Magnesium in PDB 7kvu: Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T

The structure of Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T, PDB code: 7kvu 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)	46.46 / 2.68
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.731, 103.731, 51.959, 90, 90, 90
R / Rfree (%)	20.9 / 24.7

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

Potassium	(K)	3 atoms
Fluorine	(F)	5 atoms

The binding sites of Magnesium atom in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T (pdb code 7kvu). 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 Squash Rna Aptamer in Complex with Dfhbi-1T, PDB code: 7kvu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T


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 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg101 b:67.4 occ:1.00 OP1 G:A17 3.9 69.9 1.0 OP1 G:C19 4.0 96.1 1.0 OP2 G:C65 4.1 88.5 1.0 OP1 G:G18 4.7 89.6 1.0 OP2 G:U64 4.8 80.3 1.0 O3' G:G18 5.0 94.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T


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 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg102 b:75.5 occ:1.00 O6 G:G41 2.5 65.3 1.0 O2' G:G46 2.7 69.7 1.0 OP2 G:G47 2.8 67.0 1.0 C6 G:G41 3.5 63.6 1.0 OP2 G:A40 3.6 87.3 1.0 N7 G:A40 3.9 65.4 1.0 N7 G:G41 3.9 66.2 1.0 C2' G:G46 4.0 65.7 1.0 P G:G47 4.0 69.9 1.0 C5 G:G41 4.1 63.6 1.0 O3' G:G46 4.1 67.5 1.0 C1' G:G46 4.3 64.7 1.0 C8 G:A40 4.4 68.5 1.0 C8 G:G46 4.6 64.6 1.0 N9 G:G46 4.6 65.0 1.0 C3' G:G46 4.7 66.4 1.0 N1 G:G41 4.7 62.0 1.0 C5 G:A40 4.8 64.1 1.0 P G:A40 4.8 87.2 1.0 OP1 G:G47 5.0 65.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T


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 Squash Rna Aptamer in Complex with Dfhbi-1T within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg107 b:70.5 occ:1.00 OP2 G:A45 1.7 72.7 1.0 O G:HOH205 2.1 74.8 1.0 O6 G:G46 2.2 70.0 1.0 O G:HOH202 2.3 65.8 1.0 O G:HOH206 2.7 77.5 1.0 OP2 G:G42 3.0 73.2 1.0 P G:A45 3.0 78.4 1.0 C6 G:G46 3.2 66.3 1.0 C8 G:A45 3.2 67.7 1.0 N7 G:A45 3.3 67.9 1.0 O5' G:A45 3.4 71.3 1.0 C3' G:U44 3.7 72.2 1.0 OP2 G:U44 3.8 81.7 1.0 O3' G:U44 3.8 74.0 1.0 C5 G:G46 3.9 64.8 1.0 N7 G:G46 4.0 65.4 1.0 OP1 G:U44 4.0 76.4 1.0 P G:U44 4.2 83.2 1.0 N1 G:G46 4.2 64.8 1.0 P G:G42 4.2 77.3 1.0 OP1 G:A45 4.2 72.8 1.0 O5' G:U44 4.3 76.5 1.0 C8 G:G42 4.3 70.5 1.0 O5' G:G42 4.4 70.4 1.0 C5' G:U44 4.5 76.9 1.0 N9 G:A45 4.5 63.1 1.0 C4' G:U44 4.6 75.2 1.0 C2' G:U44 4.6 70.3 1.0 C5 G:A45 4.7 66.3 1.0 N7 G:G42 4.8 68.3 1.0 C5' G:A45 4.8 69.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T


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 Squash Rna Aptamer in Complex with Dfhbi-1T within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg108 b:52.9 occ:1.00 O G:HOH209 1.8 61.8 1.0 O G:HOH212 1.8 65.6 1.0 O G:HOH210 1.8 94.1 1.0 O G:HOH213 1.8 69.4 1.0 O G:HOH214 1.8 80.8 1.0 O G:HOH211 1.8 96.4 1.0 OP2 G:C67 4.1 68.1 1.0 OP2 G:G16 4.5 70.1 1.0 N7 G:G16 4.6 63.9 1.0 C8 G:G16 4.8 67.4 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