Magnesium in PDB 3oww: Crystal Structure of the Glycine Riboswitch Bound to Glycine

The structure of Crystal Structure of the Glycine Riboswitch Bound to Glycine, PDB code: 3oww was solved by L.Huang, A.Serganov, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.514, 83.514, 198.524, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 23.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 33;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Glycine Riboswitch Bound to Glycine (pdb code 3oww). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 33 binding sites of Magnesium where determined in the Crystal Structure of the Glycine Riboswitch Bound to Glycine, PDB code: 3oww:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 33 in the Crystal Structure of the Glycine Riboswitch Bound to Glycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Glycine Riboswitch Bound to Glycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:62.1 occ:1.00 OP1 A:A34 2.0 59.2 1.0 OP2 A:G35 2.1 68.8 1.0 O A:HOH134 2.2 27.7 1.0 O A:HOH133 2.2 28.3 1.0 O A:HOH131 2.2 28.3 1.0 O A:HOH132 2.2 28.6 1.0 P A:A34 3.4 59.4 1.0 P A:G35 3.5 70.0 1.0 O5' A:A34 4.0 61.2 1.0 C4' A:A33 4.2 55.7 1.0 O3' A:A33 4.3 57.9 1.0 O5' A:G35 4.3 71.6 1.0 CA A:GLY89 4.4 59.0 1.0 OP1 A:G35 4.4 70.6 1.0 O3' A:A34 4.4 68.8 1.0 C5' A:A34 4.5 62.5 1.0 OP2 A:A34 4.5 59.8 1.0 N7 A:G35 4.6 70.9 1.0 OXT A:GLY89 4.7 57.3 1.0 C3' A:A33 4.7 56.4 1.0 C3' A:A34 4.7 67.3 1.0 C5' A:A33 4.7 54.4 1.0 C8 A:G35 4.9 71.8 1.0 N7 A:G36 4.9 68.6 1.0 OP1 A:A65 4.9 59.9 1.0 O2' A:A81 5.0 60.8 1.0

Magnesium binding site 2 out of 33 in the Crystal Structure of the Glycine Riboswitch Bound to Glycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Glycine Riboswitch Bound to Glycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:91.3 occ:1.00 OP2 A:A33 2.0 51.5 1.0 O A:HOH135 2.2 62.6 1.0 O A:HOH137 2.2 62.6 1.0 O A:HOH136 2.2 62.6 1.0 OP2 A:C66 2.2 57.1 1.0 O2' A:G32 2.4 53.2 1.0 C2' A:G32 3.3 52.2 1.0 P A:A33 3.4 51.2 1.0 P A:C66 3.6 56.5 1.0 OXT A:GLY89 3.6 57.3 1.0 C3' A:G32 3.7 51.2 1.0 O3' A:G32 3.9 51.2 1.0 OP1 A:C66 4.2 56.6 1.0 O4 A:U69 4.3 62.3 1.0 OP1 A:A33 4.4 51.0 1.0 O A:GLY89 4.4 57.8 1.0 C5 A:U67 4.5 57.5 1.0 O4 A:U67 4.5 59.2 1.0 O5' A:A33 4.5 52.6 1.0 C A:GLY89 4.5 57.9 1.0 C5' A:A33 4.5 54.4 1.0 O5' A:C66 4.5 55.6 1.0 O3' A:A65 4.6 58.0 1.0 C4' A:A65 4.7 58.2 1.0 C1' A:G32 4.7 52.1 1.0 C4 A:U67 4.8 58.7 1.0 C5' A:A65 4.9 58.4 1.0 OP2 A:U67 4.9 53.4 1.0

Magnesium binding site 3 out of 33 in the Crystal Structure of the Glycine Riboswitch Bound to Glycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Glycine Riboswitch Bound to Glycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:0.1 occ:1.00 O A:HOH141 2.2 81.4 1.0 O A:HOH138 2.2 81.5 1.0 O A:HOH139 2.2 81.3 1.0 O A:HOH140 2.2 81.5 1.0 OP1 A:A22 2.6 57.7 1.0 OP2 A:A75 2.7 59.9 1.0 O3' A:A21 3.6 56.7 1.0 P A:A22 3.7 58.3 1.0 P A:A75 4.2 59.1 1.0 OP2 A:C74 4.6 62.0 1.0 N7 A:A75 4.7 61.5 1.0 OP2 A:A22 4.8 59.1 1.0 C5' A:A22 4.8 58.4 1.0 O5' A:A22 4.8 58.7 1.0 O5' A:A75 4.8 59.0 1.0 O3' A:C74 5.0 59.1 1.0 C8 A:A75 5.0 60.8 1.0 C3' A:A21 5.0 55.6 1.0

Magnesium binding site 4 out of 33 in the Crystal Structure of the Glycine Riboswitch Bound to Glycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Glycine Riboswitch Bound to Glycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:86.0 occ:1.00 OP2 A:A76 2.0 59.1 1.0 O A:HOH142 2.2 57.1 1.0 O A:HOH144 2.2 57.5 1.0 O A:HOH143 2.2 56.8 1.0 OP1 A:A75 2.2 58.5 1.0 OP1 A:C74 3.1 60.5 1.0 P A:A76 3.5 58.8 1.0 P A:A75 3.6 59.1 1.0 C5' A:C74 4.0 59.3 1.0 N6 A:A78 4.0 56.6 1.0 O5' A:A76 4.2 59.4 1.0 N7 A:A77 4.3 60.5 1.0 OP1 A:A76 4.3 58.6 1.0 N6 A:A77 4.4 61.6 1.0 OP2 A:A75 4.4 59.9 1.0 P A:C74 4.4 61.3 1.0 O5' A:A75 4.4 59.0 1.0 N7 A:A76 4.4 59.2 1.0 O3' A:A75 4.4 58.5 1.0 O5' A:C74 4.6 60.7 1.0 O3' A:C74 4.6 59.1 1.0 C3' A:A75 4.6 58.8 1.0 C8 A:A76 4.7 58.9 1.0 C6 A:A78 4.8 57.5 1.0 C5' A:A75 4.8 58.5 1.0 C4' A:C74 4.9 58.8 1.0

