Potassium in PDB 6c64: Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO3- Biotin

The structure of Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO3- Biotin, PDB code: 6c64 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)	46.52 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	37.098, 181.764, 108.289, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 25.5

The binding sites of Potassium atom in the Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO3- Biotin (pdb code 6c64). 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 Fluorescent Aptamer Bound to TO3- Biotin, PDB code: 6c64:
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 Fluorescent Aptamer Bound to TO3- 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 Fluorescent Aptamer Bound to TO3- Biotin within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:35.9 occ:1.00 O6 A:G13 2.6 35.2 1.0 O6 A:G18 2.6 34.9 1.0 O6 A:G16 2.7 33.1 1.0 O6 A:G24 2.7 39.7 1.0 O6 A:G29 2.8 32.3 1.0 O6 A:G21 2.8 36.7 1.0 O6 A:G27 2.9 37.4 1.0 O6 A:G11 3.1 26.9 1.0 C6 A:G18 3.4 37.8 1.0 K A:K103 3.5 30.4 1.0 C6 A:G16 3.5 34.5 1.0 C6 A:G13 3.6 32.3 1.0 C6 A:G24 3.6 42.4 1.0 C6 A:G21 3.6 39.5 1.0 N1 A:G18 3.7 39.1 1.0 C6 A:G29 3.7 34.6 1.0 N1 A:G24 3.7 45.3 1.0 C6 A:G27 3.8 32.0 1.0 C6 A:G11 3.8 26.4 1.0 N1 A:G16 3.8 36.0 1.0 N1 A:G13 3.9 28.6 1.0 N1 A:G21 3.9 40.0 1.0 N1 A:G29 4.0 35.4 1.0 N1 A:G27 4.1 28.7 1.0 N1 A:G11 4.1 27.8 1.0 C5 A:G18 4.7 35.7 1.0 C5 A:G16 4.7 31.1 1.0 C5 A:G21 4.8 41.0 1.0 C5 A:G13 4.8 33.3 1.0 N6 A:A22 4.9 49.4 1.0 C5 A:G24 4.9 45.2 1.0 C5 A:G29 4.9 33.4 1.0 C5 A:G11 5.0 24.5 1.0 C2 A:G18 5.0 36.6 1.0 C5 A:G27 5.0 30.9 1.0

Potassium binding site 2 out of 8 in the Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO3- 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 Fluorescent Aptamer Bound to TO3- Biotin within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:30.4 occ:1.00 O6 A:G11 2.6 26.9 1.0 O6 A:G16 2.7 33.1 1.0 O6 A:G20 2.7 32.8 1.0 O6 A:G27 2.7 37.4 1.0 O6 A:G21 2.7 36.7 1.0 O6 A:G15 2.8 30.5 1.0 O6 A:G26 2.8 33.8 1.0 O6 A:G10 3.0 25.1 1.0 K A:K104 3.4 41.7 0.5 C6 A:G20 3.5 35.1 1.0 C6 A:G16 3.5 34.5 1.0 K A:K102 3.5 35.9 1.0 C6 A:G21 3.6 39.5 1.0 C6 A:G11 3.6 26.4 1.0 C6 A:G15 3.6 28.7 1.0 C6 A:G27 3.6 32.0 1.0 C6 A:G10 3.7 26.1 1.0 C6 A:G26 3.7 34.5 1.0 N1 A:G20 3.8 37.8 1.0 N1 A:G15 3.8 27.5 1.0 N1 A:G21 3.8 40.0 1.0 N1 A:G16 3.8 36.0 1.0 N1 A:G11 3.9 27.8 1.0 N1 A:G10 3.9 27.1 1.0 N1 A:G27 4.0 28.7 1.0 N1 A:G26 4.1 34.5 1.0 C5 A:G16 4.7 31.1 1.0 C5 A:G20 4.7 36.0 1.0 C5 A:G27 4.8 30.9 1.0 C5 A:G21 4.8 41.0 1.0 C5 A:G15 4.8 26.0 1.0 C5 A:G11 4.8 24.5 1.0 C5 A:G10 4.8 25.3 1.0 C5 A:G26 5.0 37.1 1.0

Potassium binding site 3 out of 8 in the Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO3- 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 Fluorescent Aptamer Bound to TO3- Biotin within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:41.7 occ:0.50 O6 A:G10 2.6 25.1 1.0 O6 A:G15 2.8 30.5 1.0 O6 A:G20 2.8 32.8 1.0 O6 A:G26 3.0 33.8 1.0 K A:K103 3.4 30.4 1.0 C6 A:G15 3.6 28.7 1.0 C6 A:G10 3.6 26.1 1.0 C6 A:G20 3.6 35.1 1.0 C6 A:G26 3.8 34.5 1.0 N1 A:G10 3.8 27.1 1.0 N1 A:G15 3.8 27.5 1.0 N1 A:G20 3.9 37.8 1.0 N1 A:G26 4.0 34.5 1.0 C5 A:G15 4.7 26.0 1.0 C5 A:G20 4.9 36.0 1.0 C5 A:G10 4.9 25.3 1.0 C5 A:G26 4.9 37.1 1.0

