Potassium in PDB 6v9d: 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: 6v9d 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)	42.36 / 2.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	48.917, 48.917, 122.972, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 27.2

The structure of Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Potassium atom in the Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin (pdb code 6v9d). 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: 6v9d:
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:K104 b:30.2 occ:1.00 O6 B:G15 2.6 32.4 1.0 O6 B:G26 2.6 35.7 1.0 O6 B:G13 2.7 34.7 1.0 O6 B:G18 2.7 28.6 1.0 O6 B:G21 2.8 35.2 1.0 O6 B:G10 2.8 48.5 1.0 O6 B:G24 2.8 30.7 1.0 O6 B:G8 2.9 41.5 1.0 C6 B:G13 3.4 35.2 1.0 C6 B:G15 3.5 35.3 1.0 K B:K105 3.6 30.5 1.0 C6 B:G26 3.6 41.0 1.0 C6 B:G21 3.6 34.1 1.0 C6 B:G18 3.7 28.4 1.0 C6 B:G10 3.7 46.0 1.0 C6 B:G24 3.7 32.5 1.0 N1 B:G13 3.8 32.8 1.0 C6 B:G8 3.8 41.8 1.0 N1 B:G15 3.8 35.9 1.0 N1 B:G21 3.9 31.6 1.0 N1 B:G26 4.0 37.3 1.0 N1 B:G8 4.0 41.9 1.0 N1 B:G18 4.1 28.2 1.0 N1 B:G24 4.1 36.1 1.0 N1 B:G10 4.3 46.1 1.0 C5 B:G13 4.6 37.7 1.0 C04 B:QW4102 4.7 46.7 1.0 C5 B:G10 4.8 47.3 1.0 C5 B:G15 4.8 35.4 1.0 C5 B:G18 4.9 31.4 1.0 C5 B:G26 4.9 46.8 1.0 C5 B:G21 4.9 36.1 1.0 C5 B:G24 4.9 34.7 1.0 C2 B:G13 5.0 35.1 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:K105 b:30.5 occ:1.00 O6 B:G7 2.5 36.8 1.0 O6 B:G24 2.6 30.7 1.0 O6 B:G23 2.7 30.4 1.0 O6 B:G12 2.7 39.3 1.0 O6 B:G13 2.8 34.7 1.0 O6 B:G8 2.8 41.5 1.0 O6 B:G17 2.9 33.7 1.0 O6 B:G18 3.0 28.6 1.0 C6 B:G23 3.4 31.4 1.0 C6 B:G7 3.4 37.9 1.0 N1 B:G23 3.5 33.7 1.0 C6 B:G24 3.5 32.5 1.0 K B:K104 3.6 30.2 1.0 C6 B:G8 3.6 41.8 1.0 C6 B:G12 3.7 43.6 1.0 N1 B:G7 3.7 40.6 1.0 C6 B:G13 3.7 35.2 1.0 C6 B:G17 3.8 32.7 1.0 N1 B:G24 3.8 36.1 1.0 N1 B:G12 3.9 41.6 1.0 C6 B:G18 3.9 28.4 1.0 N1 B:G17 3.9 32.6 1.0 N1 B:G8 4.0 41.9 1.0 N1 B:G13 4.1 32.8 1.0 N1 B:G18 4.2 28.2 1.0 C5 B:G24 4.7 34.7 1.0 C5 B:G23 4.7 32.2 1.0 C2 B:G23 4.7 35.5 1.0 C5 B:G8 4.8 43.9 1.0 C5 B:G7 4.8 40.6 1.0 C5 B:G13 4.9 37.7 1.0 C2 E:A1 5.0 33.4 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 E:K103 b:33.7 occ:1.00 O6 E:G7 2.5 44.8 1.0 O6 E:G23 2.6 37.3 1.0 O6 E:G12 2.6 42.9 1.0 O6 E:G24 2.9 39.1 1.0 O6 E:G18 2.9 31.8 1.0 O6 E:G13 3.0 34.6 1.0 O6 E:G17 3.0 31.4 1.0 O6 E:G8 3.1 37.0 1.0 C6 E:G7 3.4 44.6 1.0 C6 E:G23 3.4 35.2 1.0 N1 E:G23 3.5 40.2 1.0 N1 E:G7 3.5 44.0 1.0 C6 E:G24 3.6 41.0 1.0 C6 E:G12 3.6 42.1 1.0 K E:K104 3.7 36.5 1.0 C6 E:G18 3.7 34.3 1.0 N1 E:G24 3.8 42.8 1.0 C6 E:G8 3.9 39.7 1.0 C6 E:G17 3.9 30.5 1.0 C6 E:G13 3.9 36.5 1.0 N1 E:G12 4.0 38.5 1.0 N1 E:G18 4.0 32.6 1.0 N1 E:G17 4.0 29.0 1.0 N1 E:G8 4.2 44.0 1.0 N1 E:G13 4.3 38.7 1.0 C2 B:A1 4.6 29.0 1.0 C5 E:G23 4.7 30.5 1.0 C5 E:G7 4.7 42.0 1.0 C2 E:G23 4.8 35.8 1.0 C5 E:G24 4.8 41.1 1.0 C2 E:G7 4.9 46.7 1.0 C5 E:G12 4.9 42.2 1.0 C5 E:G8 4.9 43.3 1.0 C5 E:G18 4.9 33.8 1.0 N3 B:A1 5.0 29.7 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 E:K104 b:36.5 occ:1.00 O6 E:G13 2.7 34.6 1.0 O6 E:G26 2.7 41.5 1.0 O6 E:G21 2.8 41.9 1.0 O6 E:G8 2.8 37.0 1.0 O6 E:G15 2.8 35.8 1.0 O6 E:G10 2.8 46.8 1.0 O6 E:G18 2.8 31.8 1.0 O6 E:G24 2.9 39.1 1.0 C6 E:G13 3.5 36.5 1.0 C6 E:G10 3.6 47.1 1.0 C6 E:G21 3.6 37.6 1.0 C6 E:G8 3.6 39.7 1.0 C6 E:G26 3.6 46.3 1.0 C6 E:G15 3.6 40.6 1.0 C6 E:G24 3.7 41.0 1.0 K E:K103 3.7 33.7 1.0 C6 E:G18 3.7 34.3 1.0 N1 E:G8 3.8 44.0 1.0 N1 E:G13 3.9 38.7 1.0 N1 E:G21 3.9 35.0 1.0 N1 E:G15 3.9 38.0 1.0 N1 E:G10 3.9 47.5 1.0 N1 E:G24 3.9 42.8 1.0 N1 E:G26 4.0 46.9 1.0 N1 E:G18 4.1 32.6 1.0 C5 E:G13 4.6 37.9 1.0 C5 E:G10 4.7 45.8 1.0 C5 E:G21 4.8 39.1 1.0 C5 E:G26 4.9 50.2 1.0 C5 E:G18 4.9 33.8 1.0 C5 E:G24 4.9 41.1 1.0 C5 E:G15 4.9 39.7 1.0 C5 E:G8 4.9 43.3 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