Potassium in PDB 5bjo: Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U

The structure of Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U, PDB code: 5bjo was solved by K.D.Warner, W.Song, G.S.Filonov, S.R.Jaffrey, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.50 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.269, 55.305, 99.002, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22.8

The structure of Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Magnesium	(Mg)	4 atoms
Iodine	(I)	2 atoms

The binding sites of Potassium atom in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U (pdb code 5bjo). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U, PDB code: 5bjo:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U


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 Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U within 5.0Å range: probe atom residue distance (Å) B Occ E:K101 b:38.4 occ:1.00 O6 E:G16 2.7 38.7 1.0 O E:HOH213 2.8 35.7 1.0 O E:HOH219 2.8 42.0 1.0 O6 E:G26 2.9 35.5 1.0 O2 E:IU17 2.9 43.5 1.0 O6 E:G23 2.9 39.6 1.0 O6 E:G13 2.9 39.8 1.0 K E:K102 3.5 38.0 1.0 C6 E:G16 3.7 37.9 1.0 C2 E:IU17 3.7 43.5 1.0 C6 E:G13 3.7 40.8 1.0 O E:HOH224 3.8 39.4 1.0 N3 E:IU17 3.8 42.1 1.0 C6 E:G26 3.8 36.2 1.0 C6 E:G23 3.9 37.9 1.0 N1 E:G13 3.9 39.8 1.0 N1 E:G16 4.1 36.0 1.0 N1 E:G23 4.1 39.0 1.0 N1 E:G26 4.2 37.4 1.0 C2 E:A21 4.2 41.3 1.0 N1 E:A21 4.2 37.1 1.0 C2 E:A10 4.3 37.2 1.0 N1 E:A10 4.5 37.6 1.0 N3 E:U27 4.7 33.5 1.0 O2 E:U27 4.8 44.3 1.0 C5 E:G16 4.9 37.8 1.0 N1 E:IU17 5.0 40.0 1.0 C5 E:G13 5.0 36.0 1.0

Potassium binding site 2 out of 4 in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U


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 Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U within 5.0Å range: probe atom residue distance (Å) B Occ E:K102 b:38.0 occ:1.00 O6 E:G22 2.7 37.5 1.0 O6 E:G25 2.7 32.8 1.0 O6 E:G15 2.7 38.1 1.0 O6 E:G13 2.8 39.8 1.0 O6 E:G12 2.9 30.6 1.0 O6 E:G23 2.9 39.6 1.0 O6 E:G16 2.9 38.7 1.0 O6 E:G26 2.9 35.5 1.0 K E:K101 3.5 38.4 1.0 C6 E:G23 3.6 37.9 1.0 C6 E:G12 3.7 32.4 1.0 C6 E:G25 3.7 31.3 1.0 C6 E:G16 3.7 37.9 1.0 C6 E:G13 3.7 40.8 1.0 C6 E:G22 3.7 36.6 1.0 C6 E:G15 3.8 34.2 1.0 C6 E:G26 3.8 36.2 1.0 N6 Y:A11 3.9 45.6 1.0 N1 E:G12 3.9 33.5 1.0 N1 E:G25 3.9 31.0 1.0 N1 E:G23 3.9 39.0 1.0 N1 E:G16 4.0 36.0 1.0 N1 E:G13 4.0 39.8 1.0 N1 E:G22 4.0 37.6 1.0 N1 E:G26 4.1 37.4 1.0 N1 E:G15 4.1 37.7 1.0 C6 Y:A11 4.5 44.6 1.0 C5 E:G23 4.8 36.1 1.0 C5 E:G16 4.8 37.8 1.0 C5 E:G12 4.8 33.6 1.0 N1 Y:A11 4.9 35.6 1.0 C5 E:G13 4.9 36.0 1.0 C5 E:G26 5.0 35.6 1.0 C5 E:G25 5.0 35.6 1.0

Potassium binding site 3 out of 4 in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U


