Potassium in PDB 9ec4: Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Chelerythrine

The structure of Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Chelerythrine, PDB code: 9ec4 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 / 2.85
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	109.654, 69.27, 82.099, 90, 90, 90
R / Rfree (%)	22.9 / 26.4

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

Barium	(Ba)	3 atoms
Magnesium	(Mg)	14 atoms

The binding sites of Potassium atom in the Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Chelerythrine (pdb code 9ec4). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Chelerythrine, PDB code: 9ec4:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in the Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Chelerythrine


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 Chelerythrine within 5.0Å range: probe atom residue distance (Å) B Occ M:K103 b:83.0 occ:1.00 O2' M:A27 2.8 64.7 1.0 O M:HOH202 3.4 39.7 1.0 C2' M:A27 3.7 48.3 1.0 O6 M:G20 3.9 46.0 1.0 N7 M:G20 4.3 46.2 1.0 C3' M:A27 4.4 42.9 1.0 O6 M:G21 4.5 49.3 1.0 OP1 M:U29 4.7 38.8 1.0 C6 M:G20 4.7 50.2 1.0 O3' M:A27 4.8 46.2 1.0 N4 M:C30 4.8 62.7 1.0 C5 M:G20 4.9 49.9 1.0 N4 M:C19 4.9 44.9 1.0

Potassium binding site 2 out of 5 in the Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Chelerythrine


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 Chelerythrine within 5.0Å range: probe atom residue distance (Å) B Occ M:K104 b:69.9 occ:1.00 O4 M:U45 2.8 46.4 1.0 O6 M:G36 3.0 40.0 1.0 O6 M:G44 3.1 50.4 1.0 O4 M:U35 3.7 51.3 1.0 C4 M:U45 3.8 39.2 1.0 N4 M:C37 4.0 41.5 1.0 C6 M:G44 4.1 43.4 1.0 C6 M:G36 4.1 37.1 1.0 N3 M:U45 4.1 38.0 1.0 C4 M:U35 4.3 50.9 1.0 C5 M:U35 4.4 52.8 1.0 N7 M:G36 4.5 40.8 1.0 C5 M:G36 4.7 36.7 1.0 C5 M:G44 4.9 39.3 1.0 N1 M:G44 4.9 34.6 1.0

Potassium binding site 3 out of 5 in the Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Chelerythrine


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 Chelerythrine within 5.0Å range: probe atom residue distance (Å) B Occ M:K105 b:93.5 occ:1.00 O M:HOH207 2.9 51.6 1.0 N7 M:G24 3.0 55.9 1.0 O6 M:G24 3.3 44.7 1.0 C5 M:G24 3.8 48.4 1.0 C6 M:G24 3.9 50.5 1.0 C8 M:G24 4.1 50.7 1.0 O2' M:U23 4.7 46.7 1.0

Potassium binding site 4 out of 5 in the Structure of the Bacillus Subtilis Yjdf Riboswitch Aptamer Domain in Complex with Chelerythrine


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 Chelerythrine within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:99.6 occ:1.00 O2' A:A27 3.8 57.2 1.0 O6 A:G21 3.8 55.5 1.0 C2' A:A27 4.1 48.8 1.0 N7 A:G21 4.6 53.9 1.0 N7 A:G20 4.6 44.0 1.0 OP2 A:A27 4.6 43.6 1.0 O6 A:G20 4.7 49.5 1.0 O4 A:U22 4.7 59.8 1.0 C6 A:G21 4.7 54.8 1.0 C3' A:A27 4.8 49.4 1.0 C8 A:A27 4.9 51.3 1.0 O A:HOH237 5.0 43.4 1.0

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


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 Chelerythrine within 5.0Å range: probe atom residue distance (Å) B Occ A:K105 b:79.6 occ:1.00 O2B A:GDP1 3.0 107.6 1.0 N7 A:GDP1 3.1 54.1 1.0 O6 A:GDP1 3.4 46.5 1.0 O3B A:GDP1 3.5 126.0 1.0 OP2 M:U75 3.6 76.2 1.0 C5 A:GDP1 3.8 47.5 1.0 PB A:GDP1 3.8 148.9 1.0 C6 A:GDP1 4.1 44.2 1.0 C8 A:GDP1 4.1 61.1 1.0 O1B A:GDP1 4.6 133.1 1.0 N4 A:C80 4.7 50.5 1.0 N7 A:G2 4.7 50.5 1.0 O6 A:G2 4.8 46.5 1.0 P M:U75 4.8 67.0 1.0 N1 A:A81 4.8 55.0 1.0

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