Magnesium in PDB 3q3z: Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp

The structure of Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp, PDB code: 3q3z was solved by K.D.Smith, C.A.Shanahan, E.L.Moore, A.C.Simon, S.A.Strobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.07 / 2.51
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.644, 70.285, 86.037, 90.00, 98.86, 90.00
R / Rfree (%)	17.8 / 23.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp (pdb code 3q3z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp, PDB code: 3q3z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in the Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ V:Mg82 b:52.9 occ:1.00 OP1 V:G56 2.0 61.9 1.0 O V:HOH88 2.2 52.3 1.0 O V:HOH94 2.2 51.1 1.0 O V:HOH93 2.2 51.1 1.0 O V:HOH90 2.2 55.2 1.0 P V:G56 3.3 60.1 1.0 O3' V:U55 3.6 64.0 1.0 OP2 V:G56 4.2 67.3 1.0 O5' V:G56 4.4 59.6 1.0 C5' V:G56 4.6 59.2 1.0

Magnesium binding site 2 out of 13 in the Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ V:Mg4 b:62.0 occ:1.00 OP2 V:G62 2.0 52.8 1.0 OP1 V:A61 2.1 55.7 1.0 O4 V:U63 2.1 49.0 1.0 O V:HOH99 2.2 62.6 1.0 O V:HOH97 2.2 64.1 1.0 O V:HOH98 2.2 61.9 1.0 C4 V:U63 3.2 49.0 1.0 P V:A61 3.4 53.3 1.0 P V:G62 3.4 51.9 1.0 O3' V:U60 3.7 43.5 1.0 C5 V:U63 3.7 49.0 1.0 O V:HOH148 3.8 61.1 1.0 O3' V:A61 4.1 50.8 1.0 OP1 V:G62 4.3 63.5 1.0 C3' V:A61 4.3 48.2 1.0 N3 V:U63 4.4 49.1 1.0 OP2 V:A61 4.4 44.8 1.0 O V:HOH133 4.4 51.9 1.0 O5' V:A61 4.4 51.2 1.0 O5' V:G62 4.4 54.4 1.0 C5' V:A61 4.6 50.9 1.0 O V:HOH174 4.8 62.9 1.0

Magnesium binding site 3 out of 13 in the Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ V:Mg5 b:73.4 occ:1.00 O V:HOH104 2.2 64.5 1.0 O V:HOH100 2.2 75.2 1.0 O V:HOH107 2.2 69.1 1.0 O V:HOH110 2.2 66.6 1.0 O V:HOH108 2.2 75.2 1.0 O V:HOH109 2.2 76.6 1.0 O6 V:G12 4.1 58.2 1.0 O6 V:C2E1 4.2 55.5 1.0 N6 V:A74 4.2 48.1 1.0 OP2 V:C72 4.3 69.1 1.0 N7 V:G73 4.6 52.4 1.0 N6 V:A13 4.7 52.0 1.0 N4 V:C75 4.9 48.1 1.0 OP2 V:G73 4.9 57.1 1.0

Magnesium binding site 4 out of 13 in the Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ V:Mg83 b:60.4 occ:1.00 OP1 V:U66 2.0 53.4 1.0 OP1 V:U60 2.0 52.0 1.0 O V:HOH172 2.2 52.7 1.0 O V:HOH171 2.2 53.8 1.0 O V:HOH173 2.2 53.7 1.0 O V:HOH174 2.2 62.9 1.0 P V:U66 3.2 46.6 1.0 P V:U60 3.5 50.9 1.0 O5' V:U66 3.7 56.8 1.0 OP2 V:U66 3.7 43.9 1.0 O V:HOH139 4.0 49.9 1.0 OP2 V:U60 4.2 50.4 1.0 O5' V:U60 4.2 51.9 1.0 C5' V:U66 4.3 54.7 1.0 OP2 V:A61 4.4 44.8 1.0 O3' V:G65 4.4 50.0 1.0 O3' V:U59 4.4 55.2 1.0 C5' V:U60 4.6 54.4 1.0

Magnesium binding site 5 out of 13 in the Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ V:Mg85 b:75.6 occ:1.00 OP1 V:G46 2.1 76.9 1.0 O V:HOH176 2.2 76.5 1.0 O V:HOH175 2.2 68.1 1.0 O A:HOH161 2.2 75.3 1.0 O A:HOH160 2.2 71.7 1.0 OP2 A:A34 2.4 78.9 1.0 P V:G46 3.3 74.5 1.0 P A:A34 3.6 86.8 1.0 O3' A:A33 3.7 82.7 1.0 O V:HOH114 3.8 46.9 1.0 OP2 V:G46 3.8 70.0 1.0 O3' V:U45 4.1 77.3 1.0 C3' V:U45 4.3 75.5 1.0 C5' A:A34 4.3 82.2 1.0 O5' A:A34 4.5 80.2 1.0 O5' V:G46 4.6 69.1 1.0 O A:HOH121 4.7 38.6 1.0 OP1 A:A34 4.8 81.2 1.0 O2' A:A33 4.8 85.7 1.0

Magnesium binding site 6 out of 13 in the Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ V:Mg86 b:79.4 occ:1.00 O V:HOH126 1.9 55.5 1.0 O V:HOH156 2.2 68.3 1.0 OP2 V:G67 2.9 53.4 1.0 O V:HOH139 3.0 49.9 1.0 OP1 V:G67 3.3 58.4 1.0 N7 V:A61 3.4 52.6 1.0 P V:G67 3.6 55.3 1.0 N21 V:C2E1 3.7 64.6 1.0 OP2 V:A70 3.9 52.0 1.0 C8 V:A61 4.2 49.0 1.0 O V:HOH124 4.2 50.4 1.0 N31 V:C2E1 4.3 59.1 1.0 C5 V:A61 4.4 48.8 1.0 C21 V:C2E1 4.4 61.8 1.0 N6 V:A61 4.5 49.5 1.0 O5' V:G67 4.5 51.9 1.0 OP2 V:C68 4.7 62.6 1.0 O3' V:A69 4.8 58.2 1.0 O V:HOH171 4.9 53.8 1.0 C6 V:A61 4.9 50.9 1.0 O3' V:U66 4.9 53.6 1.0 O2' V:A69 4.9 58.0 1.0

