Magnesium in PDB 4qlm: Ydao Riboswitch Binding to C-Di-Amp

The structure of Ydao Riboswitch Binding to C-Di-Amp, PDB code: 4qlm was solved by A.M.Ren, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.64 / 2.72
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	78.767, 87.975, 145.235, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 24.4

The binding sites of Magnesium atom in the Ydao Riboswitch Binding to C-Di-Amp (pdb code 4qlm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ydao Riboswitch Binding to C-Di-Amp, PDB code: 4qlm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ydao Riboswitch Binding to C-Di-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ydao Riboswitch Binding to C-Di-Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:88.8 occ:1.00 OP2 A:G28 2.0 71.5 1.0 O A:HOH332 2.0 62.7 1.0 O A:HOH331 2.1 0.8 1.0 OP1 A:G96 2.1 0.6 1.0 O4 A:U98 2.1 91.7 1.0 OP2 A:C97 2.1 78.4 1.0 C4 A:U98 3.0 82.2 1.0 P A:G28 3.4 83.0 1.0 C5 A:U98 3.4 72.0 1.0 P A:G96 3.5 0.7 1.0 P A:C97 3.6 80.9 1.0 N7 A:G28 3.8 73.6 1.0 O5' A:G28 3.9 80.1 1.0 O3' A:A95 3.9 0.7 1.0 C8 A:G28 4.1 65.2 1.0 O5' A:G27 4.1 64.7 1.0 C5 A:C97 4.2 0.5 1.0 OP1 A:C97 4.3 86.8 1.0 N3 A:U98 4.3 85.0 1.0 OP2 A:G96 4.3 82.5 1.0 OP1 A:G28 4.3 85.5 1.0 O3' A:G27 4.4 81.3 1.0 C3' A:G27 4.5 73.2 1.0 O5' A:C97 4.5 92.7 1.0 O3' A:G96 4.5 83.1 1.0 O5' A:G96 4.6 97.8 1.0 C3' A:G96 4.7 86.6 1.0 C5' A:G27 4.7 70.7 1.0 C6 A:U98 4.8 71.7 1.0 OP1 A:G27 4.8 77.9 1.0 C6 A:C97 4.8 0.3 1.0 OP2 A:A29 4.8 82.5 1.0 P A:G27 4.8 76.8 1.0 O A:HOH321 5.0 81.4 1.0

Magnesium binding site 2 out of 2 in the Ydao Riboswitch Binding to C-Di-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ydao Riboswitch Binding to C-Di-Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:69.5 occ:1.00 O4' A:A73 2.4 75.7 1.0 OP1 A:U72 3.2 72.5 1.0 C4' A:A73 3.3 70.9 1.0 C1' A:A73 3.3 74.9 1.0 OP1 A:U75 3.6 91.4 1.0 N9 A:A73 3.7 76.8 1.0 C5' A:A73 4.0 68.7 1.0 C4 A:A73 4.3 83.7 1.0 C8 A:A73 4.4 76.4 1.0 P A:U75 4.4 89.1 1.0 C3' A:A73 4.5 76.1 1.0 P A:U72 4.5 75.8 1.0 OP1 A:C7 4.5 83.1 1.0 N3 A:A73 4.5 90.3 1.0 C2' A:A73 4.6 79.0 1.0 O3' A:C74 4.6 82.1 1.0 O3' A:A73 4.6 85.9 1.0 OP2 A:U75 4.7 84.5 1.0 OP2 A:U72 4.8 63.1 1.0 O3' A:G6 4.8 95.7 1.0 O5' A:A73 4.9 71.3 1.0

A.Ren, D.J.Patel. C-Di-Amp Binds the Ydao Riboswitch in Two Pseudo-Symmetry-Related Pockets. Nat.Chem.Biol. V. 10 780 2014.
ISSN: ISSN 1552-4450
PubMed: 25086509
DOI: 10.1038/NCHEMBIO.1606