Magnesium in PDB 4qln: Structure of Ydao Riboswitch Binding with C-Di-Damp

The structure of Structure of Ydao Riboswitch Binding with C-Di-Damp, PDB code: 4qln 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)	45.25 / 2.65
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	77.874, 87.051, 144.553, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 29

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

Magnesium binding site 1 out of 2 in the Structure of Ydao Riboswitch Binding with C-Di-Damp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Ydao Riboswitch Binding with C-Di-Damp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:93.7 occ:1.00 OP2 A:C97 1.7 79.8 1.0 OP1 A:G96 2.0 0.2 1.0 O A:HOH303 2.0 56.0 1.0 OP2 A:G28 2.4 56.0 1.0 O4 A:U98 2.4 57.5 1.0 C4 A:U98 3.1 54.1 1.0 P A:C97 3.1 81.4 1.0 C5 A:U98 3.3 56.2 1.0 P A:G96 3.4 1.0 1.0 C5 A:C97 3.8 77.5 1.0 OP1 A:C97 3.9 81.8 1.0 P A:G28 3.9 60.1 1.0 O3' A:A95 3.9 89.4 1.0 O5' A:C97 4.0 93.5 1.0 O3' A:G96 4.1 73.2 1.0 O5' A:G96 4.2 96.7 1.0 C3' A:G96 4.2 77.8 1.0 C6 A:C97 4.2 83.2 1.0 N7 A:G28 4.3 62.7 1.0 C5' A:G96 4.3 87.4 1.0 N3 A:U98 4.4 66.6 1.0 O5' A:G27 4.4 59.3 1.0 O5' A:G28 4.4 69.3 1.0 OP2 A:G96 4.5 0.7 1.0 OP1 A:G27 4.5 65.1 1.0 C6 A:U98 4.6 53.4 1.0 C8 A:G28 4.7 66.8 1.0 OP2 A:G27 4.8 55.6 1.0 P A:G27 4.8 56.0 1.0 OP1 A:G28 4.8 73.8 1.0 O3' A:G27 4.8 69.4 1.0 C4' A:G96 4.9 84.0 1.0 C3' A:G27 4.9 62.8 1.0 C4 A:C97 5.0 80.9 1.0

Magnesium binding site 2 out of 2 in the Structure of Ydao Riboswitch Binding with C-Di-Damp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Ydao Riboswitch Binding with C-Di-Damp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:72.8 occ:1.00 O A:HOH301 2.1 63.2 1.0 OP1 A:U72 2.4 58.8 1.0 O4' A:A73 2.4 77.6 1.0 C4' A:A73 3.0 77.5 1.0 C5' A:A73 3.4 78.2 1.0 P A:U72 3.5 58.2 1.0 C1' A:A73 3.6 71.1 1.0 OP2 A:U72 3.8 53.3 1.0 OP1 A:U75 4.1 76.5 1.0 N9 A:A73 4.1 77.5 1.0 O5' A:U72 4.3 67.4 1.0 O5' A:A73 4.4 84.2 1.0 C3' A:A73 4.4 68.4 1.0 C8 A:A73 4.5 73.2 1.0 O3' A:A73 4.7 70.1 1.0 O3' A:U71 4.7 48.1 1.0 C2' A:A73 4.7 69.7 1.0 P A:U75 4.7 76.9 1.0 OP2 A:U75 4.8 89.6 1.0 O3' A:C74 4.8 78.2 1.0 C4 A:A73 4.9 83.8 1.0 C5' A:U72 4.9 62.2 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