Potassium in PDB 6c63: Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO1- Biotin

The structure of Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO1- Biotin, PDB code: 6c63 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)	91.21 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	36.831, 182.412, 107.494, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23

The binding sites of Potassium atom in the Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO1- Biotin (pdb code 6c63). 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 TO1- Biotin, PDB code: 6c63:
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 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 Fluorescent Aptamer Bound to TO1- Biotin within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:48.1 occ:1.00 O6 A:G13 2.6 48.4 1.0 O6 A:G21 2.7 46.5 1.0 O6 A:G18 2.7 50.7 1.0 O6 A:G27 2.7 54.5 1.0 O6 A:G24 2.7 51.1 1.0 O6 A:G16 2.7 45.9 1.0 O6 A:G29 2.8 49.2 1.0 O6 A:G11 2.8 43.2 1.0 C6 A:G13 3.5 45.2 1.0 C6 A:G18 3.5 49.4 1.0 C6 A:G21 3.6 48.9 1.0 C6 A:G29 3.6 49.2 1.0 C6 A:G24 3.6 50.6 1.0 C6 A:G16 3.6 46.3 1.0 C6 A:G27 3.6 48.4 1.0 K A:K103 3.6 48.2 1.0 C6 A:G11 3.7 42.7 1.0 N1 A:G29 3.7 45.1 1.0 N1 A:G18 3.8 50.9 1.0 N1 A:G13 3.8 42.6 1.0 N1 A:G24 3.9 54.2 1.0 N1 A:G27 3.9 48.3 1.0 N1 A:G16 3.9 50.5 1.0 N1 A:G21 3.9 46.3 1.0 N1 A:G11 4.1 40.5 1.0 C5 A:G21 4.7 50.3 1.0 C5 A:G13 4.7 45.4 1.0 C5 A:G18 4.8 50.5 1.0 H111 A:EKJ101 4.8 66.4 1.0 C5 A:G16 4.8 42.7 1.0 C5 A:G27 4.8 41.0 1.0 C5 A:G24 4.9 49.4 1.0 C5 A:G29 4.9 46.4 1.0 C5 A:G11 4.9 40.7 1.0 C2 A:G29 5.0 48.2 1.0

Potassium binding site 2 out of 8 in the Crystal Structure of the Mango-II 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 Fluorescent Aptamer Bound to TO1- Biotin within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:48.2 occ:1.00 O6 A:G16 2.6 45.9 1.0 O6 A:G11 2.7 43.2 1.0 O6 A:G20 2.7 49.1 1.0 O6 A:G15 2.7 47.8 1.0 O6 A:G26 2.8 49.4 1.0 O6 A:G10 2.8 44.1 1.0 O6 A:G21 2.9 46.5 1.0 O6 A:G27 3.0 54.5 1.0 K A:K104 3.3 63.0 0.5 C6 A:G15 3.5 44.1 1.0 C6 A:G16 3.5 46.3 1.0 C6 A:G10 3.5 46.6 1.0 C6 A:G11 3.6 42.7 1.0 K A:K102 3.6 48.1 1.0 C6 A:G20 3.6 49.7 1.0 N1 A:G15 3.6 41.4 1.0 C6 A:G26 3.7 48.2 1.0 N1 A:G10 3.7 41.4 1.0 C6 A:G27 3.7 48.4 1.0 C6 A:G21 3.8 48.9 1.0 N1 A:G26 3.9 49.6 1.0 N1 A:G16 3.9 50.5 1.0 N1 A:G11 3.9 40.5 1.0 N1 A:G27 4.0 48.3 1.0 N1 A:G20 4.0 48.8 1.0 N1 A:G21 4.1 46.3 1.0 C5 A:G16 4.6 42.7 1.0 C5 A:G10 4.7 43.5 1.0 C5 A:G15 4.8 44.0 1.0 C5 A:G11 4.8 40.7 1.0 C5 A:G20 4.8 46.7 1.0 C2 A:G15 4.9 46.0 1.0 C5 A:G27 4.9 41.0 1.0 C2 A:G10 4.9 42.5 1.0 C5 A:G21 4.9 50.3 1.0 C5 A:G26 5.0 47.1 1.0

Potassium binding site 3 out of 8 in the Crystal Structure of the Mango-II 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 Fluorescent Aptamer Bound to TO1- Biotin within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:63.0 occ:0.50 O6 A:G10 2.7 44.1 1.0 O6 A:G26 2.9 49.4 1.0 O6 A:G20 2.9 49.1 1.0 O6 A:G15 2.9 47.8 1.0 K A:K103 3.3 48.2 1.0 C6 A:G26 3.6 48.2 1.0 C6 A:G10 3.6 46.6 1.0 C6 A:G15 3.7 44.1 1.0 C6 A:G20 3.7 49.7 1.0 N1 A:G15 3.8 41.4 1.0 N1 A:G26 3.9 49.6 1.0 N1 A:G10 3.9 41.4 1.0 N1 A:G20 4.0 48.8 1.0 C5 A:G26 4.7 47.1 1.0 C5 A:G10 4.9 43.5 1.0 C5 A:G15 4.9 44.0 1.0 C5 A:G20 4.9 46.7 1.0

