Magnesium in PDB 7kvv: 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: 7kvv 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)	52.14 / 2.85
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.271, 104.271, 52.107, 90, 90, 90
R / Rfree (%)	22.1 / 24.5

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

Fluorine

(F)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T (pdb code 7kvv). 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, PDB code: 7kvv:
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


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 D:Mg301 b:90.4 occ:1.00 OP2 D:A45 2.1 91.1 1.0 O6 D:G46 2.3 86.2 1.0 OP2 D:G42 2.4 92.8 1.0 O D:HOH2301 2.7 88.1 1.0 OP2 D:U44 3.1 96.8 1.0 P D:G42 3.3 93.0 1.0 O5' D:G42 3.4 94.1 1.0 C6 D:G46 3.4 84.7 1.0 N7 D:A45 3.5 86.4 1.0 P D:A45 3.6 91.5 1.0 O5' D:U44 3.6 99.7 1.0 P D:U44 3.6 98.3 1.0 C8 D:A45 3.7 87.1 1.0 OP1 D:U44 3.8 97.5 1.0 OP1 D:G42 4.0 107.9 1.0 C8 D:G42 4.1 86.5 1.0 C3' D:U44 4.2 93.8 1.0 O5' D:A45 4.3 88.1 1.0 N1 D:G46 4.3 84.8 1.0 O3' D:U44 4.3 92.7 1.0 C2' D:G42 4.4 94.0 1.0 C5 D:G46 4.5 84.9 1.0 C5' D:U44 4.5 100.1 1.0 OP1 D:A45 4.5 88.6 1.0 O3' D:G41 4.7 92.3 1.0 N7 D:G46 4.8 84.6 1.0 C5' D:G42 4.8 94.2 1.0 N7 D:G42 4.8 85.8 1.0 C5 D:A45 4.9 85.7 1.0 C4' D:U44 5.0 100.8 1.0

Magnesium binding site 2 out of 2 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 D:Mg303 b:82.1 occ:1.00 O2' D:G46 2.4 83.6 1.0 O6 D:G41 2.5 83.6 1.0 OP2 D:G47 3.2 88.9 1.0 C6 D:G41 3.6 83.3 1.0 C2' D:G46 3.7 86.4 1.0 N7 D:G41 4.0 87.5 1.0 C1' D:G46 4.0 84.9 1.0 OP2 D:A40 4.1 105.0 1.0 N7 D:A40 4.1 86.1 1.0 C5 D:G41 4.2 86.2 1.0 C8 D:G46 4.2 84.7 1.0 N9 D:G46 4.3 84.5 1.0 P D:G47 4.3 92.6 1.0 O3' D:G46 4.3 89.1 1.0 C3' D:G46 4.6 87.4 1.0 C8 D:A40 4.8 89.4 1.0 N1 D:G41 4.8 82.6 1.0 C5 D:A40 4.9 85.9 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