Magnesium in PDB 6ck4: G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp

The structure of G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp, PDB code: 6ck4 was solved by C.W.Reiss, A.J.Knappenberger, S.A.Strobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.54 / 3.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.252, 62.147, 125.909, 91.18, 89.61, 101.94
R / Rfree (%)	24.8 / 30.4

The structure of G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp also contains other interesting chemical elements:

Potassium

(K)

27 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp (pdb code 6ck4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp, PDB code: 6ck4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:83.2 occ:1.00 OP1 A:C93 2.2 1.0 1.0 OP2 A:G48 2.2 74.3 1.0 P A:C93 3.6 0.7 1.0 P A:G48 3.6 93.3 1.0 O3' A:C92 4.2 1.0 1.0 OP1 A:G48 4.4 0.1 1.0 O3' A:A47 4.4 0.4 1.0 O5' A:C93 4.4 75.6 1.0 C5' A:C93 4.5 75.4 1.0 OP1 A:A47 4.5 0.1 1.0 O5' A:G48 4.6 0.0 1.0 C5' A:G48 4.7 0.6 1.0 OP2 A:C93 4.7 95.0 1.0 C3' A:A47 4.9 0.7 1.0

Magnesium binding site 2 out of 12 in the G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:0.0 occ:1.00 OP1 A:C92 2.2 0.8 1.0 OP2 A:C93 2.2 95.0 1.0 OP1 A:G48 2.2 0.1 1.0 P A:C92 3.4 0.7 1.0 P A:C93 3.6 0.7 1.0 P A:G48 3.7 93.3 1.0 OP2 A:C92 3.8 87.7 1.0 N7 A:G48 4.2 0.7 1.0 OP1 A:C93 4.3 1.0 1.0 C8 A:G48 4.3 0.3 1.0 O5' A:C93 4.4 75.6 1.0 O3' A:A47 4.4 0.4 1.0 O5' A:C92 4.4 89.0 1.0 O5' A:G48 4.5 0.0 1.0 O3' A:G91 4.6 98.2 1.0 O3' A:C92 4.7 1.0 1.0 OP2 A:G48 4.7 74.3 1.0 C3' A:C92 4.9 97.2 1.0 C5 A:C93 4.9 99.0 1.0 C5' A:C92 4.9 82.1 1.0

Magnesium binding site 3 out of 12 in the G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:89.5 occ:1.00 N1 A:G31 3.2 0.1 1.0 O2' A:U28 3.5 0.9 1.0 O6 A:G31 3.7 0.4 1.0 C6 A:G31 3.9 0.7 1.0 K A:K211 3.9 0.9 1.0 N2 A:G31 4.1 0.6 1.0 C2 A:G31 4.1 0.9 1.0 C2' A:U28 4.8 0.3 1.0

Magnesium binding site 4 out of 12 in the G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:86.9 occ:1.00 O B:HOH302 2.2 63.4 1.0 OP2 B:G48 2.2 65.9 1.0 OP1 B:C93 2.2 98.2 1.0 OP1 B:A47 3.5 0.0 1.0 P B:G48 3.5 0.5 1.0 P B:C93 3.5 93.9 1.0 O3' B:C92 3.6 0.7 1.0 O3' B:A47 3.8 0.0 1.0 C3' B:A47 4.3 0.4 1.0 OP1 B:G48 4.4 91.5 1.0 O5' B:C93 4.5 64.2 1.0 C5' B:C93 4.6 68.9 1.0 C4' B:A47 4.6 0.5 1.0 OP2 B:C93 4.6 69.4 1.0 O5' B:G48 4.6 0.2 1.0 C5' B:G48 4.7 0.0 1.0 P B:A47 4.9 0.2 1.0

Magnesium binding site 5 out of 12 in the G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:0.5 occ:1.00 OP1 B:G48 2.1 91.5 1.0 OP2 B:C93 2.2 69.4 1.0 OP1 B:C92 2.2 0.7 1.0 O B:HOH301 2.2 82.4 1.0 P B:C92 3.4 0.6 1.0 P B:C93 3.6 93.9 1.0 P B:G48 3.6 0.5 1.0 OP2 B:C92 3.9 0.1 1.0 N7 B:G48 4.1 0.2 1.0 OP1 B:C93 4.2 98.2 1.0 C8 B:G48 4.2 0.3 1.0 O3' B:A47 4.3 0.0 1.0 O5' B:C93 4.4 64.2 1.0 O5' B:G48 4.4 0.2 1.0 O5' B:C92 4.4 78.4 1.0 O3' B:G91 4.6 0.2 1.0 OP2 B:G48 4.6 65.9 1.0 O3' B:C92 4.6 0.7 1.0 C3' B:C92 4.9 0.5 1.0 C5' B:C92 4.9 79.1 1.0 C5 B:C93 5.0 0.4 1.0

