Potassium in PDB 6v9b: Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin

The structure of Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin, PDB code: 6v9b 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)	42.39 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	48.953, 48.953, 123.349, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 24.4

The binding sites of Potassium atom in the Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin (pdb code 6v9b). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin, PDB code: 6v9b:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer 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 Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:46.1 occ:1.00 O6 B:G21 2.6 53.5 1.0 O6 B:G26 2.7 52.0 1.0 O6 B:G13 2.8 56.9 1.0 O6 B:G15 2.8 41.9 1.0 O6 B:G10 2.9 51.9 1.0 O6 B:G24 2.9 52.7 1.0 O6 B:G8 2.9 50.5 1.0 O6 B:G18 2.9 41.8 1.0 C6 B:G13 3.5 54.5 1.0 C6 B:G21 3.5 56.9 1.0 K B:K104 3.7 49.0 1.0 C6 B:G15 3.7 52.2 1.0 C6 B:G26 3.7 54.9 1.0 C6 B:G24 3.7 45.8 1.0 C6 B:G8 3.7 59.6 1.0 C6 B:G10 3.7 62.8 1.0 N1 B:G13 3.7 51.6 1.0 C6 B:G18 3.8 42.3 1.0 N1 B:G15 3.9 46.7 1.0 N1 B:G8 3.9 53.3 1.0 N1 B:G21 3.9 48.1 1.0 N1 B:G24 4.0 55.7 1.0 N1 B:G26 4.0 46.6 1.0 N1 B:G18 4.0 46.3 1.0 N1 B:G10 4.1 64.8 1.0 C05 B:QSA102 4.4 68.3 1.0 C5 B:G21 4.8 46.3 1.0 C5 B:G13 4.8 51.9 1.0 C5 B:G10 4.9 63.7 1.0 C5 B:G24 4.9 47.5 1.0 C5 B:G26 4.9 63.3 1.0 C5 B:G15 4.9 56.3 1.0 C2 B:G13 5.0 59.0 1.0 C5 B:G8 5.0 69.2 1.0

Potassium binding site 2 out of 4 in the Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer 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 Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:K104 b:49.0 occ:1.00 O6 B:G12 2.6 51.4 1.0 O6 B:G7 2.6 56.2 1.0 O6 B:G23 2.7 43.6 1.0 O6 B:G13 2.8 56.9 1.0 O6 B:G24 2.9 52.7 1.0 O6 B:G17 2.9 39.9 1.0 O6 B:G8 3.0 50.5 1.0 O6 B:G18 3.3 41.8 1.0 C6 B:G23 3.5 47.1 1.0 C6 B:G12 3.5 61.0 1.0 C6 B:G7 3.6 55.5 1.0 K B:K103 3.7 46.1 1.0 C6 B:G13 3.7 54.5 1.0 N1 B:G23 3.7 50.1 1.0 C6 B:G24 3.7 45.8 1.0 C6 B:G8 3.8 59.6 1.0 C6 B:G17 3.8 48.9 1.0 N1 B:G12 3.8 56.1 1.0 N1 B:G7 3.8 57.7 1.0 N1 B:G24 3.9 55.7 1.0 N1 B:G17 3.9 47.5 1.0 N1 B:G13 4.0 51.6 1.0 C6 B:G18 4.0 42.3 1.0 N1 B:G8 4.0 53.3 1.0 N1 B:G18 4.2 46.3 1.0 C2 D:A1 4.8 58.1 1.0 C5 B:G23 4.8 45.7 1.0 C5 B:G12 4.9 54.8 1.0 C5 B:G13 4.9 51.9 1.0 C5 B:G7 4.9 57.9 1.0 C5 B:G8 4.9 69.2 1.0 C5 B:G24 5.0 47.5 1.0