Potassium binding site 4 out of 8 in the Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO3- 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 Fluorescent Aptamer Bound to TO3- Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:44.6 occ:1.00 O6 B:G16 2.6 43.6 1.0 O6 B:G15 2.7 40.7 1.0 O6 B:G11 2.7 44.0 1.0 O6 B:G21 2.8 43.7 1.0 O6 B:G10 2.8 36.2 1.0 O6 B:G27 2.8 43.7 1.0 O6 B:G26 2.9 43.6 1.0 O6 B:G20 3.0 40.3 1.0 K B:K104 3.4 50.7 1.0 C6 B:G10 3.5 37.6 1.0 C6 B:G16 3.5 44.5 1.0 K B:K103 3.5 50.7 1.0 C6 B:G15 3.6 40.3 1.0 C6 B:G21 3.6 47.7 1.0 C6 B:G11 3.6 43.0 1.0 C6 B:G27 3.6 41.1 1.0 C6 B:G20 3.6 45.1 1.0 N1 B:G10 3.7 35.8 1.0 C6 B:G26 3.8 41.5 1.0 N1 B:G21 3.8 48.6 1.0 N1 B:G20 3.8 47.3 1.0 N1 B:G16 3.8 44.7 1.0 N1 B:G27 3.9 39.8 1.0 N1 B:G15 3.9 43.1 1.0 N1 B:G11 3.9 42.5 1.0 N1 B:G26 4.0 38.0 1.0 C5 B:G10 4.6 40.3 1.0 C5 B:G16 4.7 44.8 1.0 C5 B:G20 4.8 47.5 1.0 C5 B:G15 4.8 40.7 1.0 C5 B:G11 4.8 39.9 1.0 C5 B:G27 4.9 38.7 1.0 C2 B:G10 4.9 39.8 1.0 C5 B:G21 4.9 51.7 1.0 C2 B:G20 4.9 49.3 1.0

Potassium binding site 5 out of 8 in the Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO3- 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 Fluorescent Aptamer Bound to TO3- Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:50.7 occ:1.00 O6 B:G24 2.6 53.3 1.0 O6 B:G13 2.7 47.9 1.0 O6 B:G27 2.8 43.7 1.0 O6 B:G18 2.8 48.7 1.0 O6 B:G11 2.9 44.0 1.0 O6 B:G29 2.9 45.6 1.0 O6 B:G16 3.0 43.6 1.0 O6 B:G21 3.0 43.7 1.0 C6 B:G24 3.4 56.5 1.0 K B:K102 3.5 44.6 1.0 C6 B:G27 3.5 41.1 1.0 C6 B:G13 3.6 49.6 1.0 N1 B:G27 3.7 39.8 1.0 C6 B:G21 3.7 47.7 1.0 C6 B:G18 3.7 50.3 1.0 C6 B:G11 3.7 43.0 1.0 C6 B:G29 3.8 42.8 1.0 C6 B:G16 3.8 44.5 1.0 N1 B:G21 3.8 48.6 1.0 N1 B:G13 3.8 49.5 1.0 N1 B:G24 3.9 56.5 1.0 N1 B:G18 4.0 48.8 1.0 N1 B:G16 4.1 44.7 1.0 N1 B:G29 4.1 43.3 1.0 N1 B:G11 4.1 42.5 1.0 C5 B:G24 4.6 56.1 1.0 C5 B:G27 4.7 38.7 1.0 N6 B:A22 4.7 61.5 1.0 C5 B:G13 4.8 47.3 1.0 C5 B:G11 4.9 39.9 1.0 C5 B:G21 4.9 51.7 1.0 C2 B:G27 4.9 39.1 1.0 C5 B:G29 4.9 43.9 1.0 C5 B:G18 4.9 50.6 1.0 C5 B:G16 5.0 44.8 1.0

