
|
1.0
|
P
|
A:C38
|
3.6
|
19.9
|
1.0
|
C2
|
A:U32
|
4.1
|
15.7
|
1.0
|
C4
|
A:U35
|
4.1
|
16.7
|
1.0
|
C6
|
A:G34
|
4.2
|
18.6
|
1.0
|
N3
|
A:U35
|
4.3
|
17.4
|
1.0
|
N3
|
A:U32
|
4.4
|
16.2
|
1.0
|
N1
|
A:A31
|
4.7
|
21.2
|
1.0
|
O
|
A:HOH234
|
4.7
|
17.6
|
1.0
|
O5'
|
A:C38
|
4.8
|
20.8
|
1.0
|
O3'
|
A:G37
|
4.8
|
19.9
|
1.0
|
|
Caesium binding site 8 out
of 8 in 7eoj
Go back to
Caesium Binding Sites List in 7eoj
Caesium binding site 8 out
of 8 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak
![](/pictures/CS/pdb/eo/7eoj-CS-sphere_08.jpg) Mono view
![](/pictures/CS/pdb/eo/7eoj-CS-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Caesium with other atoms in the Cs binding
site number 8 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cs118
b:39.9
occ:1.00
|
O2'
|
A:C49
|
3.2
|
21.5
|
1.0
|
O2
|
A:C49
|
3.3
|
18.4
|
1.0
|
O
|
A:HOH324
|
3.6
|
30.4
|
1.0
|
N2
|
A:GDP1
|
3.9
|
17.9
|
1.0
|
C2'
|
A:C49
|
4.1
|
18.7
|
1.0
|
C1'
|
A:C49
|
4.4
|
18.1
|
1.0
|
C2
|
A:C49
|
4.4
|
17.4
|
1.0
|
O
|
A:HOH335
|
4.4
|
27.4
|
1.0
|
O
|
A:HOH201
|
4.5
|
23.9
|
1.0
|
N1
|
A:C49
|
5.0
|
16.9
|
1.0
|
|
Reference:
K.Huang,
X.Chen,
C.Li,
Q.Song,
H.Li,
L.Zhu,
Y.Yang,
A.Ren.
Structure-Based Investigation of Fluorogenic Pepper Aptamer. Nat.Chem.Biol. 2021.
ISSN: ESSN 1552-4469
PubMed: 34725509
DOI: 10.1038/S41589-021-00884-6
Page generated: Tue Jul 30 21:07:05 2024
|