Potassium binding site 4 out of 8 in the Crystal Structure of the Mango-II 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 Fluorescent Aptamer Bound to TO1- Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:59.8 occ:1.00 O6 B:G11 2.6 65.8 1.0 O6 B:G16 2.6 61.2 1.0 O6 B:G15 2.6 72.2 1.0 O6 B:G21 2.8 59.7 1.0 O6 B:G27 2.8 59.9 1.0 O6 B:G26 2.8 61.7 1.0 O6 B:G10 2.9 58.2 1.0 O6 B:G20 3.0 60.2 1.0 K B:K103 3.1 66.4 1.0 K C:K103 3.4 71.6 1.0 C6 B:G10 3.5 62.1 1.0 C6 B:G11 3.5 63.6 1.0 C6 B:G16 3.5 62.2 1.0 C6 B:G15 3.5 67.2 1.0 C6 B:G26 3.6 59.1 1.0 C6 B:G27 3.6 59.5 1.0 N1 B:G10 3.7 59.4 1.0 C6 B:G20 3.7 61.2 1.0 C6 B:G21 3.7 63.1 1.0 N1 B:G26 3.7 54.1 1.0 N1 B:G11 3.9 64.3 1.0 N1 B:G15 3.9 62.9 1.0 N1 B:G27 3.9 60.0 1.0 N1 B:G16 3.9 60.1 1.0 N1 B:G20 3.9 60.4 1.0 N1 B:G21 4.0 61.4 1.0 C5 B:G10 4.7 63.6 1.0 C5 B:G11 4.7 59.1 1.0 C5 B:G16 4.8 63.1 1.0 C5 B:G15 4.8 67.8 1.0 C5 B:G20 4.8 62.6 1.0 C2 B:G10 4.8 63.4 1.0 C5 B:G27 4.8 52.6 1.0 C5 B:G26 4.9 57.4 1.0 C5 B:G21 4.9 63.3 1.0 C2 B:G26 5.0 54.6 1.0

Potassium binding site 5 out of 8 in the Crystal Structure of the Mango-II 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 Fluorescent Aptamer Bound to TO1- Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:66.4 occ:1.00 O6 B:G11 2.6 65.8 1.0 O6 B:G13 2.6 62.1 1.0 O6 B:G27 2.7 59.9 1.0 O6 B:G16 2.7 61.2 1.0 O6 B:G24 2.8 64.4 1.0 O6 B:G18 2.8 66.1 1.0 O6 B:G21 2.8 59.7 1.0 O6 B:G29 3.0 65.8 1.0 K B:K102 3.1 59.8 1.0 C6 B:G27 3.4 59.5 1.0 C6 B:G11 3.5 63.6 1.0 C6 B:G13 3.5 68.6 1.0 N1 B:G27 3.6 60.0 1.0 C6 B:G16 3.6 62.2 1.0 C6 B:G24 3.7 66.9 1.0 C6 B:G21 3.7 63.1 1.0 C6 B:G18 3.8 66.2 1.0 C6 B:G29 3.8 60.6 1.0 N1 B:G13 3.8 63.9 1.0 N1 B:G11 3.9 64.3 1.0 N1 B:G16 3.9 60.1 1.0 N1 B:G21 3.9 61.4 1.0 N1 B:G29 4.1 56.4 1.0 N1 B:G24 4.1 70.2 1.0 N1 B:G18 4.3 67.7 1.0 H081 B:EKJ101 4.4 91.1 1.0 C5 B:G11 4.6 59.1 1.0 H111 B:EKJ101 4.7 94.7 1.0 C5 B:G13 4.7 66.9 1.0 C5 B:G27 4.7 52.6 1.0 C5 B:G24 4.8 65.8 1.0 C5 B:G16 4.8 63.1 1.0 C2 B:G27 4.8 56.5 1.0 C5 B:G18 4.9 66.1 1.0 C5 B:G21 4.9 63.3 1.0 C5 B:G29 4.9 60.8 1.0

Potassium binding site 6 out of 8 in the Crystal Structure of the Mango-II 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 Fluorescent Aptamer Bound to TO1- Biotin within 5.0Å range: probe atom residue distance (Å) B Occ C:K102 b:67.3 occ:1.00 O6 C:G15 2.6 64.2 1.0 O6 C:G26 2.7 60.8 1.0 O6 C:G27 2.7 72.8 1.0 O6 C:G11 2.8 69.7 1.0 O6 C:G21 2.8 63.5 1.0 O6 C:G16 2.8 61.4 1.0 O6 C:G10 2.8 70.5 1.0 O6 C:G20 2.9 62.1 1.0 K C:K103 3.3 71.6 1.0 C6 C:G15 3.5 62.5 1.0 C6 C:G27 3.5 70.2 1.0 C6 C:G26 3.5 61.2 1.0 C6 C:G21 3.6 67.7 1.0 K C:K104 3.6 82.4 1.0 C6 C:G10 3.6 72.1 1.0 C6 C:G11 3.6 70.5 1.0 C6 C:G16 3.6 60.0 1.0 C6 C:G20 3.6 62.6 1.0 N1 C:G26 3.8 62.6 1.0 N1 C:G15 3.8 60.6 1.0 N1 C:G16 3.8 61.6 1.0 N1 C:G21 3.8 69.7 1.0 N1 C:G10 3.9 69.4 1.0 N1 C:G27 3.9 70.7 1.0 N1 C:G11 3.9 69.5 1.0 N1 C:G20 3.9 63.2 1.0 C5 C:G27 4.7 66.3 1.0 C5 C:G15 4.7 62.1 1.0 C5 C:G10 4.7 72.9 1.0 C5 C:G21 4.8 67.7 1.0 C5 C:G20 4.8 59.8 1.0 C5 C:G11 4.8 71.2 1.0 C5 C:G26 4.8 63.3 1.0 C5 C:G16 4.9 57.4 1.0

