Potassium in PDB 6e8t: Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin

The structure of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin, PDB code: 6e8t was solved by R.J.Trachman, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.97 / 2.90
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	91.945, 91.945, 161.691, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 23.7

The structure of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Potassium atom in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin (pdb code 6e8t). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin, PDB code: 6e8t:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ D:K102 b:69.5 occ:1.00 O6 D:G17 2.7 68.0 1.0 O6 D:G12 2.7 78.1 1.0 O6 D:G9 2.8 70.4 1.0 O6 D:G18 2.8 71.8 1.0 O6 D:G24 2.8 74.6 1.0 O6 D:G8 2.9 76.0 1.0 O6 D:G22 2.9 73.6 1.0 O6 D:G13 2.9 72.5 1.0 C6 D:G12 3.6 77.0 1.0 C6 D:G8 3.7 75.7 1.0 C6 D:G13 3.7 75.0 1.0 C6 D:G22 3.7 71.8 1.0 C6 D:G18 3.7 71.2 1.0 C6 D:G24 3.8 75.8 1.0 C6 D:G17 3.8 69.6 1.0 N1 D:G12 3.8 71.0 1.0 N1 D:G13 3.9 73.9 1.0 C6 D:G9 3.9 71.8 1.0 N1 D:G24 3.9 74.8 1.0 N1 D:G22 3.9 74.6 1.0 N1 D:G8 4.1 74.8 1.0 N1 D:G18 4.1 72.7 1.0 N1 D:G17 4.3 72.0 1.0 N1 D:G9 4.3 74.5 1.0 S19 D:HZG101 4.4 72.3 1.0 C5 D:G8 4.8 78.1 1.0 C5 D:G12 4.9 84.3 1.0 C5 D:G13 4.9 76.0 1.0 C5 D:G17 5.0 74.7 1.0 C5 D:G22 5.0 73.8 1.0 C5 D:G18 5.0 72.8 1.0

Potassium binding site 2 out of 4 in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ C:K102 b:59.1 occ:1.00 O6 C:G17 2.6 49.9 1.0 O6 C:G18 2.6 53.4 1.0 O6 C:G13 2.7 58.2 1.0 O6 C:G9 2.7 57.3 1.0 O6 C:G24 2.7 50.9 1.0 O6 C:G8 2.8 51.1 1.0 O6 C:G22 2.8 50.2 1.0 O6 C:G12 3.0 56.7 1.0 C6 C:G18 3.5 56.1 1.0 C6 C:G17 3.6 54.5 1.0 C6 C:G8 3.6 50.7 1.0 N1 C:G12 3.6 56.5 1.0 C6 C:G12 3.6 57.5 1.0 C6 C:G13 3.6 54.9 1.0 C6 C:G22 3.7 51.0 1.0 N1 C:G18 3.7 54.9 1.0 N1 C:G8 3.8 49.1 1.0 C6 C:G24 3.8 49.9 1.0 C6 C:G9 3.8 56.2 1.0 N1 C:G22 4.0 52.0 1.0 N1 C:G17 4.0 54.1 1.0 N1 C:G13 4.1 58.5 1.0 N1 C:G24 4.1 47.8 1.0 S19 C:HZG101 4.2 48.2 1.0 N1 C:G9 4.3 55.3 1.0 C20 C:HZG101 4.8 51.9 1.0 C5 C:G17 4.8 58.9 1.0 C06 C:HZG101 4.8 52.6 1.0 C5 C:G18 4.8 56.4 1.0 C2 C:G12 4.8 55.4 1.0 C5 C:G13 4.8 57.1 1.0 C5 C:G8 4.9 50.6 1.0 C5 C:G22 4.9 49.8 1.0 C5 C:G12 4.9 55.2 1.0 C5 C:G9 5.0 53.8 1.0 C2 C:G18 5.0 51.8 1.0

