Potassium in PDB 7oax: Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+

The structure of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+, PDB code: 7oax 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)	40.97 / 2.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.324, 100.352, 113.294, 90, 90, 90
R / Rfree (%)	20.2 / 23.7

The structure of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+ also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+ (pdb code 7oax). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 12 binding sites of Potassium where determined in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+, PDB code: 7oax:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+


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 the Chili Rna Aptamer in Complex with Dmhbo+ within 5.0Å range: probe atom residue distance (Å) B Occ A:K106 b:62.2 occ:1.00 O6 A:G42 2.6 58.1 1.0 O6 A:G32 2.7 52.1 1.0 O6 A:G9 2.7 51.5 1.0 O6 A:G36 2.8 52.4 1.0 O6 A:G37 2.8 45.9 1.0 O6 A:G12 2.9 45.1 1.0 O6 A:G13 3.0 48.8 1.0 C6 A:G32 3.4 45.8 1.0 C6 A:G42 3.5 56.6 1.0 O6 A:G41 3.5 59.3 1.0 K A:K107 3.6 52.6 1.0 C6 A:G9 3.6 43.6 1.0 N1 A:G42 3.6 52.2 1.0 N1 A:G32 3.6 45.8 1.0 C6 A:G36 3.7 51.3 1.0 C6 A:G37 3.7 48.9 1.0 C6 A:G12 3.8 41.5 1.0 C6 A:G13 3.8 45.1 1.0 N1 A:G13 3.8 46.7 1.0 N1 A:G9 3.8 37.0 1.0 N1 A:G36 3.9 49.7 1.0 N1 A:G12 4.0 44.1 1.0 N1 A:G37 4.1 41.2 1.0 C6 A:G41 4.3 54.1 1.0 O2 A:C44 4.3 70.1 1.0 N1 A:G41 4.4 49.8 1.0 C2 A:C44 4.4 58.8 1.0 N3 A:C44 4.5 56.7 1.0 C5 A:G32 4.6 44.6 1.0 C2 A:G32 4.8 49.0 1.0 C5 A:G9 4.9 42.7 1.0 C5 A:G42 4.9 54.3 1.0 C5 A:G37 4.9 53.4 1.0 C2 A:G42 4.9 54.1 1.0 C5 A:G36 4.9 53.3 1.0 N1 A:C44 5.0 51.9 1.0

Potassium binding site 2 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+


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 the Chili Rna Aptamer in Complex with Dmhbo+ within 5.0Å range: probe atom residue distance (Å) B Occ A:K107 b:52.6 occ:1.00 O31 A:V5Z102 2.8 40.4 1.0 O6 A:G41 2.8 59.3 1.0 O6 A:G32 2.8 52.1 1.0 O6 A:G37 2.8 45.9 1.0 O28 A:V5Z102 2.8 45.8 1.0 O6 A:G13 2.9 48.8 1.0 O6 A:G15 2.9 56.4 1.0 C30 A:V5Z102 3.5 40.5 1.0 C27 A:V5Z102 3.5 40.4 1.0 K A:K106 3.6 62.2 1.0 C6 A:G32 3.6 45.8 1.0 C6 A:G37 3.6 48.9 1.0 C6 A:G13 3.7 45.1 1.0 C6 A:G41 3.7 54.1 1.0 N1 A:G32 3.8 45.8 1.0 C6 A:G15 3.8 50.6 1.0 C29 A:V5Z102 3.9 46.8 1.0 N1 A:G37 3.9 41.2 1.0 N1 A:G13 4.0 46.7 1.0 N1 A:G41 4.0 49.8 1.0 N4 A:C40 4.0 55.8 1.0 N7 A:G15 4.4 53.0 1.0 C5 A:G15 4.4 53.1 1.0 C03 A:V5Z102 4.7 41.9 1.0 C26 A:V5Z102 4.7 36.0 1.0 O6 A:G42 4.8 58.1 1.0 C5 A:G13 4.8 50.1 1.0 C5 A:G32 4.8 44.6 1.0 C5 A:G37 4.9 53.4 1.0 N1 A:G15 4.9 48.0 1.0 C5 A:G41 5.0 49.3 1.0

