Potassium in PDB 7oav: Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form)

The structure of Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form), PDB code: 7oav 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)	46.14 / 2.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.192, 106.76, 63.552, 90, 116.53, 90
R / Rfree (%)	20.2 / 25.5

The structure of Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form) also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Iridium	(Ir)	4 atoms

The binding sites of Potassium atom in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form) (pdb code 7oav). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form), PDB code: 7oav:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal 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 III Hexammine Soaking Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:136.4 occ:1.00 O6 A:G42 2.7 145.1 1.0 O6 A:G9 2.7 117.6 1.0 O6 A:G32 2.8 106.5 1.0 O6 A:G37 2.8 140.5 1.0 O6 A:G36 2.9 142.0 1.0 O6 A:G13 3.1 118.0 1.0 O6 A:G12 3.2 122.8 1.0 C6 A:G42 3.4 148.4 1.0 N1 A:G42 3.4 151.1 1.0 C6 A:G9 3.6 117.9 1.0 C6 A:G32 3.6 103.6 1.0 C6 A:G36 3.6 144.3 1.0 C6 A:G37 3.6 138.2 1.0 N1 A:G36 3.7 145.2 1.0 N1 A:G9 3.8 121.6 1.0 O6 A:G41 3.8 125.8 1.0 N1 A:G32 3.8 110.6 1.0 C6 A:G13 3.9 121.1 1.0 N1 A:G13 3.9 121.5 1.0 N1 A:G37 4.1 134.0 1.0 C6 A:G12 4.1 123.8 1.0 O2 A:C44 4.3 138.2 1.0 N1 A:G12 4.4 122.6 1.0 C2 A:C44 4.5 131.3 1.0 C6 A:G41 4.6 124.9 1.0 C2 A:G42 4.7 148.5 1.0 N3 A:C44 4.7 125.3 1.0 C5 A:G37 4.8 140.1 1.0 C5 A:G32 4.8 101.3 1.0 C5 A:G42 4.8 146.3 1.0 C2 A:G36 4.9 146.4 1.0 C5 A:G9 4.9 119.2 1.0 C5 A:G36 4.9 148.5 1.0 N1 A:G41 4.9 120.7 1.0 N1 A:C44 4.9 128.8 1.0

Potassium binding site 2 out of 7 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal 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 III Hexammine Soaking Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:185.8 occ:1.00 O6 A:G15 2.9 114.6 1.0 O28 A:V5Z101 3.1 116.8 1.0 O31 A:V5Z101 3.1 126.4 1.0 C29 A:V5Z101 3.3 118.1 1.0 O6 A:G37 3.4 140.5 1.0 O6 A:G41 3.5 125.8 1.0 N4 A:C40 3.7 130.8 1.0 C6 A:G37 3.9 138.2 1.0 N1 A:G37 4.0 134.0 1.0 C6 A:G15 4.0 112.9 1.0 C27 A:V5Z101 4.0 120.0 1.0 C30 A:V5Z101 4.1 122.1 1.0 O6 A:G32 4.2 106.5 1.0 C6 A:G41 4.6 124.9 1.0 N1 A:G32 4.6 110.6 1.0 O6 A:G39 4.7 127.0 1.0 C6 A:G32 4.7 103.6 1.0 N7 A:G31 4.7 116.4 1.0 O6 A:G13 4.7 118.0 1.0 N7 A:G15 4.7 111.4 1.0 C5 A:G15 4.8 115.1 1.0 C5 A:G37 4.9 140.1 1.0

Potassium binding site 3 out of 7 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal 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 III Hexammine Soaking Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:160.3 occ:1.00 O6 B:G42 2.7 141.3 1.0 O6 B:G32 2.7 141.2 1.0 O6 B:G37 2.7 132.9 1.0 O6 B:G36 2.8 151.5 1.0 O6 B:G9 2.8 142.6 1.0 O6 B:G13 2.9 136.8 1.0 O6 B:G12 3.2 124.2 1.0 N1 B:G42 3.3 136.9 1.0 C6 B:G42 3.4 141.9 1.0 C6 B:G37 3.5 130.0 1.0 C6 B:G32 3.6 135.9 1.0 O6 B:G41 3.7 136.6 1.0 C6 B:G9 3.7 145.5 1.0 C6 B:G13 3.7 133.8 1.0 C6 B:G36 3.7 147.0 1.0 O B:HOH201 3.8 93.0 1.0 N1 B:G13 3.8 131.3 1.0 N1 B:G37 3.9 127.3 1.0 N1 B:G9 4.0 149.4 1.0 C6 B:G12 4.1 126.1 1.0 N1 B:G36 4.1 144.4 1.0 N1 B:G32 4.1 133.9 1.0 N1 B:G12 4.2 122.0 1.0 C6 B:G41 4.4 138.0 1.0 O2 B:C44 4.5 172.1 1.0 C2 B:G42 4.6 133.5 1.0 N1 B:G41 4.6 139.0 1.0 C2 B:C44 4.6 169.2 1.0 C5 B:G37 4.6 127.4 1.0 C5 B:G42 4.8 146.6 1.0 C5 B:G32 4.8 128.5 1.0 N3 B:C44 4.9 167.4 1.0 N2 B:G42 4.9 127.2 1.0 C5 B:G36 5.0 143.8 1.0