Potassium binding site 3 out of 4 in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:65.0 occ:1.00 O6 B:G8 2.6 64.7 1.0 O6 B:G12 2.7 61.9 1.0 O6 B:G24 2.7 71.3 1.0 O6 B:G22 2.7 67.3 1.0 O6 B:G13 2.7 58.4 1.0 O6 B:G18 2.8 61.0 1.0 O6 B:G9 2.8 63.0 1.0 O6 B:G17 3.0 70.0 1.0 C6 B:G8 3.4 63.8 1.0 C6 B:G24 3.5 72.4 1.0 C6 B:G12 3.6 61.0 1.0 C6 B:G18 3.6 64.7 1.0 N1 B:G24 3.6 68.7 1.0 C6 B:G22 3.6 68.6 1.0 N1 B:G8 3.7 59.0 1.0 C6 B:G13 3.7 56.5 1.0 N1 B:G12 3.8 63.1 1.0 C6 B:G9 3.8 59.8 1.0 N1 B:G18 3.8 64.4 1.0 C6 B:G17 3.9 70.3 1.0 N1 B:G22 4.2 67.5 1.0 N1 B:G13 4.2 61.2 1.0 N1 B:G9 4.2 57.4 1.0 N1 B:G17 4.3 72.2 1.0 S19 B:HZG101 4.5 63.0 1.0 C2 B:A29 4.6 74.1 1.0 C5 B:G8 4.6 61.1 1.0 C5 B:G22 4.8 68.9 1.0 C5 B:G13 4.9 54.9 1.0 C5 B:G12 4.9 59.1 1.0 C5 B:G18 4.9 66.5 1.0 C5 B:G24 4.9 74.7 1.0 C2 B:G8 4.9 57.5 1.0 C2 B:G24 4.9 69.5 1.0 N1 B:A29 4.9 72.6 1.0

Potassium binding site 4 out of 4 in the Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of the Mango-III (A10U) Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:79.5 occ:1.00 O6 A:G8 2.6 75.8 1.0 O6 A:G17 2.6 76.9 1.0 O6 A:G12 2.7 77.1 1.0 O6 A:G9 2.7 70.4 1.0 O6 A:G22 2.7 76.4 1.0 O6 A:G13 2.8 70.1 1.0 O6 A:G24 2.9 77.3 1.0 O6 A:G18 2.9 72.5 1.0 C6 A:G8 3.4 77.6 1.0 C6 A:G9 3.5 71.9 1.0 C6 A:G12 3.5 71.3 1.0 C6 A:G22 3.6 74.2 1.0 C6 A:G17 3.6 75.6 1.0 N1 A:G9 3.7 69.3 1.0 N1 A:G12 3.7 69.0 1.0 C6 A:G13 3.7 70.1 1.0 C6 A:G24 3.8 77.3 1.0 N1 A:G8 3.8 78.3 1.0 N1 A:G22 3.9 74.8 1.0 C6 A:G18 3.9 75.4 1.0 N1 A:G13 3.9 71.5 1.0 N1 A:G24 4.0 74.7 1.0 N1 A:G17 4.2 75.4 1.0 N1 A:G18 4.2 73.4 1.0 S19 A:HZG101 4.3 65.3 1.0 C5 A:G8 4.6 77.9 1.0 C5 A:G9 4.8 73.7 1.0 C5 A:G12 4.8 68.0 1.0 C5 A:G17 4.8 73.6 1.0 C5 A:G22 4.8 75.6 1.0 C2 A:G9 4.9 69.7 1.0 C2 A:G12 4.9 71.7 1.0 C5 A:G13 5.0 66.9 1.0

R.J.Trachman 3Rd., A.Autour, S.C.Y.Jeng, A.Abdolahzadeh, A.Andreoni, R.Cojocaru, R.Garipov, E.V.Dolgosheina, J.R.Knutson, M.Ryckelynck, P.J.Unrau, A.R.Ferre-D'amare. Structure and Functional Reselection of the Mango-III Fluorogenic Rna Aptamer. Nat. Chem. Biol. V. 15 472 2019.
ISSN: ESSN 1552-4469
PubMed: 30992561
DOI: 10.1038/S41589-019-0267-9