Barium in PDB 6ck5: Prpp Riboswitch From T. Mathranii Bound to Prpp

The structure of Prpp Riboswitch From T. Mathranii Bound to Prpp, PDB code: 6ck5 was solved by A.J.Knappenberger, C.W.Reiss, S.A.Strobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.35 / 2.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.977, 89.575, 136.367, 90.00, 96.90, 90.00
R / Rfree (%)	21.5 / 25.2

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

Magnesium	(Mg)	8 atoms
Potassium	(K)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Barium atom in the Prpp Riboswitch From T. Mathranii Bound to Prpp (pdb code 6ck5). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 20 binding sites of Barium where determined in the Prpp Riboswitch From T. Mathranii Bound to Prpp, PDB code: 6ck5:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 20 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba201 b:84.5 occ:1.00 O6 A:G48 2.8 40.7 1.0 O A:HOH303 3.0 54.6 1.0 O6 A:G97 3.1 55.6 1.0 O4 A:U80 3.5 84.7 1.0 C6 A:G48 3.9 58.2 1.0 O1P A:PRP217 4.0 60.6 1.0 C6 A:G97 4.2 57.2 1.0 N6 A:A98 4.4 62.8 1.0 C4 A:U80 4.4 62.8 1.0 N7 A:G97 4.5 65.9 1.0 N3 A:U80 4.5 50.0 1.0 O4 A:U79 4.5 59.8 1.0 N1 A:G48 4.6 58.0 1.0 C5 A:G97 4.7 59.9 1.0 N2 A:G95 4.8 73.4 1.0

Barium binding site 2 out of 20 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba202 b:0.5 occ:1.00 OP1 A:C92 2.2 36.6 1.0 OP2 A:C93 2.2 44.8 1.0 OP1 A:G48 2.7 38.1 1.0 P A:C92 3.2 41.2 1.0 OP2 A:C92 3.5 48.5 1.0 P A:C93 3.6 34.6 1.0 O5' A:C92 4.0 30.5 1.0 O5' A:C93 4.0 39.4 1.0 P A:G48 4.1 52.3 1.0 C5' A:C92 4.2 34.6 1.0 O3' A:A47 4.5 49.4 1.0 N7 A:G48 4.5 55.8 1.0 OP1 A:C93 4.5 41.0 1.0 OP2 A:C94 4.6 50.7 1.0 O2' A:G95 4.6 42.3 1.0 O3' A:G91 4.6 40.9 1.0 C3' A:C92 4.6 28.7 1.0 O3' A:C92 4.6 27.0 1.0 OP2 A:G96 4.7 66.5 1.0 C8 A:G48 4.8 54.5 1.0 C5 A:C93 4.9 40.9 1.0 C6 A:C93 4.9 46.0 1.0

Barium binding site 3 out of 20 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba203 b:0.8 occ:1.00 OP1 A:C93 2.2 41.0 1.0 OP2 A:G48 2.2 54.0 1.0 O A:HOH306 2.8 48.8 1.0 P A:G48 3.3 52.3 1.0 P A:C93 3.5 34.6 1.0 OP1 A:G48 3.6 38.1 1.0 OP2 A:C93 3.9 44.8 1.0 O5' A:G48 4.2 48.7 1.0 C5' A:G48 4.2 38.2 1.0 O3' A:A47 4.4 49.4 1.0 O5' A:C93 4.5 39.4 1.0 O3' A:C92 4.5 27.0 1.0 C5' A:C93 4.6 38.9 1.0 O A:HOH309 4.7 77.0 1.0 O A:HOH322 4.7 55.9 1.0 C3' A:A47 4.9 53.7 1.0

Barium binding site 4 out of 20 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba204 b:0.4 occ:1.00 OP2 A:C77 2.4 65.8 1.0 O2 A:C49 2.5 68.6 1.0 O2P A:PRP217 2.7 61.5 1.0 O A:HOH303 3.1 54.6 1.0 C2 A:C49 3.3 54.4 1.0 P A:PRP217 3.3 56.4 1.0 N3 A:C49 3.3 55.2 1.0 O3P A:PRP217 3.4 50.0 1.0 O1P A:PRP217 3.7 60.6 1.0 P A:C77 3.7 65.6 1.0 OP2 A:C78 3.8 94.4 1.0 O5' A:C77 4.1 76.4 1.0 O2' A:A76 4.3 71.3 1.0 N1 A:G48 4.4 58.0 1.0 N1 A:C49 4.6 50.7 1.0 C2' A:A76 4.6 76.4 1.0 C4 A:C49 4.6 45.1 1.0 O3' A:A76 4.7 75.4 1.0 OP1 A:C77 4.7 57.5 1.0 O5 A:PRP217 4.8 45.8 1.0 N2 A:G48 4.9 49.9 1.0 O6 A:G48 5.0 40.7 1.0