Magnesium binding site 5 out of 33 in the Crystal Structure of the Glycine Riboswitch Bound to Glycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Glycine Riboswitch Bound to Glycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:0.2 occ:1.00 OP2 A:C70 2.2 74.7 1.0 O A:HOH145 2.2 64.8 1.0 O A:HOH148 2.2 64.9 1.0 O A:HOH146 2.2 65.4 1.0 O A:HOH147 2.2 65.3 1.0 OP2 A:A71 2.2 78.6 1.0 P A:C70 3.1 75.5 1.0 O5' A:C70 3.3 76.9 1.0 O3' A:U69 3.3 72.8 1.0 P A:A71 3.7 80.0 1.0 O6 A:G72 4.0 65.4 1.0 O2' A:U69 4.0 67.9 1.0 N7 A:G72 4.4 68.2 1.0 O5' A:A71 4.4 79.2 1.0 C3' A:U69 4.5 70.8 1.0 OP1 A:A71 4.5 81.6 1.0 N7 A:A71 4.5 72.5 1.0 OP1 A:C70 4.5 76.4 1.0 C5' A:C70 4.6 79.5 1.0 O3' A:C70 4.6 80.9 1.0 C3' A:C70 4.7 79.8 1.0 C8 A:A71 4.8 74.2 1.0 C2' A:U69 4.8 68.5 1.0 C6 A:G72 4.9 65.2 1.0

Magnesium binding site 6 out of 33 in the Crystal Structure of the Glycine Riboswitch Bound to Glycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Glycine Riboswitch Bound to Glycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:63.0 occ:1.00 OP1 A:A33 3.1 51.0 1.0 OP1 A:C66 4.0 56.6 1.0 P A:A33 4.6 51.2 1.0 OP1 B:A33 4.6 48.1 1.0

Magnesium binding site 7 out of 33 in the Crystal Structure of the Glycine Riboswitch Bound to Glycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Glycine Riboswitch Bound to Glycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:0.5 occ:1.00 O A:HOH151 2.2 83.3 1.0 O A:HOH149 2.2 83.3 1.0 O A:HOH153 2.2 83.1 1.0 O A:HOH150 2.2 83.4 1.0 O A:HOH152 2.2 83.2 1.0 O B:HOH134 2.2 83.1 1.0 OP2 A:G32 4.3 53.7 1.0 OP1 A:U67 4.3 52.5 1.0 OP2 A:U67 4.4 53.4 1.0 OP2 A:C68 4.4 59.8 1.0 OP1 B:G10 4.7 48.5 1.0 P A:U67 4.8 52.8 1.0

Magnesium binding site 8 out of 33 in the Crystal Structure of the Glycine Riboswitch Bound to Glycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Glycine Riboswitch Bound to Glycine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg108 b:0.9 occ:1.00 O B:HOH139 2.2 66.5 1.0 O B:HOH136 2.2 66.4 1.0 O A:HOH154 2.2 66.3 1.0 O B:HOH135 2.2 66.5 1.0 O B:HOH137 2.2 66.3 1.0 O B:HOH138 2.2 66.3 1.0 OP1 B:U67 4.3 54.3 1.0 OP2 B:G32 4.5 44.9 1.0 OP2 B:C68 4.5 56.1 1.0 OP1 A:G10 4.6 54.2 1.0 OP2 B:U67 4.6 54.8 1.0 P B:U67 5.0 54.7 1.0

Magnesium binding site 9 out of 33 in the Crystal Structure of the Glycine Riboswitch Bound to Glycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Glycine Riboswitch Bound to Glycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:71.4 occ:1.00 O A:HOH156 2.2 22.6 1.0 O A:HOH159 2.2 22.2 1.0 O A:HOH160 2.2 22.1 1.0 O A:HOH155 2.2 22.9 1.0 O A:HOH158 2.2 22.2 1.0 O A:HOH157 2.2 22.4 1.0 O4 A:U46 4.3 74.1 1.0 O6 A:G55 4.5 66.2 1.0 O6 A:G47 4.5 76.9 1.0 N4 A:C54 4.5 65.0 1.0

Magnesium binding site 10 out of 33 in the Crystal Structure of the Glycine Riboswitch Bound to Glycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Glycine Riboswitch Bound to Glycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg110 b:75.9 occ:1.00 O A:HOH164 2.2 30.9 1.0 O A:HOH162 2.2 30.9 1.0 O A:HOH163 2.2 30.7 1.0 O A:HOH161 2.2 30.4 1.0 O A:HOH165 2.2 30.9 1.0 O A:HOH166 2.2 31.1 1.0 O6 A:G26 4.3 88.2 1.0 N7 A:G25 4.4 86.3 1.0 N7 A:G26 4.6 93.2 1.0 O6 A:G25 4.8 83.3 1.0 C5 A:C24 4.9 73.9 1.0

L.Huang, A.Serganov, D.J.Patel. Structural Insights Into Ligand Recognition By A Sensing Domain of the Cooperative Glycine Riboswitch. Mol.Cell V. 40 774 2010.
ISSN: ISSN 1097-2765
PubMed: 21145485
DOI: 10.1016/J.MOLCEL.2010.11.026