Potassium binding site 6 out of 8 in the Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO3- 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 Fluorescent Aptamer Bound to TO3- Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:K104 b:50.7 occ:1.00 O6 B:G10 2.5 36.2 1.0 O6 D:G20 2.6 44.6 1.0 O6 B:G20 2.7 40.3 1.0 O6 B:G26 2.7 43.6 1.0 O6 D:G15 2.7 38.8 1.0 O6 D:G26 2.9 46.6 1.0 O6 D:G10 2.9 40.8 1.0 O6 B:G15 2.9 40.7 1.0 K D:K101 3.3 49.0 1.0 K B:K102 3.4 44.6 1.0 C6 D:G20 3.4 44.3 1.0 C6 B:G26 3.5 41.5 1.0 C6 B:G10 3.5 37.6 1.0 C6 B:G20 3.5 45.1 1.0 N1 D:G20 3.5 44.8 1.0 C6 D:G15 3.5 39.1 1.0 C6 D:G26 3.6 45.7 1.0 N1 B:G20 3.6 47.3 1.0 N1 D:G15 3.7 37.4 1.0 N1 B:G26 3.8 38.0 1.0 C6 B:G15 3.8 40.3 1.0 C6 D:G10 3.8 41.5 1.0 N1 B:G10 3.8 35.8 1.0 N1 D:G26 3.9 46.3 1.0 N1 D:G10 4.0 37.7 1.0 N1 B:G15 4.1 43.1 1.0 C5 B:G26 4.7 43.6 1.0 C5 D:G20 4.7 45.0 1.0 C5 D:G26 4.7 45.8 1.0 C5 B:G10 4.8 40.3 1.0 C5 D:G15 4.8 38.0 1.0 C2 D:G20 4.8 49.7 1.0 C5 B:G20 4.9 47.5 1.0 C2 B:G20 4.9 49.3 1.0 C5 B:G15 5.0 40.7 1.0 C2 D:G15 5.0 36.4 1.0 C2 B:G26 5.0 39.6 1.0

Potassium binding site 7 out of 8 in the Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO3- 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 Fluorescent Aptamer Bound to TO3- Biotin within 5.0Å range: probe atom residue distance (Å) B Occ D:K101 b:49.0 occ:1.00 O6 D:G15 2.6 38.8 1.0 O6 D:G11 2.7 43.0 1.0 O6 D:G16 2.8 38.1 1.0 O6 D:G26 2.8 46.6 1.0 O6 D:G27 2.8 46.1 1.0 O6 D:G10 2.8 40.8 1.0 O6 D:G20 2.9 44.6 1.0 O6 D:G21 2.9 49.1 1.0 K B:K104 3.3 50.7 1.0 C6 D:G15 3.4 39.1 1.0 C6 D:G10 3.5 41.5 1.0 C6 D:G11 3.6 45.3 1.0 C6 D:G16 3.6 40.9 1.0 C6 D:G27 3.6 46.9 1.0 C6 D:G20 3.6 44.3 1.0 N1 D:G10 3.6 37.7 1.0 C6 D:G26 3.7 45.7 1.0 C6 D:G21 3.7 49.5 1.0 N1 D:G15 3.7 37.4 1.0 K D:K102 3.8 58.3 1.0 N1 D:G27 3.9 47.6 1.0 N1 D:G16 3.9 41.4 1.0 N1 D:G26 3.9 46.3 1.0 N1 D:G11 3.9 44.5 1.0 N1 D:G20 3.9 44.8 1.0 N1 D:G21 4.0 49.5 1.0 C5 D:G15 4.6 38.0 1.0 C5 D:G10 4.7 43.6 1.0 C5 D:G11 4.8 44.6 1.0 C5 D:G20 4.8 45.0 1.0 C2 D:G10 4.8 44.2 1.0 C5 D:G16 4.8 36.3 1.0 C5 D:G27 4.8 44.7 1.0 C5 D:G21 4.9 51.7 1.0 C2 D:G15 5.0 36.4 1.0

Potassium binding site 8 out of 8 in the Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO3- 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 Fluorescent Aptamer Bound to TO3- Biotin within 5.0Å range: probe atom residue distance (Å) B Occ D:K102 b:58.3 occ:1.00 O6 D:G24 2.6 50.7 1.0 O6 D:G13 2.7 41.1 1.0 O6 D:G27 2.7 46.1 1.0 O6 D:G18 2.8 45.4 1.0 O6 D:G11 2.8 43.0 1.0 O6 D:G29 2.8 45.0 1.0 O6 D:G21 2.9 49.1 1.0 O6 D:G16 3.3 38.1 1.0 C6 D:G27 3.4 46.9 1.0 C6 D:G24 3.5 54.3 1.0 C6 D:G29 3.6 45.8 1.0 C6 D:G13 3.6 45.3 1.0 C6 D:G21 3.6 49.5 1.0 N1 D:G27 3.7 47.6 1.0 N1 D:G29 3.7 46.0 1.0 C6 D:G11 3.7 45.3 1.0 N1 D:G24 3.8 53.3 1.0 C6 D:G18 3.8 44.7 1.0 K D:K101 3.8 49.0 1.0 N1 D:G21 3.9 49.5 1.0 N1 D:G13 3.9 44.0 1.0 C6 D:G16 4.0 40.9 1.0 N1 D:G16 4.1 41.4 1.0 N1 D:G18 4.2 43.0 1.0 N1 D:G11 4.2 44.5 1.0 C5 D:G27 4.6 44.7 1.0 C5 D:G24 4.7 60.6 1.0 C5 D:G21 4.8 51.7 1.0 C5 D:G29 4.8 49.2 1.0 C5 D:G11 4.8 44.6 1.0 C5 D:G13 4.9 52.3 1.0 C2 D:G27 4.9 46.2 1.0 C2 D:G29 4.9 48.9 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