Potassium in PDB 7oa3: Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form)
Protein crystallography data
The structure of Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form), PDB code: 7oa3
was solved by
M.Mieczkowski,
V.Pena,
C.Hoebartner,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.92 /
2.80
|
Space group
|
I 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.605,
54.026,
87.532,
90,
95.49,
90
|
R / Rfree (%)
|
22.5 /
24.1
|
Other elements in 7oa3:
The structure of Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form) also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form)
(pdb code 7oa3). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the
Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form), PDB code: 7oa3:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 7oa3
Go back to
Potassium Binding Sites List in 7oa3
Potassium binding site 1 out
of 4 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form)
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K103
b:120.0
occ:1.00
|
O6
|
A:G13
|
2.7
|
135.7
|
1.0
|
O6
|
A:G42
|
2.8
|
119.6
|
1.0
|
O6
|
A:G9
|
2.8
|
134.6
|
1.0
|
O6
|
A:G32
|
2.8
|
115.7
|
1.0
|
O6
|
A:G36
|
2.8
|
126.8
|
1.0
|
O6
|
A:G37
|
2.8
|
131.3
|
1.0
|
O6
|
A:G12
|
3.0
|
115.6
|
1.0
|
N1
|
A:G13
|
3.2
|
133.9
|
1.0
|
O6
|
A:G41
|
3.4
|
118.6
|
1.0
|
C6
|
A:G13
|
3.4
|
138.4
|
1.0
|
C6
|
A:G9
|
3.5
|
129.0
|
1.0
|
C6
|
A:G37
|
3.5
|
126.2
|
1.0
|
C6
|
A:G36
|
3.7
|
123.0
|
1.0
|
C6
|
A:G32
|
3.7
|
116.0
|
1.0
|
N1
|
A:G9
|
3.7
|
131.3
|
1.0
|
N1
|
A:G37
|
3.7
|
127.0
|
1.0
|
C6
|
A:G42
|
3.8
|
126.1
|
1.0
|
K
|
A:K104
|
3.8
|
125.0
|
1.0
|
C6
|
A:G12
|
3.9
|
129.3
|
1.0
|
N1
|
A:G36
|
3.9
|
122.2
|
1.0
|
N1
|
A:G32
|
3.9
|
119.5
|
1.0
|
N1
|
A:G42
|
4.0
|
122.2
|
1.0
|
C6
|
A:G41
|
4.1
|
121.5
|
1.0
|
N1
|
A:G12
|
4.2
|
129.9
|
1.0
|
O2
|
A:C44
|
4.2
|
133.0
|
1.0
|
N1
|
A:G41
|
4.2
|
117.8
|
1.0
|
C2
|
A:G13
|
4.5
|
131.4
|
1.0
|
C2
|
A:C44
|
4.6
|
124.8
|
1.0
|
C5
|
A:G9
|
4.7
|
126.0
|
1.0
|
C5
|
A:G37
|
4.8
|
131.1
|
1.0
|
C5
|
A:G13
|
4.8
|
138.5
|
1.0
|
N2
|
A:G13
|
4.8
|
127.3
|
1.0
|
N3
|
A:C44
|
4.8
|
119.4
|
1.0
|
C2
|
A:G9
|
4.9
|
137.1
|
1.0
|
C5
|
A:G32
|
4.9
|
122.9
|
1.0
|
C2
|