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 Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U within 5.0Å range: probe atom residue distance (Å) B Occ Y:K101 b:41.4 occ:1.00 O6 Y:G12 2.6 39.0 1.0 O6 Y:G22 2.7 47.9 1.0 O6 Y:G15 2.7 40.1 1.0 O6 Y:G25 2.7 35.2 1.0 O6 Y:G23 2.9 44.4 1.0 O6 Y:G13 3.0 42.9 1.0 O6 Y:G16 3.1 37.7 1.0 O6 Y:G26 3.1 31.5 1.0 C6 Y:G12 3.5 37.1 1.0 K Y:K102 3.6 44.2 1.0 C6 Y:G23 3.7 41.6 1.0 C6 Y:G25 3.7 36.6 1.0 C6 Y:G16 3.7 38.8 1.0 C6 Y:G22 3.7 38.8 1.0 C6 Y:G15 3.7 38.1 1.0 C6 Y:G13 3.8 42.6 1.0 N1 Y:G16 3.8 40.7 1.0 N1 Y:G12 3.9 34.3 1.0 N1 Y:G25 3.9 39.8 1.0 N1 Y:G22 3.9 39.5 1.0 C6 Y:G26 3.9 35.6 1.0 N1 Y:G23 4.0 42.3 1.0 N1 Y:G13 4.0 41.0 1.0 N1 Y:G15 4.1 38.8 1.0 N1 Y:G26 4.2 37.8 1.0 N15 Y:747104 4.6 37.8 1.0 C16 Y:747104 4.6 41.4 1.0 C5 Y:G23 4.7 39.2 1.0 C5 Y:G12 4.8 34.0 1.0 C5 Y:G16 4.8 40.4 1.0 C10 Y:747104 4.8 36.4 1.0 C12 Y:747104 4.9 34.7 1.0 C5 Y:G25 5.0 35.7 1.0 C2 Y:G16 5.0 42.3 1.0

Potassium binding site 4 out of 4 in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U


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 Corn Rna Aptamer in Complex with Dfho, Site- Specific 5-Iodo-U within 5.0Å range: probe atom residue distance (Å) B Occ Y:K102 b:44.2 occ:1.00 O6 Y:G23 2.7 44.4 1.0 O6 Y:G16 2.8 37.7 1.0 O Y:HOH207 2.9 33.6 1.0 O Y:HOH211 2.9 42.3 1.0 O6 Y:G26 2.9 31.5 1.0 O6 Y:G13 3.0 42.9 1.0 O2 Y:IU17 3.2 54.7 1.0 K Y:K101 3.6 41.4 1.0 C6 Y:G23 3.7 41.6 1.0 C6 Y:G16 3.7 38.8 1.0 O Y:HOH213 3.7 48.9 1.0 C6 Y:G13 3.9 42.6 1.0 C2 Y:IU17 3.9 51.1 1.0 N3 Y:IU17 3.9 53.3 1.0 C6 Y:G26 3.9 35.6 1.0 N1 Y:G23 3.9 42.3 1.0 N1 Y:G13 4.0 41.0 1.0 N1 Y:G16 4.0 40.7 1.0 C2 Y:A21 4.0 38.8 1.0 N1 Y:A21 4.3 41.7 1.0 N1 Y:G26 4.3 37.8 1.0 C2 Y:A10 4.4 43.0 1.0 O2 Y:U27 4.6 47.9 1.0 N3 Y:U27 4.6 45.9 1.0 N1 Y:A10 4.7 40.0 1.0 N3 Y:A21 4.9 41.9 1.0 C2 Y:U27 5.0 51.4 1.0 C5 Y:G23 5.0 39.2 1.0 C5 Y:G16 5.0 40.4 1.0

K.D.Warner, L.Sjekloca, W.Song, G.S.Filonov, S.R.Jaffrey, A.R.Ferre-D'amare. A Homodimer Interface Without Base Pairs in An Rna Mimic of Red Fluorescent Protein. Nat. Chem. Biol. V. 13 1195 2017.
ISSN: ESSN 1552-4469
PubMed: 28945234
DOI: 10.1038/NCHEMBIO.2475