Cobalt in PDB 2xnw: Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening

The structure of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening, PDB code: 2xnw was solved by P.Daldrop, F.E.Reyes, D.A.Robinson, C.M.Hammond, D.M.J.Lilley, R.Brenk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.90 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.895, 35.380, 42.197, 90.00, 92.19, 90.00
R / Rfree (%)	21.3 / 24.4

The structure of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Cobalt atom in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening (pdb code 2xnw). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening, PDB code: 2xnw:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1081 b:18.7 occ:1.00 CO A:NCO1081 0.0 18.7 1.0 N5 A:NCO1081 2.0 16.8 1.0 N3 A:NCO1081 2.0 18.9 1.0 N2 A:NCO1081 2.0 18.8 1.0 N6 A:NCO1081 2.0 20.9 1.0 N4 A:NCO1081 2.0 20.1 1.0 N1 A:NCO1081 2.0 21.3 1.0 O A:HOH2312 3.7 35.0 1.0 O A:HOH2309 3.8 28.5 1.0 O A:HOH2311 3.9 31.9 1.0 O A:HOH2263 3.9 26.7 1.0 O A:HOH2313 4.0 39.8 1.0 O A:HOH2085 4.1 24.2 1.0 OP1 A:U67 4.1 13.5 1.0 O3' A:A66 4.3 13.1 1.0 O2' A:A66 4.6 16.3 1.0 P A:U67 4.9 13.5 1.0

Cobalt binding site 2 out of 7 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1082 b:15.0 occ:1.00 CO A:NCO1082 0.0 15.0 1.0 N3 A:NCO1082 2.0 18.7 1.0 N6 A:NCO1082 2.0 20.2 1.0 N4 A:NCO1082 2.0 17.3 1.0 N1 A:NCO1082 2.0 16.8 1.0 N5 A:NCO1082 2.0 17.3 1.0 N2 A:NCO1082 2.0 19.5 1.0 O A:HOH2202 3.9 17.2 1.0 O A:HOH2315 3.9 17.9 1.0 O A:HOH2196 4.0 23.2 1.0 O A:HOH2209 4.0 20.2 1.0 O A:HOH2314 4.1 16.3 1.0 O6 A:G56 4.1 13.2 1.0 O4 A:U69 4.1 12.7 1.0 O A:HOH2199 4.1 13.5 1.0 O A:HOH2316 4.2 20.0 1.0 OP2 A:C39 4.3 12.7 1.0 OP1 A:C39 4.4 14.3 1.0 N7 A:G56 4.6 14.1 1.0 O6 A:G68 4.9 12.2 1.0 P A:C39 4.9 13.6 1.0 O A:HOH2203 4.9 21.6 1.0 C6 A:G56 4.9 12.0 1.0

Cobalt binding site 3 out of 7 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1083 b:14.4 occ:1.00 CO A:NCO1083 0.0 14.4 1.0 N6 A:NCO1083 2.0 17.0 1.0 N4 A:NCO1083 2.0 14.2 1.0 N2 A:NCO1083 2.0 15.8 1.0 N3 A:NCO1083 2.0 13.6 1.0 N5 A:NCO1083 2.0 13.7 1.0 N1 A:NCO1083 2.0 16.0 1.0 O A:HOH2092 3.8 14.5 1.0 OP2 A:A66 3.8 18.4 1.0 O A:HOH2317 3.9 17.9 1.0 O6 A:G32 4.0 14.1 1.0 O A:HOH2094 4.1 17.1 1.0 O A:HOH2101 4.2 14.0 1.0 O6 A:G31 4.2 11.5 1.0 O A:HOH2328 4.2 13.5 1.0 O A:HOH2318 4.3 25.4 1.0 O A:HOH2257 4.3 20.6 1.0 N7 A:G31 4.3 12.6 1.0 O A:HOH2093 4.4 17.4 1.0 C6 A:G31 4.9 12.7 1.0 C5 A:G31 4.9 12.4 1.0