A:G37
|
5.0
|
123.8
|
1.0
|
C5
|
A:G36
|
5.0
|
122.9
|
1.0
|
|
Potassium binding site 2 out
of 4 in 7oa3
Go back to
Potassium Binding Sites List in 7oa3
Potassium binding site 2 out
of 4 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form)
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K104
b:125.0
occ:1.00
|
O6
|
A:G37
|
2.8
|
131.3
|
1.0
|
O6
|
A:G15
|
2.8
|
125.0
|
1.0
|
O31
|
A:V5Z101
|
2.9
|
146.6
|
1.0
|
O6
|
A:G41
|
2.9
|
118.6
|
1.0
|
C6
|
A:G37
|
3.4
|
126.2
|
1.0
|
O28
|
A:V5Z101
|
3.4
|
140.7
|
1.0
|
N1
|
A:G37
|
3.4
|
127.0
|
1.0
|
O6
|
A:G32
|
3.6
|
115.7
|
1.0
|
N4
|
A:C40
|
3.7
|
137.2
|
1.0
|
K
|
A:K103
|
3.8
|
120.0
|
1.0
|
C6
|
A:G41
|
3.9
|
121.5
|
1.0
|
C30
|
A:V5Z101
|
3.9
|
152.8
|
1.0
|
C6
|
A:G15
|
3.9
|
126.5
|
1.0
|
O6
|
A:G13
|
4.0
|
135.7
|
1.0
|
C27
|
A:V5Z101
|
4.1
|
149.8
|
1.0
|
C29
|
A:V5Z101
|
4.1
|
142.8
|
1.0
|
N1
|
A:G41
|
4.2
|
117.8
|
1.0
|
C6
|
A:G32
|
4.3
|
116.0
|
1.0
|
N1
|
A:G32
|
4.4
|
119.5
|
1.0
|
C6
|
A:G13
|
4.5
|
138.4
|
1.0
|
N1
|
A:G13
|
4.6
|
133.9
|
1.0
|
C5
|
A:G37
|
4.6
|
131.1
|
1.0
|
O6
|
A:G39
|
4.6
|
150.3
|
1.0
|
C2
|
A:G37
|
4.6
|
123.8
|
1.0
|
C5
|
A:G15
|
4.7
|
126.0
|
1.0
|
N7
|
A:G15
|
4.7
|
126.7
|
1.0
|
C4
|
A:C40
|
4.9
|
139.8
|
1.0
|
N1
|
A:G15
|
5.0
|
133.8
|
1.0
|
|
Potassium binding site 3 out
of 4 in 7oa3
Go back to
Potassium Binding Sites List in 7oa3
Potassium binding site 3 out
of 4 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form)
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K103
b:134.0
occ:1.00
|
O6
|
B:G36
|
2.6
|
139.0
|
1.0
|
O6
|
B:G13
|
2.7
|
127.9
|
1.0
|
O6
|
B:G37
|
2.7
|
122.9
|
1.0
|
O6
|
B:G32
|
2.8
|
119.5
|
1.0
|
O6
|
B:G42
|
3.0
|
138.2
|
1.0
|
O6
|
B:G9
|
3.0
|
124.5
|
1.0
|
N1
|
B:G36
|
3.0
|
146.1
|
1.0
|
O6
|
B:G12
|
3.1
|
130.2
|
1.0
|
C6
|
B:G36
|
3.2
|
142.9
|
1.0
|
K
|
B:K104
|
3.2
|
134.4
|
1.0
|
N1
|
B:G13
|
3.4
|
128.3
|
1.0
|
O6
|
B:G41
|
3.4
|
128.4
|
1.0
|
C6
|
B:G13
|
3.4
|
130.2
|
1.0
|
C6
|
B:G37
|
3.5
|
135.0
|
1.0
|
N1
|
B:G37
|
3.6
|
134.5
|
1.0
|
C6
|
B:G32
|
3.6
|
123.4
|
1.0
|
N1
|
B:G32
|
3.7
|
122.3
|
1.0
|
C6
|
B:G9
|
3.8
|
129.6
|
1.0
|
C6
|
B:G42
|
3.9
|
138.0
|
1.0
|
N1
|
B:G42
|
4.0
|
136.3
|
1.0
|
C6
|