Barium binding site 5 out of 20 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba205 b:0.8 occ:1.00 N7 A:G15 3.8 50.8 1.0 OP2 A:A14 3.9 50.4 1.0 O6 A:G16 4.1 55.0 1.0 O6 A:G15 4.1 46.2 1.0 N7 A:G16 4.1 43.7 1.0 C5 A:G15 4.6 46.1 1.0 C6 A:G15 4.7 44.5 1.0 C6 A:G16 4.8 55.3 1.0 C5 A:G16 4.8 45.6 1.0 C8 A:G15 4.8 53.4 1.0

Barium binding site 6 out of 20 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba206 b:0.5 occ:1.00 OP2 A:C45 3.1 46.8 1.0 O6 A:G46 3.2 58.0 1.0 N7 A:G46 3.2 50.0 1.0 C6 A:G46 3.8 47.0 1.0 C5 A:G46 3.9 47.2 1.0 OP2 A:C12 4.2 58.6 1.0 C8 A:G46 4.4 52.0 1.0 C5 A:C45 4.5 41.3 1.0 P A:C45 4.5 48.6 1.0 C6 A:C45 4.8 43.2 1.0

Barium binding site 7 out of 20 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba207 b:0.5 occ:1.00 O A:HOH305 3.1 54.8 1.0 OP1 A:C49 4.1 42.3 1.0 O6 A:G51 4.2 68.6 1.0 O4 A:U52 4.4 63.8 1.0 O6 A:G50 4.5 56.3 1.0 N7 A:G51 4.5 63.7 1.0 N7 A:G50 4.6 48.3 1.0 C5' A:A47 4.7 48.9 1.0 C6 A:G50 4.8 53.9 1.0 C5 A:G50 4.9 56.8 1.0 P A:C49 5.0 52.7 1.0 N6 A:A10 5.0 68.8 1.0

Barium binding site 8 out of 20 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba208 b:0.1 occ:1.00 O A:HOH308 3.0 53.5 1.0 O A:HOH313 3.1 41.9 1.0 N7 A:G83 3.6 47.8 1.0 O6 A:G84 3.9 56.5 1.0 O6 A:G83 4.1 47.4 1.0 N7 A:G84 4.2 43.8 1.0 C5 A:G83 4.4 54.8 1.0 OP1 A:A90 4.5 35.5 1.0 C8 A:G83 4.5 51.4 1.0 C6 A:G83 4.6 51.6 1.0 OP2 A:A90 4.7 36.5 1.0 C6 A:G84 4.7 51.3 1.0 C5 A:G84 4.8 49.9 1.0

Barium binding site 9 out of 20 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba209 b:0.2 occ:1.00 OP1 A:A103 2.6 0.1 1.0 OP1 A:G104 3.3 0.4 1.0 C8 A:G104 4.0 0.7 1.0 P A:A103 4.0 0.8 1.0 O4' A:G104 4.1 0.8 1.0 N7 A:G104 4.5 0.3 1.0 C4' A:A103 4.5 0.7 1.0 O5' A:A103 4.6 0.9 1.0 P A:G104 4.7 0.4 1.0 N9 A:G104 4.7 0.7 1.0 O3' A:U102 4.8 0.7 1.0 C5' A:G104 4.8 0.3 1.0 O4' A:A103 4.8 0.4 1.0 C1' A:G104 5.0 0.1 1.0

Barium binding site 10 out of 20 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba210 b:0.6 occ:1.00 BA A:BA211 1.7 70.3 1.0 O4 A:U36 2.7 47.7 1.0 O A:HOH323 3.2 59.0 1.0 O6 A:G35 3.5 80.9 1.0 C4 A:U36 3.7 44.7 1.0 O6 A:G23 4.0 63.0 1.0 N3 A:U36 4.1 46.7 1.0 N7 A:G35 4.2 78.0 1.0 C6 A:G35 4.3 67.6 1.0 O A:HOH317 4.4 56.4 1.0 O A:HOH315 4.5 48.6 1.0 C5 A:G35 4.6 68.2 1.0 C5 A:U36 5.0 44.2 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