Potassium in PDB 9ebv: Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome

The structure of Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome, PDB code: 9ebv was solved by R.T.Batey, S.F.Spradlin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.79 / 2.52
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	110.718, 68.927, 82.654, 90, 90, 90
R / Rfree (%)	21.6 / 24.6

The structure of Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome also contains other interesting chemical elements:

Magnesium

(Mg)

10 atoms

The binding sites of Potassium atom in the Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome (pdb code 9ebv). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome, PDB code: 9ebv:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in the Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome within 5.0Å range: probe atom residue distance (Å) B Occ A:K105 b:67.9 occ:1.00 O6 A:G33 3.1 51.5 1.0 O4 A:U18 3.1 44.1 1.0 O4 A:U17 3.2 43.8 1.0 O6 A:G32 3.3 51.4 1.0 N6 A:A34 3.8 43.1 1.0 C6 A:G33 4.1 48.6 1.0 C4 A:U18 4.1 47.4 1.0 C6 A:G32 4.2 50.8 1.0 C4 A:U17 4.2 49.5 1.0 N7 A:G33 4.3 52.5 1.0 C6 A:A34 4.4 53.4 1.0 N3 A:U18 4.4 51.2 1.0 C5 A:G33 4.6 52.0 1.0 N3 A:U17 4.8 48.7 1.0 C5 A:G32 4.8 53.4 1.0 N4 A:C19 4.8 44.3 1.0 N7 A:G32 4.9 43.4 1.0 N1 A:A34 4.9 53.1 1.0

Potassium binding site 2 out of 7 in the Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome within 5.0Å range: probe atom residue distance (Å) B Occ A:K106 b:100.0 occ:1.00 OP1 A:G25 3.5 51.1 1.0 OP2 A:G25 3.9 49.7 1.0 OP1 A:U22 3.9 62.6 1.0 OP2 A:U23 3.9 55.6 1.0 C5 A:U23 4.1 48.4 1.0 P A:G25 4.1 50.3 1.0 OP2 A:U22 4.3 55.1 1.0 P A:U22 4.5 51.7 1.0 C6 A:U23 4.6 48.7 1.0 C4 A:U23 4.6 49.3 1.0 O4 A:U23 4.8 54.6 1.0 O3' A:G24 4.9 51.0 1.0 O5' A:U22 5.0 48.0 1.0

Potassium binding site 3 out of 7 in the Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome within 5.0Å range: probe atom residue distance (Å) B Occ A:K107 b:59.1 occ:1.00 O6 A:G44 2.9 49.0 1.0 O4 A:U45 2.9 48.8 1.0 O6 A:G36 3.1 51.5 1.0 O4 A:U35 3.2 51.3 1.0 C4 A:U45 3.8 41.4 1.0 N3 A:U45 3.8 41.5 1.0 C4 A:U35 3.8 49.5 1.0 C6 A:G44 4.0 47.2 1.0 N4 A:C37 4.0 46.9 1.0 C6 A:G36 4.2 46.2 1.0 C5 A:U35 4.2 45.4 1.0 N7 A:G36 4.5 48.8 1.0 N7 A:G44 4.7 42.1 1.0 C5 A:G44 4.7 43.1 1.0 C5 A:G36 4.7 47.9 1.0 N3 A:U35 4.8 49.8 1.0

Potassium binding site 4 out of 7 in the Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome within 5.0Å range: probe atom residue distance (Å) B Occ A:K108 b:85.3 occ:1.00 O6 A:G70 2.6 61.1 1.0 O4 A:U69 3.1 64.2 1.0 C6 A:G70 3.7 51.3 1.0 C4 A:U69 3.9 70.3 1.0 O4 A:U71 4.1 57.4 1.0 N7 A:G70 4.2 50.6 1.0 O A:HOH219 4.3 42.6 1.0 N4 A:C52 4.3 60.2 1.0 C5 A:G70 4.3 52.1 1.0 N4 A:C53 4.3 57.1 1.0 OP2 A:A50 4.4 71.8 1.0 C5 A:U69 4.5 63.7 1.0 N3 A:U69 4.6 58.5 1.0 N1 A:G70 4.9 48.8 1.0

Potassium binding site 5 out of 7 in the Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome within 5.0Å range: probe atom residue distance (Å) B Occ M:K107 b:104.2 occ:1.00 OP1 M:G25 3.5 59.6 1.0 OP2 M:G25 3.5 59.7 1.0 OP2 M:U23 3.8 66.3 1.0 C5 M:U23 3.9 64.5 1.0 P M:G25 4.0 61.9 1.0 OP1 M:U22 4.1 71.0 1.0 C6 M:U23 4.4 57.4 1.0 C4 M:U23 4.5 61.8 1.0 OP2 M:G24 4.6 56.6 1.0 OP2 M:U22 4.6 65.6 1.0 O4 M:U23 4.7 67.2 1.0 P M:U22 4.8 66.8 1.0 O3' M:G24 4.9 69.4 1.0 O5' M:U23 4.9 59.2 1.0 P M:U23 5.0 67.5 1.0

Potassium binding site 6 out of 7 in the Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome within 5.0Å range: probe atom residue distance (Å) B Occ M:K108 b:81.8 occ:1.00 O2' M:A27 2.9 67.0 1.0 C2' M:A27 3.8 53.6 1.0 O6 M:G21 4.1 48.0 1.0 O6 M:G20 4.3 53.1 1.0 N7 M:G20 4.4 59.0 1.0 C3' M:A27 4.5 53.5 1.0 O3' M:A27 4.9 54.7 1.0 C6 M:G20 5.0 57.1 1.0 OP1 M:U29 5.0 44.3 1.0

Potassium binding site 7 out of 7 in the Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome within 5.0Å range: probe atom residue distance (Å) B Occ M:K109 b:82.8 occ:1.00 O6 M:G32 3.0 64.3 1.0 O6 M:G33 3.2 54.1 1.0 O4 M:U18 3.3 54.4 1.0 C6 M:G32 4.0 62.8 1.0 N6 M:A34 4.0 47.7 1.0 N4 M:C19 4.1 52.7 1.0 C6 M:G33 4.2 59.4 1.0 N7 M:G33 4.3 58.3 1.0 C4 M:U18 4.3 55.5 1.0 O4 M:U17 4.4 52.9 1.0 N3 M:U18 4.5 50.9 1.0 C5 M:G33 4.7 58.2 1.0 C5 M:G32 4.7 63.5 1.0 N1 M:G32 4.8 56.8 1.0 N7 M:G32 4.8 57.9 1.0 C6 M:A34 4.9 54.1 1.0

R.T.Batey, S.F.Spradlin. Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Lumichrome To Be Published.