Potassium binding site 3 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+


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 the Chili Rna Aptamer in Complex with Dmhbo+ within 5.0Å range: probe atom residue distance (Å) B Occ A:K108 b:77.9 occ:1.00 O6 A:G17 3.0 48.6 1.0 O6 A:G31 3.3 54.2 1.0 O A:HOH206 3.5 52.2 1.0 O4 A:U30 3.5 49.0 1.0 OP2 A:C16 3.6 50.8 1.0 O6 A:G29 3.7 55.1 1.0 C6 A:G17 4.0 49.9 1.0 N14 A:SPM103 4.0 54.0 0.9 N7 A:G17 4.0 51.9 1.0 C6 A:G31 4.1 50.8 1.0 OP2 A:G15 4.1 43.8 1.0 C5 A:C16 4.1 51.1 1.0 N1 A:G31 4.1 43.9 1.0 N4 A:C18 4.2 58.1 1.0 C5 A:G17 4.4 52.5 1.0 C4 A:U30 4.4 47.4 1.0 C13 A:SPM103 4.4 52.3 0.9 N3 A:U30 4.4 43.8 1.0 N4 A:C16 4.7 49.5 1.0 C4 A:C16 4.8 50.6 1.0 C6 A:G29 4.8 47.6 1.0 C6 A:C16 4.9 53.0 1.0

Potassium binding site 4 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+


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 the Chili Rna Aptamer in Complex with Dmhbo+ within 5.0Å range: probe atom residue distance (Å) B Occ B:K105 b:53.7 occ:1.00 O6 B:G42 2.6 43.1 1.0 O6 B:G9 2.7 42.7 1.0 O6 B:G32 2.7 49.2 1.0 O6 B:G37 2.7 57.0 1.0 O6 B:G36 2.8 45.4 1.0 O6 B:G13 2.8 38.0 1.0 O6 B:G12 2.9 48.4 1.0 O6 B:G41 3.3 56.0 1.0 K B:K106 3.4 53.7 1.0 C6 B:G42 3.5 47.0 1.0 C6 B:G32 3.5 48.2 1.0 C6 B:G9 3.6 44.2 1.0 C6 B:G37 3.7 50.0 1.0 C6 B:G13 3.7 38.9 1.0 C6 B:G36 3.7 45.9 1.0 C6 B:G12 3.7 41.8 1.0 N1 B:G42 3.7 46.2 1.0 N1 B:G32 3.8 52.0 1.0 N1 B:G12 3.8 39.0 1.0 N1 B:G13 3.8 37.5 1.0 N1 B:G9 3.8 36.5 1.0 N1 B:G36 3.9 46.9 1.0 C6 B:G41 4.1 52.5 1.0 N1 B:G37 4.1 45.1 1.0 N1 B:G41 4.2 46.4 1.0 O2 B:C44 4.5 49.8 1.0 C2 B:C44 4.6 45.0 1.0 C5 B:G32 4.8 41.8 1.0 C5 B:G37 4.8 43.6 1.0 N3 B:C44 4.9 49.6 1.0 C5 B:G9 4.9 45.8 1.0 C5 B:G42 4.9 48.1 1.0 C5 B:G13 5.0 44.0 1.0 C5 B:G36 5.0 51.4 1.0

Potassium binding site 5 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+


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 the Chili Rna Aptamer in Complex with Dmhbo+ within 5.0Å range: probe atom residue distance (Å) B Occ B:K106 b:53.7 occ:1.00 O6 B:G41 2.7 56.0 1.0 O31 B:V5Z103 2.8 42.1 1.0 O6 B:G37 2.8 57.0 1.0 O6 B:G15 2.9 57.6 1.0 O6 B:G32 2.9 49.2 1.0 O28 B:V5Z103 3.0 45.2 1.0 O6 B:G13 3.1 38.0 1.0 K B:K105 3.4 53.7 1.0 C30 B:V5Z103 3.5 40.2 1.0 C6 B:G37 3.6 50.0 1.0 C27 B:V5Z103 3.6 38.0 1.0 C6 B:G41 3.6 52.5 1.0 C6 B:G32 3.7 48.2 1.0 C6 B:G15 3.8 46.8 1.0 N1 B:G37 3.8 45.1 1.0 C6 B:G13 3.8 38.9 1.0 N1 B:G41 3.9 46.4 1.0 N1 B:G32 3.9 52.0 1.0 N4 B:C40 4.0 52.8 1.0 C29 B:V5Z103 4.0 50.2 1.0 N1 B:G13 4.0 37.5 1.0 N7 B:G15 4.4 46.0 1.0 C5 B:G15 4.4 43.5 1.0 C03 B:V5Z103 4.8 38.4 1.0 N1 B:G15 4.8 43.3 1.0 C5 B:G37 4.9 43.6 1.0 C26 B:V5Z103 4.9 33.5 1.0 O6 B:G42 4.9 43.1 1.0 C5 B:G32 4.9 41.8 1.0 C5 B:G41 4.9 45.8 1.0 C5 B:G13 5.0 44.0 1.0