Magnesium binding site 6 out of 12 in the G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:66.2 occ:1.00 OP2 B:C77 2.1 0.7 1.0 O2 B:C49 2.2 92.8 1.0 N3 B:C49 2.6 0.6 1.0 C2 B:C49 2.7 0.8 1.0 O3D B:G4P208 3.1 0.4 1.0 P B:C77 3.5 0.2 1.0 O1D B:G4P208 3.5 0.7 1.0 PD B:G4P208 3.8 0.1 1.0 C4 B:C49 3.9 0.9 1.0 N1 B:C49 4.1 0.9 1.0 OP1 B:C77 4.1 0.5 1.0 O2' B:A76 4.3 96.3 1.0 O5' B:C77 4.3 0.4 1.0 N4 B:C49 4.4 0.7 1.0 O3' B:A76 4.6 1.0 1.0 O2' B:C49 4.7 0.9 1.0 C2' B:A76 4.7 0.6 1.0 N2 B:G48 4.7 0.3 1.0 O2D B:G4P208 4.8 0.6 1.0 C1' B:C49 4.9 0.9 1.0 C2' B:C49 4.9 0.0 1.0 N1 B:G48 4.9 0.8 1.0 C5 B:C49 5.0 93.9 1.0

Magnesium binding site 7 out of 12 in the G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:76.3 occ:1.00 OP2 C:C93 2.2 0.1 1.0 OP1 C:C92 2.2 0.9 1.0 OP1 C:G48 2.2 0.7 1.0 O C:HOH303 3.2 0.8 1.0 P C:C92 3.4 0.4 1.0 P C:C93 3.6 0.1 1.0 P C:G48 3.7 0.5 1.0 OP2 C:C92 3.8 91.9 1.0 OP1 C:C93 4.2 0.1 1.0 N7 C:G48 4.3 0.7 1.0 O5' C:C93 4.3 0.4 1.0 C8 C:G48 4.4 0.8 1.0 O3' C:A47 4.4 89.9 1.0 O5' C:C92 4.4 88.0 1.0 O5' C:G48 4.5 0.9 1.0 O3' C:G91 4.6 77.4 1.0 O3' C:C92 4.6 1.0 1.0 OP2 C:G48 4.7 0.2 1.0 C3' C:C92 4.8 0.1 1.0 C5 C:C93 4.9 0.4 1.0 C5' C:C92 4.9 0.7 1.0

Magnesium binding site 8 out of 12 in the G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:0.7 occ:1.00 OP1 C:C93 2.1 0.1 1.0 OP2 C:G48 2.2 0.2 1.0 P C:C93 3.4 0.1 1.0 P C:G48 3.5 0.5 1.0 OP1 C:A47 3.7 99.4 1.0 O3' C:C92 3.7 1.0 1.0 O3' C:A47 4.0 89.9 1.0 O5' C:C93 4.3 0.4 1.0 OP1 C:G48 4.4 0.7 1.0 C5' C:C93 4.4 96.5 1.0 C3' C:A47 4.5 93.3 1.0 OP2 C:C93 4.6 0.1 1.0 O5' C:G48 4.7 0.9 1.0 C4' C:A47 4.8 1.0 1.0 C5' C:G48 4.8 0.4 1.0

Magnesium binding site 9 out of 12 in the G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg203 b:71.9 occ:1.00 OP2 C:G17 2.2 86.0 1.0 P C:G17 3.2 0.4 1.0 O5' C:G17 3.2 83.6 1.0 O5' C:G16 3.9 66.7 1.0 OP1 C:G16 4.0 0.7 1.0 C5 C:MPD212 4.1 80.5 1.0 C3' C:G16 4.1 73.7 1.0 O3' C:G16 4.2 77.4 1.0 P C:G16 4.2 0.1 1.0 OP2 C:G16 4.3 94.5 1.0 C5' C:G16 4.3 63.2 1.0 OP1 C:G17 4.4 87.1 1.0 C5' C:G17 4.5 85.0 1.0 O4 C:MPD212 4.7 79.2 1.0 C8 C:G17 4.7 72.0 1.0 OP2 C:U38 4.7 0.1 1.0 C4' C:G16 4.8 61.5 1.0

Magnesium binding site 10 out of 12 in the G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of G96A Mutant of the Prpp Riboswitch From T. Mathranii Bound to Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg204 b:81.9 occ:1.00 O6 C:G16 2.2 99.8 1.0 N7 C:G16 2.7 80.2 1.0 C6 C:G16 2.9 81.1 1.0 C5 C:G16 3.1 64.5 1.0 K C:K206 3.3 1.0 1.0 C1 C:MPD212 3.7 0.3 1.0 O6 C:G15 3.9 96.2 1.0 C8 C:G16 4.0 88.1 1.0 C4 C:MPD212 4.2 0.7 1.0 N7 C:G15 4.2 83.4 1.0 N1 C:G16 4.2 70.8 1.0 C6 C:G15 4.3 84.4 1.0 C5 C:G15 4.4 77.7 1.0 C4 C:G16 4.4 67.3 1.0 O4 C:MPD212 4.7 79.2 1.0 N4 C:C44 4.8 64.0 1.0 C2 C:MPD212 4.8 0.9 1.0 N9 C:G16 4.9 77.2 1.0 C3 C:MPD212 4.9 0.5 1.0 C5 C:MPD212 5.0 80.5 1.0

A.J.Knappenberger, C.W.Reiss, S.A.Strobel. Structures of Two Aptamers with Differing Ligand Specificity Reveal Ruggedness in the Functional Landscape of Rna. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 29877798
DOI: 10.7554/ELIFE.36381