Cobalt in PDB 2xo1: Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to N6-Methyladenine

The structure of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to N6-Methyladenine, PDB code: 2xo1 was solved by P.Daldrop, F.E.Reyes, D.A.Robinson, C.M.Hammond, D.M.J.Lilley, R.T.Batey, R.Brenk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.38 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.762, 35.180, 41.736, 90.00, 90.51, 90.00
R / Rfree (%)	19.5 / 21.1

The structure of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to N6-Methyladenine also contains other interesting chemical elements:

Potassium

(K)

3 atoms

The binding sites of Cobalt atom in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to N6-Methyladenine (pdb code 2xo1). 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 N6-Methyladenine, PDB code: 2xo1:
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 N6-Methyladenine


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 N6-Methyladenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1082 b:17.6 occ:1.00 CO A:NCO1082 0.0 17.6 1.0 N6 A:NCO1082 2.0 21.0 1.0 N4 A:NCO1082 2.0 19.5 1.0 N3 A:NCO1082 2.0 17.3 1.0 N1 A:NCO1082 2.0 19.1 1.0 N2 A:NCO1082 2.0 18.0 1.0 N5 A:NCO1082 2.0 16.9 1.0 O A:HOH2216 3.9 38.4 1.0 OP1 A:U30 4.4 14.8 1.0

Cobalt binding site 2 out of 7 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to N6-Methyladenine


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 N6-Methyladenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1083 b:17.9 occ:1.00 CO A:NCO1083 0.0 17.9 1.0 N5 A:NCO1083 2.0 20.3 1.0 N2 A:NCO1083 2.0 20.3 1.0 N3 A:NCO1083 2.0 20.0 1.0 N6 A:NCO1083 2.0 19.7 1.0 N1 A:NCO1083 2.0 22.2 1.0 N4 A:NCO1083 2.0 21.0 1.0 O A:HOH2218 3.8 31.6 1.0 O A:HOH2138 3.9 25.6 1.0 O4 A:U69 4.0 14.0 1.0 O6 A:G56 4.1 15.6 1.0 O A:HOH2217 4.1 32.2 1.0 O A:HOH2184 4.1 22.8 1.0 O A:HOH2135 4.2 28.3 1.0 O A:HOH2132 4.2 17.6 1.0 O A:HOH2145 4.3 23.8 1.0 OP2 A:C39 4.4 15.2 1.0 OP1 A:C39 4.4 14.6 1.0 N7 A:G56 4.6 13.8 1.0 O6 A:G68 4.8 13.4 1.0 P A:C39 4.9 14.4 1.0 C6 A:G56 5.0 14.5 1.0

Cobalt binding site 3 out of 7 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to N6-Methyladenine


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 N6-Methyladenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1084 b:14.1 occ:1.00 CO A:NCO1084 0.0 14.1 1.0 N5 A:NCO1084 2.0 17.9 1.0 N3 A:NCO1084 2.0 17.1 1.0 N2 A:NCO1084 2.0 16.5 1.0 N6 A:NCO1084 2.0 16.9 1.0 N1 A:NCO1084 2.0 15.8 1.0 N4 A:NCO1084 2.0 13.6 1.0 O A:HOH2052 3.8 22.5 1.0 OP2 A:A66 3.8 19.7 1.0 O6 A:G32 4.0 13.9 1.0 O6 A:G31 4.1 11.9 1.0 O A:HOH2219 4.1 35.3 1.0 O A:HOH2180 4.2 15.7 1.0 O A:HOH2179 4.2 21.5 1.0 O A:HOH2058 4.2 19.8 1.0 O A:HOH2055 4.3 17.2 1.0 O A:HOH2054 4.3 16.2 1.0 N7 A:G31 4.4 11.6 1.0 O A:HOH2176 4.8 33.3 1.0 C6 A:G31 4.9 12.5 1.0 O A:HOH2174 4.9 18.4 1.0

Cobalt binding site 4 out of 7 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to N6-Methyladenine


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 N6-Methyladenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1085 b:19.4 occ:1.00 CO A:NCO1085 0.0 19.4 1.0 N4 A:NCO1085 2.0 21.1 1.0 N6 A:NCO1085 2.0 21.2 1.0 N3 A:NCO1085 2.0 17.7 1.0 N2 A:NCO1085 2.0 21.5 0.0 N5 A:NCO1085 2.0 21.0 1.0 N1 A:NCO1085 2.0 19.2 1.0 O A:HOH2221 3.9 25.4 1.0 O A:HOH2222 3.9 33.0 1.0 O2' A:G57 4.1 15.5 1.0 O3' A:G57 4.8 15.9 1.0

Cobalt binding site 5 out of 7 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to N6-Methyladenine


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 N6-Methyladenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1086 b:39.4 occ:1.00 CO A:NCO1086 0.0 39.4 1.0 N5 A:NCO1086 2.0 40.7 0.0 N2 A:NCO1086 2.0 40.9 0.0 N4 A:NCO1086 2.0 35.3 1.0 N3 A:NCO1086 2.0 35.9 1.0 N1 A:NCO1086 2.0 40.6 0.0 N6 A:NCO1086 2.0 40.9 0.0 OP1 A:G72 4.2 12.4 1.0 OP2 A:A73 4.9 22.3 1.0

Cobalt binding site 6 out of 7 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to N6-Methyladenine


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 N6-Methyladenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1087 b:36.7 occ:1.00 CO A:NCO1087 0.0 36.7 1.0 N1 A:NCO1087 2.0 37.9 0.0 N6 A:NCO1087 2.0 38.2 0.0 N5 A:NCO1087 2.0 35.9 1.0 N4 A:NCO1087 2.0 35.7 1.0 N3 A:NCO1087 2.0 36.0 1.0 N2 A:NCO1087 2.0 38.3 0.0 OP2 A:C71 3.9 13.0 1.0 O A:HOH2223 4.2 34.6 1.0 OP1 A:A24 4.2 22.0 1.0 O A:HOH2205 4.4 26.5 1.0 O A:HOH2203 4.7 19.0 1.0

Cobalt binding site 7 out of 7 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to N6-Methyladenine


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 N6-Methyladenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1088 b:30.2 occ:1.00 CO A:NCO1088 0.0 30.2 1.0 N1 A:NCO1088 2.0 31.9 0.0 N3 A:NCO1088 2.0 30.7 1.0 N4 A:NCO1088 2.0 30.8 1.0 N6 A:NCO1088 2.0 30.8 1.0 N5 A:NCO1088 2.0 29.6 1.0 N2 A:NCO1088 2.0 30.7 0.0 O A:HOH2225 3.9 33.5 1.0 O A:HOH2149 3.9 22.5 1.0 OP2 A:G37 4.0 13.4 1.0 O A:HOH2156 4.0 22.4 1.0 O6 A:G38 4.1 11.4 1.0 O A:HOH2226 4.2 27.4 1.0 N7 A:G38 4.3 11.7 1.0 O A:HOH2224 4.3 32.4 1.0 N7 A:G37 4.3 11.7 1.0 O A:HOH2147 4.6 26.1 1.0 O A:HOH2150 4.8 32.9 1.0 C6 A:G38 4.9 11.9 1.0 C8 A:G37 4.9 11.6 1.0 C5 A:G38 5.0 11.9 1.0 O A:HOH2075 5.0 30.0 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