Potassium binding site 6 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+


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 the Chili Rna Aptamer in Complex with Dmhbo+ within 5.0Å range: probe atom residue distance (Å) B Occ B:K107 b:68.7 occ:1.00 O6 B:G17 3.2 50.7 1.0 O4 B:U30 3.2 43.3 1.0 O6 B:G31 3.3 52.6 1.0 O6 B:G29 3.4 57.5 1.0 OP2 B:C16 3.9 45.3 1.0 C6 B:G31 3.9 40.2 1.0 N1 B:G31 4.0 40.4 1.0 N14 B:SPM102 4.0 52.5 1.0 C4 B:U30 4.1 58.1 1.0 N4 B:C18 4.1 75.3 1.0 C6 B:G17 4.2 55.8 1.0 OP2 B:G15 4.2 39.7 1.0 N3 B:U30 4.2 63.4 1.0 N7 B:G17 4.3 61.0 1.0 C5 B:C16 4.3 41.7 1.0 C6 B:G29 4.5 54.6 1.0 C5 B:G17 4.6 57.2 1.0 N4 B:C16 4.8 45.8 1.0 C4 B:C16 5.0 47.5 1.0

Potassium binding site 7 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+


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 the Chili Rna Aptamer in Complex with Dmhbo+ within 5.0Å range: probe atom residue distance (Å) B Occ C:K105 b:56.5 occ:1.00 O6 C:G42 2.6 52.9 1.0 O6 C:G32 2.7 49.3 1.0 O6 C:G9 2.7 59.2 1.0 O6 C:G37 2.8 65.7 1.0 O6 C:G12 2.8 51.9 1.0 O6 C:G36 2.8 57.4 1.0 O6 C:G13 2.9 43.5 1.0 O6 C:G41 3.3 50.4 1.0 C6 C:G32 3.5 48.5 1.0 C6 C:G9 3.5 50.5 1.0 C6 C:G42 3.6 50.8 1.0 K C:K106 3.6 56.3 1.0 C6 C:G37 3.7 61.8 1.0 C6 C:G13 3.7 47.2 1.0 C6 C:G36 3.7 54.3 1.0 C6 C:G12 3.7 45.0 1.0 N1 C:G9 3.7 47.2 1.0 N1 C:G32 3.8 57.4 1.0 N1 C:G13 3.9 42.7 1.0 N1 C:G36 3.9 48.7 1.0 N1 C:G42 3.9 53.0 1.0 N1 C:G12 4.0 41.5 1.0 N1 C:G37 4.0 60.1 1.0 C6 C:G41 4.0 51.3 1.0 N1 C:G41 4.1 50.0 1.0 O2 C:C44 4.6 64.5 1.0 C2 C:C44 4.6 56.6 1.0 C5 C:G32 4.7 41.4 1.0 C5 C:G9 4.8 46.8 1.0 N3 C:C44 4.8 51.4 1.0 C5 C:G37 4.9 57.7 1.0 C5 C:G42 5.0 49.6 1.0

