Magnesium 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
Potassium	(K)	4 atoms
Iodine	(I)	2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg103 b:75.7 occ:1.00 O E:HOH228 1.9 50.3 1.0 O E:HOH216 2.0 54.4 1.0 O E:HOH211 2.2 48.4 1.0 O E:HOH210 2.2 58.5 1.0 O E:HOH235 2.3 52.4 1.0 O E:HOH227 2.3 50.1 1.0 OP2 E:G9 4.0 49.5 1.0 N7 E:G9 4.2 42.2 1.0 O2' E:G13 4.2 42.9 1.0 N7 E:A10 4.3 35.0 1.0 OP2 E:G13 4.4 42.9 1.0 C8 E:G9 4.4 41.9 1.0 C4 E:G8 4.4 42.0 1.0 C2' E:G13 4.4 44.0 1.0 N3 E:G8 4.6 42.1 1.0 C5 E:G8 4.6 44.7 1.0 C2' E:G8 4.6 45.7 1.0 O5' E:G13 4.7 50.4 1.0 C2 E:G8 4.8 44.5 1.0 N9 E:G8 4.8 44.2 1.0 C3' E:G13 4.8 49.6 1.0 C6 E:G8 4.9 40.8 1.0 N6 E:A10 4.9 41.9 1.0 N1 E:G8 4.9 42.1 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg104 b:66.5 occ:1.00 O E:HOH214 2.2 54.5 1.0 O E:HOH212 2.3 58.8 1.0 O6 E:G8 2.5 42.5 1.0 O E:HOH204 2.8 56.3 1.0 N7 E:A7 3.5 41.3 1.0 C6 E:G8 3.6 40.8 1.0 OP2 E:G6 3.8 53.9 1.0 N7 E:G8 4.1 41.2 1.0 OP2 E:A7 4.1 50.3 1.0 C5 E:G8 4.2 44.7 1.0 N6 E:A7 4.2 40.7 1.0 OP2 E:A14 4.3 53.4 1.0 C8 E:A7 4.4 39.3 1.0 C5 E:A7 4.5 40.2 1.0 O5' E:G6 4.7 56.2 1.0 N1 E:G8 4.7 42.1 1.0 P E:G6 4.7 64.0 1.0 C6 E:A7 4.8 41.9 1.0 C8 E:G6 4.9 49.7 1.0 N7 E:G6 5.0 45.3 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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 E:Mg105 b:62.4 occ:1.00 O E:HOH225 1.8 48.3 1.0 O E:HOH237 2.1 54.5 1.0 O E:HOH234 2.4 59.5 1.0 O2' E:C35 4.1 51.5 1.0 C5' E:C36 4.8 51.2 1.0 O3' E:C35 4.8 55.9 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg103 b:52.1 occ:1.00 OP2 Y:A24 2.0 49.8 1.0 O Y:HOH210 2.2 45.1 1.0 OP2 Y:G25 2.3 46.0 1.0 O Y:HOH206 2.4 52.4 1.0 O3' Y:G23 2.9 43.8 1.0 P Y:A24 3.0 49.8 1.0 P Y:G25 3.6 44.9 1.0 O5' Y:A24 3.7 46.3 1.0 O Y:HOH214 4.0 41.7 1.0 O2' Y:G23 4.0 51.6 1.0 O3' Y:A24 4.2 43.1 1.0 C5' Y:A24 4.2 43.0 1.0 OP1 Y:A24 4.2 50.9 1.0 C3' Y:G23 4.3 43.3 1.0 O Y:HOH204 4.3 37.1 1.0 OP1 Y:G25 4.3 46.2 1.0 C3' Y:A24 4.4 44.8 1.0 C2' Y:G23 4.6 45.9 1.0 O5' Y:G25 4.8 45.2 1.0 C1' Y:G23 4.8 44.3 1.0 C4' Y:A24 4.9 44.1 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