Magnesium in PDB 5bjp: Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak

The structure of Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak, PDB code: 5bjp 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)	49.34 / 2.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.642, 55.438, 98.676, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23.9

The structure of Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Potassium	(K)	4 atoms
Iridium	(Ir)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak (pdb code 5bjp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak, PDB code: 5bjp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak


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, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg104 b:72.8 occ:1.00 O E:HOH207 2.0 45.2 1.0 C5 E:G8 4.1 33.6 1.0 C4 E:G8 4.1 35.6 1.0 OP2 E:G9 4.1 34.9 1.0 O2' E:G13 4.2 39.4 1.0 C6 E:G8 4.3 35.0 1.0 N3 E:G8 4.4 36.1 1.0 C2' E:G13 4.5 36.0 1.0 N1 E:G8 4.5 34.7 1.0 N7 E:G8 4.5 32.0 1.0 N9 E:G8 4.5 34.5 1.0 C2 E:G8 4.5 35.3 1.0 N7 E:G9 4.5 31.8 1.0 C8 E:G8 4.7 35.2 1.0 C3' E:G13 4.7 37.5 1.0 C2' E:G8 4.8 36.9 1.0 O5' E:G13 4.8 38.5 1.0 C8 E:G9 4.8 30.4 1.0 O6 E:G8 4.9 40.0 1.0 N7 E:A10 4.9 30.8 1.0 OP2 E:G13 5.0 33.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Corn Rna Aptamer in Complex with Dfho, Iridium Hexammine Soak


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, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg105 b:66.4 occ:1.00 O6 E:G8 2.6 40.0 1.0 C6 E:G8 3.6 35.0 1.0 N7 E:A7 3.7 35.1 1.0 OP2 E:G6 3.9 50.2 1.0 OP2 E:A7 4.3 42.0 1.0 N7 E:G8 4.3 32.0 1.0 C5 E:G8 4.3 33.6 1.0 OP2 E:A14 4.3 41.7 1.0 N6 E:A7 4.4 37.0 1.0 C8 E:A7 4.6 36.7 1.0 C5 E:A7 4.7 34.9 1.0 N1 E:G8 4.7 34.7 1.0 P E:G6 4.8 56.2 1.0 O5' E:G6 4.9 47.0 1.0 C6 E:A7 5.0 37.2 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