Iodine 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
Potassium	(K)	4 atoms

The binding sites of Iodine 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 Iodine atom.
In total 2 binding sites of Iodine 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 Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 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 Iodine with other atoms in the I 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:I17 b:42.1 occ:0.50 I5 E:IU17 0.0 42.1 0.5 C5 E:IU17 2.1 38.4 1.0 C4 E:IU17 3.0 37.5 1.0 C6 E:IU17 3.0 38.2 1.0 O4 E:IU17 3.1 36.9 1.0 OP2 E:G16 3.5 72.2 1.0 OP2 E:IU17 3.5 60.9 1.0 O5' E:G16 3.9 63.6 1.0 O E:HOH233 4.1 41.4 1.0 C8 E:G16 4.1 47.1 1.0 N3 E:IU17 4.2 42.1 1.0 N1 E:IU17 4.2 40.0 1.0 N7 E:G16 4.3 37.2 1.0 P E:G16 4.4 62.3 1.0 N2 E:G13 4.5 37.5 1.0 O5' E:IU17 4.5 55.3 1.0 C3' E:G16 4.6 52.7 1.0 P E:IU17 4.6 52.4 1.0 C2 E:IU17 4.7 43.5 1.0 N9 E:G16 5.0 46.5 1.0

Iodine binding site 2 out of 2 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 Iodine with other atoms in the I 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 Y:I17 b:57.7 occ:0.50 I5 Y:IU17 0.0 57.7 0.5 C5 Y:IU17 2.1 57.6 1.0 C4 Y:IU17 3.1 53.8 1.0 C6 Y:IU17 3.1 55.1 1.0 O Y:HOH208 3.2 46.0 1.0 O4 Y:IU17 3.2 52.8 1.0 OP2 Y:G16 3.3 61.6 1.0 O5' Y:G16 3.6 68.7 1.0 OP2 Y:IU17 3.6 59.5 1.0 O Y:HOH215 3.6 51.0 1.0 C8 Y:G16 3.9 50.4 1.0 P Y:G16 4.0 69.7 1.0 N7 Y:G16 4.0 47.3 1.0 N3 Y:IU17 4.3 53.3 1.0 N1 Y:IU17 4.4 50.0 1.0 C3' Y:G16 4.4 61.3 1.0 N2 Y:G13 4.5 49.6 1.0 C5' Y:G16 4.7 64.1 1.0 C2 Y:IU17 4.8 51.1 1.0 N9 Y:G16 4.9 46.5 1.0 C5' Y:IU17 4.9 62.3 1.0 P Y:IU17 4.9 68.1 1.0 OP1 Y:G16 4.9 76.5 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