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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:

Magnesium (Mg) 2 atoms
Iridium (Ir) 5 atoms

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

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