Magnesium in PDB 4lx6: X-Ray Crystal Structure of the M6C" Riboswitch Aptamer Bound to 2- Aminopyrimido[4,5-D]Pyrimidin-4(3H)-One (Ppao)

The structure of X-Ray Crystal Structure of the M6C" Riboswitch Aptamer Bound to 2- Aminopyrimido[4,5-D]Pyrimidin-4(3H)-One (Ppao), PDB code: 4lx6 was solved by M.S.Dunstan, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.50 / 2.15
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	50.100, 151.690, 24.770, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.5

The binding sites of Magnesium atom in the X-Ray Crystal Structure of the M6C" Riboswitch Aptamer Bound to 2- Aminopyrimido[4,5-D]Pyrimidin-4(3H)-One (Ppao) (pdb code 4lx6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the X-Ray Crystal Structure of the M6C" Riboswitch Aptamer Bound to 2- Aminopyrimido[4,5-D]Pyrimidin-4(3H)-One (Ppao), PDB code: 4lx6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the X-Ray Crystal Structure of the M6C" Riboswitch Aptamer Bound to 2- Aminopyrimido[4,5-D]Pyrimidin-4(3H)-One (Ppao)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of the M6C" Riboswitch Aptamer Bound to 2- Aminopyrimido[4,5-D]Pyrimidin-4(3H)-One (Ppao) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:69.5 occ:1.00 OP1 A:A24 2.1 33.0 1.0 O A:HOH717 2.1 42.2 1.0 P A:A24 3.5 46.8 1.0 N7 A:A24 3.8 29.8 1.0 C8 A:A24 3.9 30.1 1.0 N7 A:G72 4.1 41.9 1.0 O6 A:G72 4.1 39.1 1.0 O5' A:A24 4.1 32.3 1.0 O A:HOH721 4.1 44.0 1.0 OP2 A:A24 4.3 34.0 1.0 O3' A:A23 4.5 35.6 1.0 C6 A:G72 4.7 39.8 1.0 C5 A:G72 4.7 41.3 1.0 C5 A:U71 5.0 49.9 1.0

Magnesium binding site 2 out of 5 in the X-Ray Crystal Structure of the M6C" Riboswitch Aptamer Bound to 2- Aminopyrimido[4,5-D]Pyrimidin-4(3H)-One (Ppao)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of the M6C" Riboswitch Aptamer Bound to 2- Aminopyrimido[4,5-D]Pyrimidin-4(3H)-One (Ppao) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:66.6 occ:1.00 O A:HOH719 2.1 46.8 1.0 O A:HOH716 2.4 42.9 1.0 O6 A:G44 4.2 28.4 1.0 N7 A:G44 4.7 35.9 1.0 N7 A:G43 4.7 33.6 1.0 O6 A:G43 4.9 34.2 1.0

Magnesium binding site 3 out of 5 in the X-Ray Crystal Structure of the M6C" Riboswitch Aptamer Bound to 2- Aminopyrimido[4,5-D]Pyrimidin-4(3H)-One (Ppao)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Crystal Structure of the M6C" Riboswitch Aptamer Bound to 2- Aminopyrimido[4,5-D]Pyrimidin-4(3H)-One (Ppao) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:70.1 occ:1.00 OP1 A:A23 1.9 61.2 1.0 P A:A23 3.4 53.9 1.0 O5' A:A23 3.9 54.3 1.0 OP2 A:A21 3.9 67.2 1.0 C3' A:U22 4.2 51.7 1.0 O3' A:U22 4.3 52.3 1.0 OP2 A:A23 4.3 61.4 1.0 C4' A:U22 4.5 43.6 1.0 C5' A:U22 4.5 50.1 1.0 OP2 A:U22 4.9 59.7 1.0

Magnesium binding site 4 out of 5 in the X-Ray Crystal Structure of the M6C" Riboswitch Aptamer Bound to 2- Aminopyrimido[4,5-D]Pyrimidin-4(3H)-One (Ppao)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Crystal Structure of the M6C" Riboswitch Aptamer Bound to 2- Aminopyrimido[4,5-D]Pyrimidin-4(3H)-One (Ppao) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg605 b:68.4 occ:1.00 OP2 A:A45 2.5 44.9 1.0 P A:A45 3.9 45.6 1.0 N7 A:G46 4.2 26.6 1.0 O5' A:A45 4.4 48.5 1.0 O6 A:G46 4.5 35.6 1.0 OP1 A:A45 4.6 51.1 1.0 N7 A:A45 4.7 31.5 1.0 C8 A:A45 4.8 33.0 1.0 N4 A:C47 4.8 33.6 1.0

Magnesium binding site 5 out of 5 in the X-Ray Crystal Structure of the M6C" Riboswitch Aptamer Bound to 2- Aminopyrimido[4,5-D]Pyrimidin-4(3H)-One (Ppao)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Crystal Structure of the M6C" Riboswitch Aptamer Bound to 2- Aminopyrimido[4,5-D]Pyrimidin-4(3H)-One (Ppao) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg606 b:69.7 occ:1.00 O A:HOH720 2.1 51.2 1.0 OP1 A:A55 3.4 55.3 1.0 OP1 A:U40 4.0 48.0 1.0 O A:HOH703 4.3 33.3 1.0 OP2 A:U40 4.3 33.3 1.0 P A:U40 4.7 42.7 1.0 P A:A55 4.8 47.2 1.0

C.J.Robinson, H.A.Vincent, M.C.Wu, P.T.Lowe, M.S.Dunstan, D.Leys, J.Micklefield. Modular Riboswitch Toolsets For Synthetic Genetic Control in Diverse Bacterial Species. J.Am.Chem.Soc. V. 136 10615 2014.
ISSN: ISSN 0002-7863
PubMed: 24971878
DOI: 10.1021/JA502873J