Cobalt binding site 4 out of 7 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1084 b:41.7 occ:1.00 CO A:NCO1084 0.0 41.7 1.0 N1 A:NCO1084 1.9 40.8 0.0 N4 A:NCO1084 2.0 40.7 0.0 N3 A:NCO1084 2.0 35.1 1.0 N6 A:NCO1084 2.0 39.4 1.0 N5 A:NCO1084 2.0 39.7 1.0 N2 A:NCO1084 2.0 40.7 0.0 O A:HOH2319 4.1 33.2 1.0 O4 A:U47 4.1 27.8 1.0 OP2 A:A45 4.2 28.4 1.0 O6 A:G46 4.2 19.1 1.0 N7 A:G46 4.3 22.0 1.0 O A:HOH2167 4.7 36.0 1.0 O A:HOH2185 4.8 29.4 1.0 C6 A:G46 5.0 21.1 1.0

Cobalt binding site 5 out of 7 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1085 b:41.1 occ:1.00 CO A:NCO1085 0.0 41.1 1.0 N3 A:NCO1085 1.9 41.9 0.0 N1 A:NCO1085 1.9 42.4 0.0 N6 A:NCO1085 2.0 38.4 1.0 N2 A:NCO1085 2.0 39.3 1.0 N5 A:NCO1085 2.0 40.2 1.0 N4 A:NCO1085 2.0 42.5 0.0 O A:HOH2320 3.7 32.8 1.0 OP1 A:G72 4.2 14.6 1.0 OP2 A:A73 4.5 22.5 1.0 O A:HOH2286 5.0 28.9 1.0

Cobalt binding site 6 out of 7 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1086 b:18.8 occ:1.00 CO A:NCO1086 0.0 18.8 1.0 N4 A:NCO1086 2.0 20.1 1.0 N6 A:NCO1086 2.0 20.1 1.0 N1 A:NCO1086 2.0 20.2 1.0 N2 A:NCO1086 2.0 20.6 1.0 N5 A:NCO1086 2.0 21.3 1.0 N3 A:NCO1086 2.0 21.2 1.0 O A:HOH2220 3.9 22.4 1.0 O A:HOH2222 4.0 17.3 1.0 O A:HOH2323 4.0 26.9 1.0 O A:HOH2322 4.1 19.4 1.0 OP2 A:G37 4.1 12.2 1.0 O6 A:G38 4.1 10.4 1.0 O A:HOH2132 4.2 17.5 1.0 N7 A:G38 4.3 10.2 1.0 N7 A:G37 4.3 11.3 1.0 O A:HOH2324 4.4 29.4 1.0 O A:HOH2215 4.9 28.3 1.0 C6 A:G38 4.9 10.3 1.0 C8 A:G37 5.0 10.3 1.0 C5 A:G38 5.0 11.6 1.0

Cobalt binding site 7 out of 7 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to A Triazolo- Triazole-Diamine Ligand Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1087 b:22.8 occ:1.00 CO A:NCO1087 0.0 22.8 1.0 N6 A:NCO1087 1.9 21.9 1.0 N1 A:NCO1087 2.0 22.1 1.0 N4 A:NCO1087 2.0 20.6 1.0 N2 A:NCO1087 2.0 22.4 0.0 N5 A:NCO1087 2.0 17.6 1.0 N3 A:NCO1087 2.0 22.9 1.0 O A:HOH2326 3.9 28.4 1.0 O A:HOH2325 3.9 28.7 1.0 O2' A:G57 4.2 15.6 1.0 O A:HOH2218 4.6 31.8 1.0 O3' A:G57 4.6 14.1 1.0 O A:HOH2327 4.9 23.2 1.0

P.Daldrop, F.E.Reyes, D.A.Robinson, C.M.Hammond, D.M.Lilley, R.T.Batey, R.Brenk. Novel Ligands For A Purine Riboswitch Discovered By Rna-Ligand Docking. Chem. Biol. V. 18 324 2011.
ISSN: ISSN 1879-1301
PubMed: 21439477
DOI: 10.1016/J.CHEMBIOL.2010.12.020