Potassium binding site 7 out of 8 in the Crystal Structure of the Mango-II 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 Fluorescent Aptamer Bound to TO1- Biotin within 5.0Å range: probe atom residue distance (Å) B Occ C:K103 b:71.6 occ:1.00 O6 B:G10 2.6 58.2 1.0 O6 C:G20 2.6 62.1 1.0 O6 C:G26 2.6 60.8 1.0 O6 B:G20 2.7 60.2 1.0 O6 C:G10 2.7 70.5 1.0 O6 C:G15 2.7 64.2 1.0 O6 B:G15 2.7 72.2 1.0 O6 B:G26 2.9 61.7 1.0 K C:K102 3.3 67.3 1.0 C6 C:G26 3.4 61.2 1.0 C6 C:G20 3.4 62.6 1.0 K B:K102 3.4 59.8 1.0 C6 B:G10 3.5 62.1 1.0 N1 C:G20 3.5 63.2 1.0 C6 B:G15 3.6 67.2 1.0 C6 C:G15 3.6 62.5 1.0 C6 B:G20 3.6 61.2 1.0 C6 B:G26 3.6 59.1 1.0 N1 B:G10 3.7 59.4 1.0 N1 C:G26 3.7 62.6 1.0 N1 B:G26 3.8 54.1 1.0 C6 C:G10 3.8 72.1 1.0 N1 B:G20 3.8 60.4 1.0 N1 C:G15 3.8 60.6 1.0 N1 B:G15 3.9 62.9 1.0 N1 C:G10 4.2 69.4 1.0 C5 C:G26 4.5 63.3 1.0 C5 C:G20 4.7 59.8 1.0 C5 B:G15 4.7 67.8 1.0 C2 C:G20 4.8 63.5 1.0 C5 B:G26 4.8 57.4 1.0 C5 B:G10 4.8 63.6 1.0 C5 C:G15 4.8 62.1 1.0 C5 B:G20 4.9 62.6 1.0 C2 B:G26 5.0 54.6 1.0 C2 C:G26 5.0 62.5 1.0

Potassium binding site 8 out of 8 in the Crystal Structure of the Mango-II 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 Fluorescent Aptamer Bound to TO1- Biotin within 5.0Å range: probe atom residue distance (Å) B Occ C:K104 b:82.4 occ:1.00 O6 C:G11 2.6 69.7 1.0 O6 C:G13 2.7 70.8 1.0 O6 C:G27 2.7 72.8 1.0 O6 C:G24 2.7 76.0 1.0 O6 C:G18 2.8 78.3 1.0 O6 C:G29 2.8 73.2 1.0 O6 C:G21 2.9 63.5 1.0 O6 C:G16 3.0 61.4 1.0 C6 C:G11 3.4 70.5 1.0 C6 C:G13 3.5 76.8 1.0 K C:K102 3.6 67.3 1.0 C6 C:G27 3.6 70.2 1.0 C6 C:G29 3.6 73.4 1.0 C6 C:G18 3.6 73.1 1.0 N1 C:G11 3.7 69.5 1.0 C6 C:G24 3.7 77.6 1.0 C6 C:G16 3.7 60.0 1.0 C6 C:G21 3.8 67.7 1.0 N1 C:G13 3.8 77.5 1.0 N1 C:G27 3.8 70.7 1.0 N1 C:G18 3.9 61.7 1.0 N1 C:G29 3.9 72.2 1.0 N1 C:G16 4.0 61.6 1.0 N1 C:G24 4.0 76.1 1.0 N1 C:G21 4.1 69.7 1.0 H081 C:EKJ101 4.1 0.3 1.0 C5 C:G11 4.6 71.2 1.0 C5 C:G13 4.7 79.2 1.0 C5 C:G29 4.8 75.9 1.0 C5 C:G27 4.8 66.3 1.0 H051 C:EKJ101 4.8 0.7 1.0 C5 C:G18 4.9 68.0 1.0 C2 C:G11 4.9 74.3 1.0 C5 C:G16 4.9 57.4 1.0 C5 C:G24 4.9 80.6 1.0 C5 C:G21 5.0 67.7 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