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Cobalt in PDB 2xo0: Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to 24-Diamino-1,3,5- Triazine Identified By Virtual Screening

Protein crystallography data

The structure of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to 24-Diamino-1,3,5- Triazine Identified By Virtual Screening, PDB code: 2xo0 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) 65.46 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 130.923, 34.940, 42.074, 90.00, 90.11, 90.00
R / Rfree (%) 21.6 / 27.1

Other elements in 2xo0:

The structure of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to 24-Diamino-1,3,5- Triazine Identified By Virtual Screening also contains other interesting chemical elements:

Potassium (K) 5 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to 24-Diamino-1,3,5- Triazine Identified By Virtual Screening (pdb code 2xo0). 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 24-Diamino-1,3,5- Triazine Identified By Virtual Screening, PDB code: 2xo0:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in 2xo0

Go back to Cobalt Binding Sites List in 2xo0
Cobalt binding site 1 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to 24-Diamino-1,3,5- Triazine 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 24-Diamino-1,3,5- Triazine Identified By Virtual Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co103

b:18.2
occ:1.00
 CO A:NCO103 0.0 18.2 1.0
N3 A:NCO103 1.9 15.7 1.0
N5 A:NCO103 1.9 14.6 1.0
N4 A:NCO103 2.0 17.8 1.0
N6 A:NCO103 2.0 20.4 1.0
N2 A:NCO103 2.0 15.4 1.0
N1 A:NCO103 2.0 17.6 1.0
O A:HOH291 4.0 34.4 1.0
O A:HOH255 4.0 26.0 1.0
O A:HOH305 4.0 28.8 1.0
O A:HOH329 4.1 37.4 1.0
OP1 A:U67 4.1 13.7 1.0
OP1 A:C28 4.1 19.3 1.0
O3' A:A66 4.3 15.3 1.0
OP2 A:C28 4.5 30.8 1.0
P A:U67 4.8 15.1 1.0
P A:C28 4.8 26.2 1.0
O A:HOH205 4.8 25.4 1.0
O2' A:A66 4.9 19.3 1.0
OP1 A:G27 4.9 32.2 1.0

Cobalt binding site 2 out of 6 in 2xo0

Go back to Cobalt Binding Sites List in 2xo0
Cobalt binding site 2 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to 24-Diamino-1,3,5- Triazine 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 24-Diamino-1,3,5- Triazine Identified By Virtual Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co104

b:22.6
occ:1.00
 CO A:NCO104 0.0 22.6 1.0
N4 A:NCO104 2.0 23.1 1.0
N6 A:NCO104 2.0 24.5 1.0
N3 A:NCO104 2.0 23.4 1.0
N1 A:NCO104 2.0 22.7 1.0
N5 A:NCO104 2.0 22.0 1.0
N2 A:NCO104 2.0 19.9 1.0
O A:HOH313 3.8 26.9 1.0
O4 A:U69 3.9 19.1 1.0
O6 A:G56 4.1 21.8 1.0
O A:HOH227 4.2 36.6 1.0
O A:HOH293 4.2 26.4 1.0
OP1 A:C39 4.3 19.3 1.0
O A:HOH208 4.4 20.3 1.0
OP2 A:C39 4.4 20.3 1.0
N7 A:G56 4.5 22.9 1.0
O A:HOH221 4.7 30.1 1.0
O6 A:G68 4.8 17.4 1.0
P A:C39 4.9 19.4 1.0
C6 A:G56 4.9 21.7 1.0

