Potassium in PDB 6c65: Crystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound to TO1-Biotin

The structure of Crystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound to TO1-Biotin, PDB code: 6c65 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)	46.38 / 2.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	36.639, 179.680, 108.313, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23.7

The binding sites of Potassium atom in the Crystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound to TO1-Biotin (pdb code 6c65). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound to TO1-Biotin, PDB code: 6c65:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in the Crystal Structure of the Mango-II-A22U Fluorescent 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 Crystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:29.6 occ:1.00 O6 A:G13 2.7 35.8 1.0 O6 A:G29 2.7 37.8 1.0 O6 A:G16 2.7 35.8 1.0 O6 A:G21 2.7 38.2 1.0 O6 A:G24 2.7 44.5 1.0 O6 A:G27 2.7 35.6 1.0 O6 A:G11 2.7 33.0 1.0 O6 A:G18 2.9 42.2 1.0 K A:K103 3.4 33.9 1.0 C6 A:G16 3.5 34.2 1.0 C6 A:G13 3.5 35.9 1.0 C6 A:G27 3.5 32.1 1.0 C6 A:G24 3.5 43.1 1.0 C6 A:G29 3.6 34.5 1.0 C6 A:G21 3.6 38.7 1.0 C6 A:G18 3.6 38.7 1.0 C6 A:G11 3.6 31.1 1.0 N1 A:G27 3.7 33.3 1.0 N1 A:G13 3.8 31.8 1.0 N1 A:G18 3.9 39.6 1.0 N1 A:G29 3.9 32.1 1.0 N1 A:G16 3.9 35.5 1.0 N1 A:G24 3.9 41.6 1.0 N1 A:G21 3.9 38.3 1.0 N1 A:G11 4.0 33.1 1.0 H082 A:EKJ101 4.5 57.5 1.0 C5 A:G24 4.7 41.4 1.0 C5 A:G16 4.7 29.7 1.0 C5 A:G13 4.8 38.5 1.0 C5 A:G27 4.8 30.9 1.0 C5 A:G11 4.8 28.8 1.0 C5 A:G18 4.8 37.7 1.0 C5 A:G29 4.8 33.9 1.0 C5 A:G21 4.9 39.2 1.0 H111 A:EKJ101 4.9 61.9 1.0 C2 A:G27 5.0 31.6 1.0

Potassium binding site 2 out of 8 in the Crystal Structure of the Mango-II-A22U Fluorescent 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 Crystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:33.9 occ:1.00 O6 A:G16 2.6 35.8 1.0 O6 A:G20 2.7 33.5 1.0 O6 A:G26 2.7 39.5 1.0 O6 A:G11 2.7 33.0 1.0 O6 A:G15 2.8 35.4 1.0 O6 A:G27 2.8 35.6 1.0 O6 A:G10 2.9 30.8 1.0 O6 A:G21 3.0 38.2 1.0 K A:K104 3.3 47.7 0.5 K A:K102 3.4 29.6 1.0 C6 A:G10 3.5 30.9 1.0 C6 A:G16 3.6 34.2 1.0 C6 A:G15 3.6 31.5 1.0 C6 A:G27 3.6 32.1 1.0 C6 A:G26 3.6 33.2 1.0 C6 A:G20 3.6 36.8 1.0 C6 A:G11 3.6 31.1 1.0 N1 A:G15 3.7 28.4 1.0 N1 A:G10 3.7 28.2 1.0 N1 A:G26 3.8 33.4 1.0 N1 A:G27 3.8 33.3 1.0 C6 A:G21 3.8 38.7 1.0 N1 A:G20 3.9 38.9 1.0 N1 A:G11 3.9 33.1 1.0 N1 A:G16 4.0 35.5 1.0 N1 A:G21 4.0 38.3 1.0 C5 A:G10 4.7 30.6 1.0 C5 A:G16 4.7 29.7 1.0 C5 A:G27 4.7 30.9 1.0 C2 A:G10 4.8 30.8 1.0 C5 A:G26 4.8 33.1 1.0 C5 A:G15 4.8 31.4 1.0 C5 A:G11 4.9 28.8 1.0 C5 A:G20 4.9 37.0 1.0 C2 A:G15 5.0 29.7 1.0

