Magnesium in PDB 7kvt: Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions

The structure of Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions, PDB code: 7kvt was solved by L.Truong, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.47 / 2.73
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.9, 103.9, 51.699, 90, 90, 90
R / Rfree (%)	20.9 / 25.1

The structure of Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions also contains other interesting chemical elements:

Fluorine	(F)	5 atoms
Iridium	(Ir)	3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions (pdb code 7kvt). 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 Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions, PDB code: 7kvt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions


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 Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:74.0 occ:1.00 OP2 B:A45 1.9 63.4 1.0 O6 B:G46 2.1 69.2 1.0 OP2 B:G42 2.3 70.8 1.0 C6 B:G46 3.3 63.2 1.0 OP2 B:U44 3.3 82.3 1.0 P B:A45 3.3 78.8 1.0 P B:G42 3.4 79.8 1.0 O5' B:G42 3.6 56.6 1.0 N7 B:A45 3.7 64.2 1.0 OP1 B:U44 3.7 69.4 1.0 C8 B:A45 3.7 63.1 1.0 P B:U44 3.8 82.4 1.0 O5' B:A45 4.0 70.0 1.0 C3' B:U44 4.1 68.3 1.0 C8 B:G42 4.1 65.3 1.0 O3' B:U44 4.1 69.3 1.0 N1 B:G46 4.2 54.9 1.0 O5' B:U44 4.2 65.3 1.0 C5 B:G46 4.2 61.6 1.0 OP1 B:G42 4.3 85.3 1.0 OP1 B:A45 4.5 70.7 1.0 N7 B:G46 4.5 61.6 1.0 C5' B:U44 4.6 67.1 1.0 C2' B:G42 4.6 71.8 1.0 O3' B:G41 4.7 74.5 1.0 N7 B:G42 4.8 63.0 1.0 C4' B:U44 4.9 72.1 1.0 C2' B:G41 5.0 69.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions


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 Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg106 b:29.0 occ:1.00 O B:HOH201 1.8 44.2 1.0 O B:HOH203 1.8 73.2 1.0 O B:HOH204 1.8 59.6 1.0 O B:HOH206 1.8 63.2 1.0 O B:HOH205 1.8 60.7 1.0 O B:HOH202 1.8 76.8 1.0 OP2 B:C67 4.0 59.4 1.0 N7 B:G16 4.6 53.9 1.0 OP2 B:G16 4.6 62.0 1.0 C8 B:G16 4.8 59.1 1.0

L.Truong, H.Kooshapur, S.K.Dey, X.Li, N.Tjandra, S.R.Jaffrey, A.R.Ferre-D'amare. The Fluorescent Aptamer Squash Extensively Repurposes the Adenine Riboswitch Fold. Nat.Chem.Biol. V. 18 191 2022.
ISSN: ESSN 1552-4469
PubMed: 34937911
DOI: 10.1038/S41589-021-00931-2