Magnesium in PDB 4lx5: X-Ray Crystal Structure of the M6" Riboswitch Aptamer Bound to Pyrimido[4,5-D]Pyrimidine-2,4-Diamine (Ppda)

The structure of X-Ray Crystal Structure of the M6" Riboswitch Aptamer Bound to Pyrimido[4,5-D]Pyrimidine-2,4-Diamine (Ppda), PDB code: 4lx5 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)	46.60 / 2.13
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	49.050, 149.710, 24.400, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 25.7

The binding sites of Magnesium atom in the X-Ray Crystal Structure of the M6" Riboswitch Aptamer Bound to Pyrimido[4,5-D]Pyrimidine-2,4-Diamine (Ppda) (pdb code 4lx5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray Crystal Structure of the M6" Riboswitch Aptamer Bound to Pyrimido[4,5-D]Pyrimidine-2,4-Diamine (Ppda), PDB code: 4lx5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the X-Ray Crystal Structure of the M6" Riboswitch Aptamer Bound to Pyrimido[4,5-D]Pyrimidine-2,4-Diamine (Ppda)


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 M6" Riboswitch Aptamer Bound to Pyrimido[4,5-D]Pyrimidine-2,4-Diamine (Ppda) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:68.3 occ:1.00 O A:HOH616 2.1 74.8 1.0 O A:HOH608 2.3 51.8 1.0 O A:HOH609 2.5 47.3 1.0 O A:HOH615 2.5 63.4 1.0 O6 A:G44 3.2 40.0 1.0 O6 A:G43 3.2 40.4 1.0 N7 A:G43 3.7 53.8 1.0 N7 A:G44 3.8 46.1 1.0 C6 A:G43 3.8 42.0 1.0 C6 A:G44 4.0 37.9 1.0 C5 A:G43 4.0 46.4 1.0 C5 A:G44 4.2 39.8 1.0 N4 A:C26 4.8 34.2 1.0 C8 A:G43 4.8 52.1 1.0 N4 A:C42 4.9 50.0 1.0 C8 A:G44 5.0 46.0 1.0

Magnesium binding site 2 out of 4 in the X-Ray Crystal Structure of the M6" Riboswitch Aptamer Bound to Pyrimido[4,5-D]Pyrimidine-2,4-Diamine (Ppda)


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 M6" Riboswitch Aptamer Bound to Pyrimido[4,5-D]Pyrimidine-2,4-Diamine (Ppda) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:74.8 occ:1.00 O A:HOH612 2.0 72.6 1.0 OP1 A:A24 2.2 55.7 1.0 O A:HOH610 2.3 51.7 1.0 O A:HOH613 2.3 78.5 1.0 O A:HOH604 2.4 49.5 1.0 O A:HOH611 2.5 64.2 1.0 P A:A24 3.6 44.3 1.0 N7 A:A24 3.9 47.7 1.0 C8 A:A24 4.1 50.1 1.0 OP2 A:A24 4.2 41.8 1.0 N7 A:G72 4.3 51.1 1.0 O6 A:G72 4.3 35.2 1.0 O A:HOH614 4.3 48.0 1.0 O5' A:A24 4.5 43.4 1.0 O3' A:A23 4.6 47.0 1.0 O A:HOH603 4.8 41.4 1.0 C5 A:U71 4.9 46.9 1.0

Magnesium binding site 3 out of 4 in the X-Ray Crystal Structure of the M6" Riboswitch Aptamer Bound to Pyrimido[4,5-D]Pyrimidine-2,4-Diamine (Ppda)


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 M6" Riboswitch Aptamer Bound to Pyrimido[4,5-D]Pyrimidine-2,4-Diamine (Ppda) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:90.5 occ:1.00 OP1 A:U68 2.2 60.2 1.0 P A:U68 3.7 57.1 1.0 OP1 A:C27 3.7 57.3 1.0 O3' A:C67 4.2 57.1 1.0 O5' A:U68 4.5 48.0 1.0 OP2 A:U68 4.6 53.5 1.0 C5' A:U68 4.6 52.3 1.0 P A:C27 4.7 46.4 1.0 OP2 A:C27 4.9 41.9 1.0

Magnesium binding site 4 out of 4 in the X-Ray Crystal Structure of the M6" Riboswitch Aptamer Bound to Pyrimido[4,5-D]Pyrimidine-2,4-Diamine (Ppda)


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 M6" Riboswitch Aptamer Bound to Pyrimido[4,5-D]Pyrimidine-2,4-Diamine (Ppda) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:73.7 occ:1.00 OP1 A:U40 3.6 75.8 1.0 OP2 A:U41 4.0 60.4 1.0 OP1 A:A55 4.0 60.5 1.0 P A:U40 4.3 61.1 1.0 OP2 A:U40 4.4 44.9 1.0 O5' A:U40 4.5 59.0 1.0 OP1 A:U41 4.8 63.0 1.0 P A:U41 4.8 65.5 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