Potassium binding site 3 out of 8 in the Crystal Structure of the Mango-II-A22U Fluorescent 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 Crystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:47.7 occ:0.50 O6 A:G10 2.7 30.8 1.0 O6 A:G20 2.8 33.5 1.0 O6 A:G26 2.8 39.5 1.0 O6 A:G15 3.0 35.4 1.0 K A:K103 3.3 33.9 1.0 C6 A:G26 3.5 33.2 1.0 C6 A:G10 3.6 30.9 1.0 C6 A:G20 3.6 36.8 1.0 C6 A:G15 3.7 31.5 1.0 N1 A:G26 3.8 33.4 1.0 N1 A:G15 3.8 28.4 1.0 N1 A:G10 3.9 28.2 1.0 N1 A:G20 3.9 38.9 1.0 C5 A:G26 4.7 33.1 1.0 C5 A:G20 4.8 37.0 1.0 C5 A:G10 4.9 30.6 1.0 C5 A:G15 4.9 31.4 1.0 C2 A:G26 5.0 30.9 1.0

Potassium binding site 4 out of 8 in the Crystal Structure of the Mango-II-A22U Fluorescent 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 Crystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:43.0 occ:1.00 O6 B:G15 2.6 48.6 1.0 O6 B:G11 2.7 46.6 1.0 O6 B:G16 2.7 41.0 1.0 O6 B:G21 2.7 49.1 1.0 O6 B:G27 2.8 45.8 1.0 O6 B:G26 2.9 50.1 1.0 O6 B:G10 2.9 47.0 1.0 O6 B:G20 2.9 43.7 1.0 K B:K103 3.2 47.7 1.0 K B:K104 3.4 53.7 1.0 C6 B:G15 3.5 48.2 1.0 C6 B:G10 3.5 45.7 1.0 C6 B:G16 3.5 44.1 1.0 C6 B:G20 3.6 46.4 1.0 C6 B:G21 3.6 48.4 1.0 C6 B:G11 3.6 45.4 1.0 C6 B:G27 3.7 43.1 1.0 C6 B:G26 3.7 45.6 1.0 N1 B:G10 3.7 44.4 1.0 N1 B:G20 3.8 48.0 1.0 N1 B:G21 3.8 47.6 1.0 N1 B:G15 3.8 44.5 1.0 N1 B:G16 3.9 44.2 1.0 N1 B:G26 3.9 41.7 1.0 N1 B:G11 3.9 47.6 1.0 N1 B:G27 4.0 41.5 1.0 C5 B:G10 4.7 45.8 1.0 C5 B:G20 4.7 45.7 1.0 C5 B:G15 4.8 49.0 1.0 C5 B:G16 4.8 46.2 1.0 C5 B:G11 4.8 41.8 1.0 C5 B:G21 4.8 48.9 1.0 C2 B:G10 4.9 44.1 1.0 C5 B:G27 4.9 40.1 1.0 C2 B:G20 4.9 47.7 1.0 C5 B:G26 5.0 44.3 1.0