Magnesium binding site 7 out of 13 in the Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ V:Mg87 b:88.8 occ:1.00 O V:HOH178 2.2 89.4 1.0 O V:HOH180 2.2 91.9 1.0 O V:HOH179 2.2 93.3 1.0 O A:HOH169 2.2 92.3 1.0 OP2 V:A34 2.3 89.5 1.0 OP2 A:G46 2.6 68.0 1.0 O3' V:A33 3.2 86.2 1.0 P V:A34 3.3 89.7 1.0 O2' V:A33 3.8 88.6 1.0 C5' V:A34 3.8 84.7 1.0 P A:G46 3.9 73.8 1.0 O5' V:A34 4.0 84.8 1.0 OP1 A:G46 4.3 78.1 1.0 O A:HOH104 4.4 47.0 1.0 C3' V:A33 4.4 82.3 1.0 OP1 V:A34 4.5 84.9 1.0 C2' V:A33 4.5 81.2 1.0 O3' A:U45 4.6 71.5 1.0 O A:HOH125 4.9 37.2 1.0 C1' V:A33 4.9 75.9 1.0 C4' V:A34 5.0 85.8 1.0

Magnesium binding site 8 out of 13 in the Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg82 b:57.2 occ:1.00 OP1 A:A61 1.9 57.4 1.0 OP2 A:G62 2.0 55.4 1.0 O4 A:U63 2.1 58.2 1.0 O A:HOH89 2.2 56.9 1.0 O A:HOH90 2.2 60.5 1.0 O A:HOH87 2.2 57.3 1.0 C4 A:U63 3.2 52.8 1.0 P A:A61 3.3 52.7 1.0 P A:G62 3.5 54.8 1.0 C5 A:U63 3.7 52.4 1.0 O3' A:U60 3.8 52.2 1.0 O3' A:A61 4.2 55.5 1.0 OP1 A:G62 4.3 60.4 1.0 C3' A:A61 4.3 55.9 1.0 OP2 A:A61 4.3 45.2 1.0 O5' A:A61 4.3 60.2 1.0 N3 A:U63 4.4 45.6 1.0 O5' A:G62 4.4 51.8 1.0 O A:HOH96 4.6 55.4 1.0 C5' A:A61 4.6 56.0 1.0 O A:HOH168 4.7 69.5 1.0 OP2 A:U66 5.0 50.8 1.0

Magnesium binding site 9 out of 13 in the Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3 b:55.4 occ:1.00 O A:HOH91 2.2 55.0 1.0 O A:HOH92 2.2 49.2 1.0 O A:HOH94 2.2 58.9 1.0 O A:HOH132 2.2 42.5 1.0 N7 A:G38 2.3 49.8 1.0 C8 A:G38 3.1 53.1 1.0 C5 A:G38 3.4 47.9 1.0 O6 A:G38 3.8 50.9 1.0 O A:HOH141 3.8 49.3 1.0 C6 A:G38 4.0 48.5 1.0 N1 A:A70 4.0 43.9 1.0 O2' A:U37 4.2 57.3 1.0 N9 A:G38 4.4 53.3 1.0 C4 A:G38 4.5 51.8 1.0 O A:HOH148 4.6 40.8 1.0 C2 A:A70 4.6 48.6 1.0 OP1 A:G38 4.7 51.0 1.0 C6 A:A70 5.0 42.8 1.0 N6 A:A70 5.0 36.2 1.0

Magnesium binding site 10 out of 13 in the Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of A C-Di-Gmp-II Riboswitch From C. Acetobutylicum Bound to C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg6 b:56.8 occ:1.00 OP1 A:U66 1.9 55.9 1.0 OP1 A:U60 2.0 53.1 1.0 O A:HOH101 2.2 63.7 1.0 O A:HOH95 2.2 56.0 1.0 O A:HOH96 2.2 55.4 1.0 O A:HOH102 2.2 58.1 1.0 P A:U66 3.1 53.9 1.0 P A:U60 3.4 54.9 1.0 O A:HOH170 3.5 88.6 1.0 OP2 A:U66 3.7 50.8 1.0 O A:HOH166 3.8 73.0 1.0 O5' A:U66 3.9 50.5 1.0 OP2 A:U60 4.1 55.2 1.0 O5' A:U60 4.2 53.2 1.0 OP2 A:A61 4.3 45.2 1.0 O3' A:G65 4.4 59.7 1.0 O3' A:U59 4.4 57.2 1.0 C5' A:U60 4.5 51.7 1.0 C5' A:U66 4.7 51.6 1.0 MG A:MG86 4.9 71.0 1.0 O A:HOH168 4.9 69.5 1.0

K.D.Smith, C.A.Shanahan, E.L.Moore, A.C.Simon, S.A.Strobel. Structural Basis of Differential Ligand Recognition By Two Classes of Bis-(3'-5')-Cyclic Dimeric Guanosine Monophosphate-Binding Riboswitches. Proc.Natl.Acad.Sci.Usa V. 108 7757 2011.
ISSN: ISSN 0027-8424
PubMed: 21518891
DOI: 10.1073/PNAS.1018857108