Cobalt in PDB 2xnz: Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening

The structure of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening, PDB code: 2xnz 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)	66.08 / 1.59
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.165, 35.068, 41.798, 90.00, 90.06, 90.00
R / Rfree (%)	19.8 / 23.4

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

Potassium

(K)

6 atoms

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

Cobalt binding site 1 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine 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 Acetoguanamine Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1081 b:18.8 occ:1.00 CO A:NCO1081 0.0 18.8 1.0 N5 A:NCO1081 2.0 19.8 1.0 N3 A:NCO1081 2.0 21.8 1.0 N4 A:NCO1081 2.0 20.2 1.0 N6 A:NCO1081 2.0 21.8 1.0 N2 A:NCO1081 2.0 16.7 1.0 N1 A:NCO1081 2.0 19.3 1.0 O A:HOH2176 3.9 29.9 1.0 O A:HOH2037 3.9 21.1 1.0 O A:HOH2169 4.0 19.1 1.0 OP1 A:U67 4.1 12.6 1.0 O A:HOH2206 4.1 38.8 1.0 O A:HOH2039 4.3 26.9 1.0 O3' A:A66 4.5 14.1 1.0 P A:U67 4.9 12.1 1.0

Cobalt binding site 2 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine 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 Acetoguanamine Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1082 b:22.1 occ:1.00 CO A:NCO1082 0.0 22.1 1.0 N4 A:NCO1082 2.0 22.9 1.0 N1 A:NCO1082 2.0 24.4 1.0 N6 A:NCO1082 2.0 26.6 1.0 N3 A:NCO1082 2.0 23.7 1.0 N2 A:NCO1082 2.0 22.5 1.0 N5 A:NCO1082 2.0 22.5 1.0 O A:HOH2133 3.8 30.0 1.0 O A:HOH2207 3.9 30.4 1.0 O4 A:U69 4.0 17.3 1.0 O6 A:G56 4.1 19.0 1.0 O A:HOH2131 4.2 18.9 1.0 O A:HOH2137 4.2 27.0 1.0 O A:HOH2175 4.2 29.4 1.0 OP2 A:C39 4.5 17.3 1.0 OP1 A:C39 4.5 16.8 1.0 N7 A:G56 4.6 19.4 1.0 O6 A:G68 4.7 14.2 1.0 O A:HOH2087 5.0 35.2 1.0 C6 A:G56 5.0 20.0 1.0

Cobalt binding site 3 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine 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 Acetoguanamine Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1083 b:15.2 occ:1.00 CO A:NCO1083 0.0 15.2 1.0 N6 A:NCO1083 2.0 18.7 1.0 N1 A:NCO1083 2.0 17.3 1.0 N2 A:NCO1083 2.0 15.6 1.0 N4 A:NCO1083 2.0 17.4 1.0 N3 A:NCO1083 2.0 16.9 1.0 N5 A:NCO1083 2.0 13.8 1.0 OP2 A:A66 3.8 19.2 1.0 O A:HOH2050 3.8 19.9 1.0 O6 A:G32 4.0 16.1 1.0 O A:HOH2209 4.1 28.9 1.0 O A:HOH2208 4.1 22.1 1.0 O6 A:G31 4.1 13.5 1.0 O A:HOH2171 4.2 21.7 1.0 O A:HOH2170 4.2 16.0 1.0 O A:HOH2054 4.2 21.1 1.0 O A:HOH2052 4.2 17.8 1.0 O A:HOH2056 4.2 18.7 1.0 N7 A:G31 4.3 13.8 1.0 O A:HOH2167 4.8 37.6 1.0 C6 A:G31 4.9 14.0 1.0 O A:HOH2162 4.9 15.7 1.0 C5 A:G31 5.0 12.6 1.0 C6 A:G32 5.0 15.3 1.0

Cobalt binding site 4 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine 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 Acetoguanamine Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1084 b:34.8 occ:1.00 CO A:NCO1084 0.0 34.8 1.0 N3 A:NCO1084 2.0 34.1 1.0 N5 A:NCO1084 2.0 35.0 1.0 N4 A:NCO1084 2.0 35.1 1.0 N6 A:NCO1084 2.0 33.7 1.0 N2 A:NCO1084 2.0 31.3 1.0 N1 A:NCO1084 2.0 36.1 0.0 O A:HOH2103 4.2 29.3 1.0 OP1 A:C43 4.4 21.9 1.0

Cobalt binding site 5 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine 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 Acetoguanamine Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1085 b:23.9 occ:1.00 CO A:NCO1085 0.0 23.9 1.0 N4 A:NCO1085 2.0 24.0 1.0 N5 A:NCO1085 2.0 22.9 1.0 N1 A:NCO1085 2.0 24.4 1.0 N6 A:NCO1085 2.0 23.8 1.0 N2 A:NCO1085 2.0 23.9 1.0 N3 A:NCO1085 2.0 22.9 1.0 O A:HOH2213 3.8 35.2 1.0 O A:HOH2212 3.9 30.3 1.0 O A:HOH2210 4.0 22.6 1.0 O2' A:G57 4.1 14.9 1.0 O A:HOH2143 4.2 28.9 1.0 O3' A:G57 4.8 17.4 1.0

Cobalt binding site 6 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine 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 Acetoguanamine Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1086 b:38.1 occ:1.00 CO A:NCO1086 0.0 38.1 1.0 N3 A:NCO1086 2.0 35.9 0.0 N2 A:NCO1086 2.0 38.2 1.0 N1 A:NCO1086 2.0 37.5 1.0 N4 A:NCO1086 2.0 37.7 1.0 N6 A:NCO1086 2.0 37.7 1.0 N5 A:NCO1086 2.0 35.9 0.0 O A:HOH2195 3.7 30.2 1.0 OP2 A:C71 4.0 16.3 1.0 O A:HOH2185 4.1 27.6 1.0 O A:HOH2215 4.1 40.8 1.0 OP1 A:A24 4.1 24.2 1.0 O A:HOH2214 4.4 33.7 1.0 O A:HOH2193 4.6 19.6 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