Potassium binding site 5 out of 8 in the Crystal Structure of the Mango-II-A22U Fluorescent 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 5 of Crystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:47.7 occ:1.00 O6 B:G11 2.6 46.6 1.0 O6 B:G27 2.6 45.8 1.0 O6 B:G24 2.7 51.0 1.0 O6 B:G13 2.7 50.2 1.0 O6 B:G21 2.8 49.1 1.0 O6 B:G16 2.8 41.0 1.0 O6 B:G18 2.9 48.5 1.0 O6 B:G29 3.0 46.5 1.0 K B:K102 3.2 43.0 1.0 C6 B:G27 3.4 43.1 1.0 C6 B:G24 3.5 53.0 1.0 C6 B:G11 3.5 45.4 1.0 C6 B:G21 3.5 48.4 1.0 C6 B:G13 3.6 48.6 1.0 C6 B:G16 3.6 44.1 1.0 N1 B:G27 3.7 41.5 1.0 N1 B:G21 3.7 47.6 1.0 C6 B:G29 3.7 45.5 1.0 N1 B:G24 3.8 53.5 1.0 C6 B:G18 3.9 47.4 1.0 N1 B:G11 3.9 47.6 1.0 N1 B:G16 3.9 44.2 1.0 N1 B:G13 4.0 45.7 1.0 N1 B:G29 4.0 45.6 1.0 N1 B:G18 4.4 47.6 1.0 H111 B:EKJ101 4.7 70.2 1.0 C5 B:G24 4.7 53.5 1.0 C5 B:G11 4.7 41.8 1.0 C5 B:G27 4.7 40.1 1.0 C5 B:G13 4.8 48.0 1.0 C5 B:G21 4.8 48.9 1.0 C5 B:G29 4.9 44.7 1.0 C5 B:G16 4.9 46.2 1.0 C2 B:G27 4.9 43.0 1.0 C2 B:G21 4.9 49.7 1.0 C5 B:G18 5.0 48.8 1.0 C2 B:G24 5.0 55.9 1.0

Potassium binding site 6 out of 8 in the Crystal Structure of the Mango-II-A22U Fluorescent 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 6 of Crystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:K104 b:53.7 occ:1.00 O6 B:G10 2.6 47.0 1.0 O6 C:G26 2.7 50.1 1.0 O6 C:G15 2.8 47.9 1.0 O6 C:G10 2.8 49.1 1.0 O6 B:G20 2.8 43.7 1.0 O6 C:G20 2.8 47.0 1.0 O6 B:G15 2.9 48.6 1.0 O6 B:G26 3.0 50.1 1.0 K C:K102 3.3 40.1 1.0 K B:K102 3.4 43.0 1.0 C6 B:G10 3.4 45.7 1.0 C6 C:G26 3.5 49.1 1.0 C6 C:G20 3.5 46.3 1.0 C6 C:G15 3.6 47.6 1.0 N1 B:G10 3.7 44.4 1.0 C6 B:G20 3.7 46.4 1.0 N1 C:G20 3.7 48.5 1.0 C6 B:G26 3.7 45.6 1.0 C6 B:G15 3.7 48.2 1.0 C6 C:G10 3.8 47.9 1.0 N1 B:G20 3.8 48.0 1.0 N1 C:G15 3.8 46.3 1.0 N1 C:G26 3.9 48.7 1.0 N1 B:G26 3.9 41.7 1.0 N1 B:G15 4.0 44.5 1.0 N1 C:G10 4.1 47.5 1.0 C5 C:G26 4.6 48.5 1.0 C5 B:G10 4.7 45.8 1.0 C5 C:G15 4.8 47.4 1.0 C5 C:G20 4.8 46.2 1.0 C5 B:G15 4.8 49.0 1.0 C5 B:G26 4.9 44.3 1.0 C2 C:G20 4.9 47.5 1.0 C2 B:G10 4.9 44.1 1.0 C5 B:G20 5.0 45.7 1.0

