Magnesium in PDB 5kx9: Selective Small Molecule Inhibition of the Fmn Riboswitch

The structure of Selective Small Molecule Inhibition of the Fmn Riboswitch, PDB code: 5kx9 was solved by T.O.Fischmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.04 / 2.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.280, 71.280, 138.930, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 25.1

The structure of Selective Small Molecule Inhibition of the Fmn Riboswitch also contains other interesting chemical elements:

Potassium

(K)

7 atoms

The binding sites of Magnesium atom in the Selective Small Molecule Inhibition of the Fmn Riboswitch (pdb code 5kx9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Selective Small Molecule Inhibition of the Fmn Riboswitch, PDB code: 5kx9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Selective Small Molecule Inhibition of the Fmn Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Selective Small Molecule Inhibition of the Fmn Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg107 b:83.1 occ:1.00 OP2 X:U23 2.2 88.4 1.0 OP1 X:A22 2.5 98.1 1.0 P X:U23 3.3 88.6 1.0 OP1 X:U23 3.4 88.4 1.0 P X:A22 3.9 97.9 1.0 O5' X:U23 4.3 88.1 1.0 O5' X:A22 4.5 96.0 1.0 C5' X:A22 4.5 94.0 1.0 O3' X:A22 4.5 89.9 1.0 OP2 X:A22 4.7 97.4 1.0 C3' X:A22 4.8 91.6 1.0 C5' X:U23 4.9 87.3 1.0 O3' X:A21 5.0 99.8 1.0

Magnesium binding site 2 out of 4 in the Selective Small Molecule Inhibition of the Fmn Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Selective Small Molecule Inhibition of the Fmn Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg201 b:81.4 occ:1.00 O4 Y:U89 2.1 98.1 1.0 OP2 Y:A92 2.1 85.1 1.0 C4 Y:U89 3.3 98.0 1.0 P Y:A92 3.6 84.9 1.0 N7 Y:G88 4.1 92.5 1.0 C5 Y:U89 4.1 98.2 1.0 O6 Y:G88 4.1 91.9 1.0 N3 Y:U89 4.3 98.2 1.0 O5' Y:A92 4.4 83.0 1.0 OP1 Y:A92 4.4 84.8 1.0 O3' Y:G91 4.5 86.3 1.0 C8 Y:A92 4.6 76.7 1.0 C3' Y:G91 4.7 87.0 1.0 C5' Y:G91 4.7 88.9 1.0 C5 Y:G88 4.7 92.1 1.0 C6 Y:G88 4.8 91.8 1.0 C4' Y:G91 4.8 87.8 1.0

Magnesium binding site 3 out of 4 in the Selective Small Molecule Inhibition of the Fmn Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Selective Small Molecule Inhibition of the Fmn Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg202 b:80.7 occ:1.00 O6 Y:G68 3.6 0.2 1.0 O6 Y:G67 3.8 0.3 1.0 OP2 Y:U75 4.2 78.2 1.0 O4 Y:U66 4.4 0.5 1.0 N7 Y:G67 4.5 0.5 1.0 N4 Y:C76 4.5 80.2 1.0 C6 Y:G68 4.7 0.1 1.0 C6 Y:G67 4.7 0.0 1.0 C4' Y:U74 4.7 86.4 1.0 C5 Y:U66 4.8 0.1 1.0 C4 Y:U66 4.9 0.8 1.0 O3' Y:U74 4.9 82.3 1.0 P Y:U75 4.9 78.3 1.0 C5 Y:G67 5.0 0.2 1.0

Magnesium binding site 4 out of 4 in the Selective Small Molecule Inhibition of the Fmn Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Selective Small Molecule Inhibition of the Fmn Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg204 b:0.1 occ:1.00 OP1 Y:C95 2.3 81.2 1.0 P Y:C95 3.4 79.9 1.0 OP2 Y:C95 3.6 79.9 1.0 O3' Y:U94 4.4 78.2 1.0 O5' Y:C95 4.5 81.0 1.0 N7 X:G12 4.6 76.7 1.0 OP2 Y:U96 4.6 88.0 1.0 OP2 X:G12 4.7 85.1 1.0

J.A.Howe, L.Xiao, T.O.Fischmann, H.Wang, H.Tang, A.Villafania, R.Zhang, C.M.Barbieri, T.Roemer. Atomic Resolution Mechanistic Studies of Ribocil: A Highly Selective Unnatural Ligand Mimic of the E. Coli Fmn Riboswitch. Rna Biol. V. 13 946 2016.
ISSN: ESSN 1555-8584
PubMed: 27485612
DOI: 10.1080/15476286.2016.1216304