Cobalt binding site 3 out of 6 in 2xo0

Go back to Cobalt Binding Sites List in 2xo0
Cobalt binding site 3 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to 24-Diamino-1,3,5- Triazine 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 24-Diamino-1,3,5- Triazine Identified By Virtual Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co105

b:18.5
occ:1.00
 CO A:NCO105 0.0 18.5 1.0
N6 A:NCO105 2.0 23.2 1.0
N4 A:NCO105 2.0 22.0 1.0
N1 A:NCO105 2.0 22.7 1.0
N2 A:NCO105 2.0 21.2 1.0
N5 A:NCO105 2.0 17.7 1.0
N3 A:NCO105 2.0 19.3 1.0
OP2 A:A66 3.8 20.6 1.0
O A:HOH237 3.9 20.9 1.0
O6 A:G32 4.0 20.1 1.0
O A:HOH339 4.0 24.2 1.0
O6 A:G31 4.1 12.9 1.0
O A:HOH292 4.2 23.7 1.0
O A:HOH306 4.2 15.2 1.0
O A:HOH288 4.3 19.1 1.0
O A:HOH263 4.3 23.0 1.0
O A:HOH235 4.4 25.5 1.0
N7 A:G31 4.4 16.4 1.0
C6 A:G31 4.9 16.1 1.0
O A:HOH228 5.0 20.1 1.0

Cobalt binding site 4 out of 6 in 2xo0

Go back to Cobalt Binding Sites List in 2xo0
Cobalt binding site 4 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to 24-Diamino-1,3,5- Triazine 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 24-Diamino-1,3,5- Triazine Identified By Virtual Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co106

b:44.5
occ:1.00
 CO A:NCO106 0.0 44.5 1.0
N3 A:NCO106 1.9 46.9 0.0
N4 A:NCO106 2.0 43.7 1.0
N1 A:NCO106 2.0 45.0 0.0
N6 A:NCO106 2.0 44.6 1.0
N5 A:NCO106 2.0 41.7 0.0
N2 A:NCO106 2.0 45.5 0.0
OP2 A:G37 3.9 16.4 1.0
O A:HOH242 4.1 34.1 1.0
O A:HOH284 4.1 28.2 1.0
O6 A:G38 4.2 16.1 1.0
O A:HOH278 4.3 28.3 1.0
N7 A:G38 4.4 17.6 1.0
N7 A:G37 4.4 17.3 1.0
O A:HOH254 4.8 27.7 1.0

Cobalt binding site 5 out of 6 in 2xo0

Go back to Cobalt Binding Sites List in 2xo0
Cobalt binding site 5 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to 24-Diamino-1,3,5- Triazine 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 24-Diamino-1,3,5- Triazine Identified By Virtual Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co107

b:40.9
occ:1.00
 CO A:NCO107 0.0 40.9 1.0
N5 A:NCO107 2.0 47.5 0.0
N1 A:NCO107 2.0 41.5 0.0
N6 A:NCO107 2.0 42.0 0.0
N4 A:NCO107 2.0 39.6 1.0
N2 A:NCO107 2.0 41.8 0.0
N3 A:NCO107 2.0 47.8 0.0
O A:HOH314 3.8 27.8 1.0
OP2 A:C71 4.0 20.8 1.0
OP1 A:A24 4.2 33.2 1.0
O A:HOH332 4.2 21.3 1.0
O A:HOH240 4.3 25.2 1.0

Cobalt binding site 6 out of 6 in 2xo0

Go back to Cobalt Binding Sites List in 2xo0
Cobalt binding site 6 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to 24-Diamino-1,3,5- Triazine 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 24-Diamino-1,3,5- Triazine Identified By Virtual Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co111

b:39.0
occ:1.00
 CO A:NCO111 0.0 39.0 1.0
N3 A:NCO111 2.0 44.3 0.0
N4 A:NCO111 2.0 44.0 0.0
N2 A:NCO111 2.0 43.1 0.0
N6 A:NCO111 2.0 38.3 1.0
N5 A:NCO111 2.0 37.9 1.0
N1 A:NCO111 2.0 39.0 1.0
O A:HOH244 3.7 30.4 1.0
O A:HOH318 4.8 29.6 1.0
O A:HOH337 4.8 41.6 1.0
O A:HOH319 4.8 34.1 1.0

Reference:

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
Page generated: Tue Jul 30 15:36:05 2024

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