Potassium binding site 3 out of 4 in the Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer 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 Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ D:K102 b:48.6 occ:1.00 O6 D:G12 2.6 53.5 1.0 O6 D:G7 2.7 65.1 1.0 O6 D:G17 2.7 51.2 1.0 O6 D:G23 2.8 43.4 1.0 O6 D:G24 2.8 53.2 1.0 O6 D:G13 2.9 49.7 1.0 O6 D:G18 2.9 43.9 1.0 O6 D:G8 2.9 52.7 1.0 K D:K103 3.5 51.7 1.0 C6 D:G23 3.5 44.6 1.0 C6 D:G7 3.6 54.0 1.0 C6 D:G12 3.6 63.3 1.0 C6 D:G24 3.6 49.0 1.0 N1 D:G23 3.7 53.3 1.0 C6 D:G18 3.7 43.2 1.0 C6 D:G17 3.7 46.2 1.0 C6 D:G13 3.7 51.1 1.0 N1 D:G7 3.7 51.7 1.0 C6 D:G8 3.8 50.7 1.0 N1 D:G24 3.9 54.5 1.0 N1 D:G12 3.9 57.3 1.0 N1 D:G18 3.9 49.9 1.0 N1 D:G17 3.9 36.4 1.0 N1 D:G13 3.9 57.2 1.0 N1 D:G8 4.1 62.0 1.0 C2 B:A1 4.8 42.1 1.0 C5 D:G23 4.8 45.5 1.0 C5 D:G24 4.9 50.5 1.0 C5 D:G18 4.9 40.2 1.0 C5 D:G7 4.9 59.4 1.0 C5 D:G12 4.9 54.5 1.0 C2 D:G23 4.9 57.0 1.0 C5 D:G13 5.0 56.2 1.0 C5 D:G8 5.0 58.4 1.0

Potassium binding site 4 out of 4 in the Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer 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 Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ D:K103 b:51.7 occ:1.00 O6 D:G21 2.7 55.2 1.0 O6 D:G13 2.8 49.7 1.0 O6 D:G26 2.8 62.6 1.0 O6 D:G8 2.8 52.7 1.0 O6 D:G15 2.9 46.7 1.0 O6 D:G24 2.9 53.2 1.0 O6 D:G10 2.9 56.5 1.0 O6 D:G18 3.0 43.9 1.0 K D:K102 3.5 48.6 1.0 C6 D:G13 3.5 51.1 1.0 C6 D:G21 3.6 48.1 1.0 C6 D:G15 3.6 49.9 1.0 C6 D:G24 3.7 49.0 1.0 C6 D:G8 3.7 50.7 1.0 C6 D:G10 3.7 60.2 1.0 C6 D:G26 3.8 56.5 1.0 C6 D:G18 3.8 43.2 1.0 N1 D:G15 3.8 50.6 1.0 N1 D:G13 3.8 57.2 1.0 N1 D:G21 3.8 44.5 1.0 O04 D:QSA101 3.9 67.4 0.5 N1 D:G8 3.9 62.0 1.0 N1 D:G24 3.9 54.5 1.0 N1 D:G18 4.0 49.9 1.0 N1 D:G26 4.0 52.1 1.0 N1 D:G10 4.1 59.0 1.0 C5 D:G13 4.7 56.2 1.0 C5 D:G21 4.8 41.2 1.0 C5 D:G24 4.9 50.5 1.0 C5 D:G10 4.9 63.3 1.0 C5 D:G15 4.9 47.0 1.0 C5 D:G8 5.0 58.4 1.0 C5 D:G18 5.0 40.2 1.0

R.J.Trachman 3Rd, R.Cojocaru, D.Wu, G.Piszczek, M.Ryckelynck, P.J.Unrau, A.R.Ferre-D'amare. Structure-Guided Engineering of the Homodimeric Mango-IV Fluorescence Turn-on Aptamer Yields An Rna Fret Pair. Structure 2020.
ISSN: ISSN 0969-2126
PubMed: 32386573
DOI: 10.1016/J.STR.2020.04.007