B:G12
|
4.0
|
130.8
|
1.0
|
C6
|
B:G41
|
4.2
|
127.2
|
1.0
|
N1
|
B:G12
|
4.2
|
134.9
|
1.0
|
C2
|
B:G36
|
4.2
|
143.9
|
1.0
|
N1
|
B:G41
|
4.2
|
121.4
|
1.0
|
N1
|
B:G9
|
4.3
|
133.7
|
1.0
|
O2
|
B:C44
|
4.4
|
149.1
|
1.0
|
C5
|
B:G36
|
4.5
|
145.5
|
1.0
|
N2
|
B:G36
|
4.6
|
153.0
|
1.0
|
C2
|
B:G13
|
4.7
|
121.5
|
1.0
|
C5
|
B:G37
|
4.8
|
131.6
|
1.0
|
C5
|
B:G13
|
4.8
|
132.7
|
1.0
|
C2
|
B:G37
|
4.8
|
132.9
|
1.0
|
C2
|
B:C44
|
4.9
|
144.1
|
1.0
|
O31
|
B:V5Z101
|
4.9
|
156.3
|
1.0
|
C5
|
B:G32
|
5.0
|
119.7
|
1.0
|
C5
|
B:G9
|
5.0
|
129.3
|
1.0
|
|
Potassium binding site 4 out
of 4 in 7oa3
Go back to
Potassium Binding Sites List in 7oa3
Potassium binding site 4 out
of 4 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form)
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium Hexammine Co-Crystallized Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K104
b:134.4
occ:1.00
|
O6
|
B:G37
|
2.8
|
122.9
|
1.0
|
O6
|
B:G15
|
2.8
|
122.1
|
1.0
|
O6
|
B:G41
|
2.9
|
128.4
|
1.0
|
O31
|
B:V5Z101
|
3.1
|
156.3
|
1.0
|
N1
|
B:G37
|
3.2
|
134.5
|
1.0
|
K
|
B:K103
|
3.2
|
134.0
|
1.0
|
C6
|
B:G37
|
3.3
|
135.0
|
1.0
|
O28
|
B:V5Z101
|
3.6
|
144.4
|
1.0
|
O6
|
B:G32
|
3.6
|
119.5
|
1.0
|
N4
|
B:C40
|
3.8
|
125.7
|
1.0
|
O6
|
B:G13
|
3.8
|
127.9
|
1.0
|
C6
|
B:G41
|
3.8
|
127.2
|
1.0
|
C6
|
B:G15
|
4.0
|
132.4
|
1.0
|
C30
|
B:V5Z101
|
4.1
|
162.9
|
1.0
|
N1
|
B:G41
|
4.2
|
121.4
|
1.0
|
N1
|
B:G32
|
4.2
|
122.3
|
1.0
|
C6
|
B:G32
|
4.3
|
123.4
|
1.0
|
C27
|
B:V5Z101
|
4.3
|
158.9
|
1.0
|
C29
|
B:V5Z101
|
4.3
|
144.9
|
1.0
|
C2
|
B:G37
|
4.3
|
132.9
|
1.0
|
C6
|
B:G13
|
4.4
|
130.2
|
1.0
|
C5
|
B:G37
|
4.6
|
131.6
|
1.0
|
N1
|
B:G13
|
4.6
|
128.3
|
1.0
|
N2
|
B:G37
|
4.7
|
126.5
|
1.0
|
C5
|
B:G15
|
4.8
|
137.7
|
1.0
|
N7
|
B:G15
|
4.8
|
141.8
|
1.0
|
O6
|
B:G42
|
4.9
|
138.2
|
1.0
|
N1
|
B:G15
|
5.0
|
139.9
|
1.0
|
|
Reference:
M.Mieczkowski,
C.Steinmetzger,
I.Bessi,
A.K.Lenz,
A.Schmiedel,
M.Holzapfel,
C.Lambert,
V.Pena,
C.Hoebartner.
Large Stokes Shift Fluorescence Activation in An Rna Aptamer By Intermolecular Proton Transfer to Guanine Nat Commun 2021.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-021-23932-0
Page generated: Mon Aug 12 19:36:31 2024
|