Potassium binding site 7 out of 8 in the Crystal Structure of the Mango-II-A22U Fluorescent 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 7 of Crystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ C:K102 b:40.1 occ:1.00 O6 C:G27 2.6 50.9 1.0 O6 C:G16 2.7 44.7 1.0 O6 C:G15 2.7 47.9 1.0 O6 C:G11 2.7 50.4 1.0 O6 C:G26 2.7 50.1 1.0 O6 C:G20 2.8 47.0 1.0 O6 C:G21 2.9 49.7 1.0 O6 C:G10 2.9 49.1 1.0 K B:K104 3.3 53.7 1.0 K C:K103 3.4 57.8 1.0 C6 C:G16 3.5 43.6 1.0 C6 C:G27 3.5 51.9 1.0 C6 C:G11 3.5 51.7 1.0 C6 C:G15 3.5 47.6 1.0 C6 C:G10 3.6 47.9 1.0 C6 C:G26 3.6 49.1 1.0 C6 C:G20 3.6 46.3 1.0 N1 C:G11 3.7 49.0 1.0 C6 C:G21 3.8 49.5 1.0 N1 C:G16 3.8 45.1 1.0 N1 C:G26 3.8 48.7 1.0 N1 C:G10 3.8 47.5 1.0 N1 C:G20 3.8 48.5 1.0 N1 C:G15 3.9 46.3 1.0 N1 C:G27 3.9 50.5 1.0 N1 C:G21 4.0 51.6 1.0 C5 C:G27 4.6 48.4 1.0 C5 C:G16 4.7 43.8 1.0 C5 C:G10 4.7 47.6 1.0 C5 C:G11 4.7 52.6 1.0 C5 C:G15 4.7 47.4 1.0 C5 C:G20 4.8 46.2 1.0 C5 C:G26 4.9 48.5 1.0 C5 C:G21 5.0 51.3 1.0 C2 C:G11 5.0 50.3 1.0

Potassium binding site 8 out of 8 in the Crystal Structure of the Mango-II-A22U Fluorescent 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 8 of Crystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ C:K103 b:57.8 occ:1.00 O6 C:G27 2.5 50.9 1.0 O6 C:G24 2.7 55.7 1.0 O6 C:G21 2.7 49.7 1.0 O6 C:G18 2.8 56.3 1.0 O6 C:G11 2.8 50.4 1.0 O6 C:G13 2.8 54.2 1.0 O6 C:G29 2.9 56.3 1.0 O6 C:G16 3.0 44.7 1.0 C6 C:G27 3.4 51.9 1.0 K C:K102 3.4 40.1 1.0 C6 C:G24 3.6 56.5 1.0 C6 C:G21 3.6 49.5 1.0 C6 C:G16 3.7 43.6 1.0 C6 C:G29 3.7 54.6 1.0 C6 C:G11 3.7 51.7 1.0 C6 C:G18 3.7 51.4 1.0 C6 C:G13 3.7 56.1 1.0 N1 C:G16 3.8 45.1 1.0 N1 C:G29 3.8 53.0 1.0 N1 C:G27 3.9 50.5 1.0 N1 C:G21 3.9 51.6 1.0 N1 C:G11 3.9 49.0 1.0 N1 C:G24 3.9 55.2 1.0 N1 C:G18 4.0 46.3 1.0 N1 C:G13 4.1 53.1 1.0 C5 C:G27 4.6 48.4 1.0 C5 C:G24 4.7 58.8 1.0 C5 C:G21 4.8 51.3 1.0 C5 C:G18 4.9 52.3 1.0 C5 C:G16 4.9 43.8 1.0 C5 C:G13 4.9 56.5 1.0 C5 C:G29 4.9 56.4 1.0 C5 C:G11 4.9 52.6 1.0 C2 C:G16 5.0 46.7 1.0

R.J.Trachman 3Rd., A.Abdolahzadeh, A.Andreoni, R.Cojocaru, J.R.Knutson, M.Ryckelynck, P.J.Unrau, A.R.Ferre-D'amare. Crystal Structures of the Mango-II Rna Aptamer Reveal Heterogeneous Fluorophore Binding and Guide Engineering of Variants with Improved Selectivity and Brightness. Biochemistry V. 57 3544 2018.
ISSN: ISSN 1520-4995
PubMed: 29768001
DOI: 10.1021/ACS.BIOCHEM.8B00399