Potassium binding site 8 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+ within 5.0Å range: probe atom residue distance (Å) B Occ C:K106 b:56.3 occ:1.00 O31 C:V5Z103 2.7 49.8 1.0 O6 C:G41 2.8 50.4 1.0 O6 C:G15 2.9 46.2 1.0 O6 C:G32 3.0 49.3 1.0 O6 C:G37 3.0 65.7 1.0 O28 C:V5Z103 3.0 54.0 1.0 O6 C:G13 3.0 43.5 1.0 C30 C:V5Z103 3.5 49.5 1.0 K C:K105 3.6 56.5 1.0 C27 C:V5Z103 3.7 52.3 1.0 C6 C:G37 3.7 61.8 1.0 C6 C:G41 3.7 51.3 1.0 C6 C:G32 3.8 48.5 1.0 N1 C:G37 3.8 60.1 1.0 C6 C:G15 3.8 41.7 1.0 C6 C:G13 3.8 47.2 1.0 N1 C:G41 3.9 50.0 1.0 C29 C:V5Z103 3.9 52.0 1.0 N4 C:C40 3.9 53.9 1.0 N1 C:G32 4.0 57.4 1.0 N1 C:G13 4.2 42.7 1.0 N7 C:G15 4.3 47.5 1.0 C5 C:G15 4.4 41.4 1.0 C03 C:V5Z103 4.7 50.1 1.0 C5 C:G37 4.8 57.7 1.0 N1 C:G15 4.9 43.3 1.0 C26 C:V5Z103 4.9 48.7 1.0 C5 C:G32 5.0 41.4 1.0 C5 C:G13 5.0 46.7 1.0 C5 C:G41 5.0 55.9 1.0 C2 C:G37 5.0 55.4 1.0

Potassium binding site 9 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+ within 5.0Å range: probe atom residue distance (Å) B Occ C:K107 b:69.2 occ:1.00 O6 C:G17 3.0 40.8 1.0 O6 C:G31 3.2 47.9 1.0 O4 C:U30 3.2 47.2 1.0 O6 C:G29 3.5 45.0 1.0 N14 C:SPM102 3.6 49.3 0.8 C6 C:G31 3.8 43.8 1.0 N1 C:G31 3.9 43.9 1.0 OP2 C:C16 3.9 49.9 1.0 C6 C:G17 4.0 41.1 1.0 C5 C:C16 4.1 46.0 1.0 C4 C:U30 4.1 44.2 1.0 OP2 C:G15 4.1 44.7 1.0 N4 C:C18 4.1 43.3 1.0 N3 C:U30 4.2 43.0 1.0 N7 C:G17 4.2 41.5 1.0 C5 C:G17 4.5 39.1 1.0 C6 C:G29 4.6 39.2 1.0 N4 C:C16 4.6 51.1 1.0 C4 C:C16 4.8 47.6 1.0 C13 C:SPM102 4.8 44.9 0.8 C6 C:C16 4.9 44.9 1.0 C5 C:G31 5.0 39.6 1.0

Potassium binding site 10 out of 12 in the Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Crystal Structure of the Chili Rna Aptamer in Complex with Dmhbo+ within 5.0Å range: probe atom residue distance (Å) B Occ D:K105 b:57.7 occ:1.00 O6 D:G32 2.7 42.1 1.0 O6 D:G42 2.7 55.3 1.0 O6 D:G37 2.7 56.6 1.0 O6 D:G9 2.8 46.8 1.0 O6 D:G13 2.9 52.7 1.0 O6 D:G12 2.9 53.9 1.0 O6 D:G36 3.0 59.7 1.0 K D:K106 3.3 52.5 1.0 O6 D:G41 3.5 54.3 1.0 C6 D:G32 3.5 43.0 1.0 C6 D:G9 3.6 46.0 1.0 C6 D:G13 3.7 53.7 1.0 C6 D:G42 3.7 54.6 1.0 C6 D:G37 3.7 47.7 1.0 N1 D:G13 3.7 49.9 1.0 C6 D:G36 3.7 46.9 1.0 C6 D:G12 3.8 52.5 1.0 N1 D:G9 3.8 39.0 1.0 N1 D:G36 3.8 47.9 1.0 N1 D:G32 3.9 46.0 1.0 N1 D:G42 3.9 57.4 1.0 N1 D:G12 4.0 55.5 1.0 N1 D:G37 4.0 46.4 1.0 C6 D:G41 4.2 52.2 1.0 N1 D:G41 4.2 43.5 1.0 O2 D:C44 4.6 56.8 1.0 C5 D:G32 4.7 43.1 1.0 C2 D:C44 4.8 45.2 1.0 C5 D:G9 4.8 46.0 1.0 C5 D:G37 4.9 50.1 1.0 C2 D:G13 5.0 47.7 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