Potassium binding site 4 out of 7 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal 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 III Hexammine Soaking Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:K104 b:168.8 occ:1.00 OP1 B:C40 3.0 151.9 1.0 OP2 B:U43 3.8 164.0 1.0 P B:C40 4.0 152.2 1.0 OP2 B:G41 4.1 156.1 1.0 O2' B:G42 4.2 145.9 1.0 OP2 B:C40 4.3 147.8 1.0 O3' B:G42 4.4 165.9 1.0 O5' B:C40 4.6 157.6 1.0 P B:U43 4.7 166.6 1.0 OP2 B:U38 4.8 169.2 1.0

Potassium binding site 5 out of 7 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:K103 b:158.7 occ:1.00 O6 C:G32 2.6 102.6 1.0 O6 C:G42 2.6 133.2 1.0 O6 C:G9 2.8 108.8 1.0 O6 C:G13 2.8 122.2 1.0 O6 C:G36 2.8 125.0 1.0 O6 C:G37 3.0 139.4 1.0 O6 C:G12 3.0 130.6 1.0 C6 C:G9 3.5 118.7 1.0 C6 C:G32 3.5 107.3 1.0 N1 C:G9 3.5 125.9 1.0 C6 C:G13 3.6 125.0 1.0 C6 C:G42 3.6 139.8 1.0 N1 C:G13 3.6 125.7 1.0 C6 C:G36 3.8 130.3 1.0 O6 C:G41 3.8 114.9 1.0 N1 C:G42 3.8 143.8 1.0 C6 C:G37 3.8 133.1 1.0 C6 C:G12 3.9 128.0 1.0 N1 C:G32 4.0 109.4 1.0 N1 C:G36 4.2 133.3 1.0 N1 C:G12 4.2 126.3 1.0 N1 C:G37 4.3 131.5 1.0 O2 C:C44 4.4 137.3 1.0 C6 C:G41 4.5 116.4 1.0 C5 C:G32 4.5 106.4 1.0 N1 C:G41 4.7 114.8 1.0 C2 C:C44 4.7 136.9 1.0 C2 C:G9 4.7 122.1 1.0 C5 C:G9 4.8 119.9 1.0 C2 C:G13 4.9 114.3 1.0 C5 C:G13 4.9 119.1 1.0 N3 C:C44 4.9 138.7 1.0 C5 C:G42 4.9 143.5 1.0 C5 C:G37 5.0 122.5 1.0

Potassium binding site 6 out of 7 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:K103 b:142.7 occ:1.00 O6 D:G32 2.7 123.9 1.0 O6 D:G42 2.8 142.9 1.0 O6 D:G9 2.8 117.9 1.0 O6 D:G12 2.9 122.0 1.0 O6 D:G37 3.0 142.5 1.0 O6 D:G36 3.0 139.4 1.0 O6 D:G13 3.0 141.5 1.0 C6 D:G9 3.5 119.1 1.0 N1 D:G42 3.5 133.7 1.0 C6 D:G42 3.5 139.3 1.0 N1 D:G9 3.6 123.2 1.0 O6 D:G41 3.7 121.2 1.0 N1 D:G13 3.7 136.5 1.0 C6 D:G32 3.7 124.3 1.0 C6 D:G13 3.7 137.8 1.0 C6 D:G37 3.8 143.3 1.0 C6 D:G36 3.8 137.8 1.0 C6 D:G12 3.9 123.7 1.0 N1 D:G36 4.0 135.6 1.0 N1 D:G32 4.1 123.6 1.0 N1 D:G37 4.2 147.0 1.0 N1 D:G12 4.3 124.6 1.0 C6 D:G41 4.5 122.9 1.0 O2 D:C44 4.5 150.9 1.0 C2 D:C44 4.7 144.9 1.0 N1 D:G41 4.7 126.6 1.0 C5 D:G37 4.8 136.9 1.0 C2 D:G42 4.8 133.2 1.0 C2 D:G9 4.8 120.4 1.0 C5 D:G9 4.8 117.9 1.0 C5 D:G32 4.8 122.7 1.0 C2 D:G13 4.9 132.3 1.0 C5 D:G42 4.9 141.0 1.0 N3 D:C44 5.0 142.5 1.0

Potassium binding site 7 out of 7 in the Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Chili Rna Aptamer in Complex with Dmhbo+ (Iridium III Hexammine Soaking Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:K104 b:139.1 occ:1.00 OP2 D:U43 2.8 134.4 1.0 O3' D:G42 3.8 136.1 1.0 P D:U43 3.9 133.7 1.0 OP1 D:C40 4.0 137.2 1.0 O2' D:G42 4.3 131.6 1.0 OP2 D:G41 4.5 133.1 1.0 OP2 D:U38 4.8 143.5 1.0 C3' D:G42 4.8 138.7 1.0 C5' D:U43 4.9 129.9 1.0 O5' D:U43 4.9 132.1 1.0 OP1 D:U43 5.0 136.3 1.0

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