Cobalt in PDB 4fej: Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine

The structure of Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine, PDB code: 4fej was solved by C.D.Stoddard, J.J.Trausch, J.Widmann, J.Marcano, R.Knight, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.694, 35.230, 41.895, 90.00, 90.60, 90.00
R / Rfree (%)	18.5 / 23

The binding sites of Cobalt atom in the Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine (pdb code 4fej). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine, PDB code: 4fej:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in the Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co104 b:16.3 occ:1.00 CO B:NCO104 0.0 16.3 1.0 N1 B:NCO104 1.9 19.6 1.0 N2 B:NCO104 2.0 20.3 1.0 N6 B:NCO104 2.0 17.5 1.0 N3 B:NCO104 2.0 16.4 1.0 N4 B:NCO104 2.0 19.0 1.0 N5 B:NCO104 2.0 16.1 1.0 O B:HOH334 3.8 38.0 1.0 O B:HOH269 3.9 21.0 1.0 O B:HOH405 4.0 37.1 1.0 O B:HOH250 4.0 25.5 1.0 O B:HOH310 4.1 30.1 1.0 OP1 B:U67 4.2 12.2 1.0 O3' B:A66 4.4 12.7 1.0 O B:HOH365 4.5 25.9 1.0 O B:HOH366 4.7 34.9 1.0 P B:U67 5.0 10.6 1.0

Cobalt binding site 2 out of 7 in the Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co105 b:13.8 occ:1.00 CO B:NCO105 0.0 13.8 1.0 N3 B:NCO105 2.0 15.2 1.0 N5 B:NCO105 2.0 15.9 1.0 N6 B:NCO105 2.0 15.6 1.0 N2 B:NCO105 2.0 16.0 1.0 N1 B:NCO105 2.0 15.1 1.0 N4 B:NCO105 2.0 13.8 1.0 OP2 B:A66 3.9 19.1 1.0 O6 B:G32 4.0 11.7 1.0 O B:HOH217 4.0 17.3 1.0 O6 B:G31 4.1 11.4 1.0 O B:HOH412 4.1 28.3 1.0 O B:HOH239 4.2 20.1 1.0 O B:HOH214 4.2 15.7 1.0 O B:HOH253 4.2 21.7 1.0 O B:HOH213 4.2 17.5 1.0 O B:HOH238 4.2 16.5 1.0 O B:HOH226 4.3 18.9 1.0 N7 B:G31 4.4 10.8 1.0 C6 B:G31 4.9 11.6 1.0 O4 B:U30 5.0 12.0 1.0 O B:HOH202 5.0 14.5 1.0

Cobalt binding site 3 out of 7 in the Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co106 b:24.0 occ:1.00 CO B:NCO106 0.0 24.0 1.0 N3 B:NCO106 2.0 24.4 1.0 N4 B:NCO106 2.0 23.9 1.0 N2 B:NCO106 2.0 24.2 1.0 N6 B:NCO106 2.0 22.4 1.0 N5 B:NCO106 2.0 23.1 1.0 N1 B:NCO106 2.0 23.6 1.0 O B:HOH459 3.6 44.0 1.0 O B:HOH279 3.7 29.3 1.0 O B:HOH308 3.9 25.8 1.0 OP1 B:G38 3.9 13.9 1.0 OP1 B:G56 4.0 22.0 1.0 O B:HOH270 4.1 23.6 1.0 O B:HOH299 4.1 23.6 1.0 O B:HOH314 4.9 34.1 1.0 P B:G38 4.9 11.3 1.0 OP2 B:G56 5.0 20.1 1.0 OP2 B:G38 5.0 14.2 1.0 O B:HOH307 5.0 32.5 1.0 P B:G56 5.0 19.7 1.0

Cobalt binding site 4 out of 7 in the Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co107 b:36.7 occ:1.00 CO B:NCO107 0.0 36.7 1.0 N5 B:NCO107 2.0 37.2 1.0 N6 B:NCO107 2.0 36.5 1.0 N1 B:NCO107 2.0 36.5 1.0 N4 B:NCO107 2.0 37.2 1.0 N2 B:NCO107 2.0 36.4 1.0 N3 B:NCO107 2.0 36.5 1.0 O B:HOH488 3.8 30.0 1.0 O B:HOH433 3.8 41.1 1.0 OP2 B:G37 4.0 13.9 1.0 O B:HOH577 4.1 42.1 1.0 O B:HOH344 4.2 25.5 1.0 O6 B:G38 4.2 11.1 1.0 N7 B:G38 4.3 13.3 1.0 O B:HOH499 4.4 41.1 1.0 N7 B:G37 4.5 11.8 1.0 O B:HOH265 4.5 20.0 1.0 O B:HOH519 4.7 47.6 1.0 O B:HOH449 4.7 27.3 1.0 C8 B:G37 5.0 11.2 1.0

Cobalt binding site 5 out of 7 in the Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co108 b:16.8 occ:1.00 CO B:NCO108 0.0 16.8 1.0 N4 B:NCO108 2.0 22.4 1.0 N6 B:NCO108 2.0 19.3 1.0 N3 B:NCO108 2.0 20.6 1.0 N5 B:NCO108 2.0 19.6 1.0 N1 B:NCO108 2.0 17.4 1.0 N2 B:NCO108 2.0 19.5 1.0 O B:HOH301 3.8 22.4 1.0 O B:HOH386 3.9 35.2 1.0 O4 B:U69 4.0 12.0 1.0 O B:HOH347 4.0 27.0 1.0 O B:HOH257 4.0 20.9 1.0 O B:HOH321 4.1 47.0 1.0 O6 B:G56 4.1 15.1 1.0 O B:HOH385 4.3 16.1 1.0 O B:HOH356 4.3 26.4 1.0 O B:HOH212 4.4 69.3 1.0 OP2 B:C39 4.5 14.7 1.0 OP1 B:C39 4.5 13.3 1.0 N7 B:G56 4.7 14.4 1.0 O6 B:G68 4.7 11.6 1.0

Cobalt binding site 6 out of 7 in the Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co109 b:41.9 occ:1.00 CO B:NCO109 0.0 41.9 1.0 N4 B:NCO109 2.0 40.6 1.0 N2 B:NCO109 2.0 41.5 1.0 N1 B:NCO109 2.0 40.9 1.0 N5 B:NCO109 2.0 41.5 1.0 N6 B:NCO109 2.0 41.5 1.0 N3 B:NCO109 2.0 41.2 1.0 O B:HOH460 3.5 81.1 1.0 O4 B:U47 3.8 21.9 1.0 O B:HOH476 4.0 30.6 1.0 O B:HOH500 4.1 74.1 1.0 OP2 B:U51 4.3 27.2 1.0 O B:HOH761 4.3 0.9 1.0 OP2 B:C50 4.4 29.4 1.0 O6 B:G46 4.7 20.1 1.0 C4 B:U47 4.8 20.4 1.0 OP1 B:C50 4.8 30.8 1.0 P B:C50 5.0 28.7 1.0

Cobalt binding site 7 out of 7 in the Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of the A24U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co110 b:16.8 occ:0.64 CO B:NCO110 0.0 16.8 0.6 N5 B:NCO110 2.0 19.1 0.6 N6 B:NCO110 2.0 18.3 0.6 N4 B:NCO110 2.0 16.1 0.6 N3 B:NCO110 2.0 18.3 0.6 N1 B:NCO110 2.0 19.6 0.6 N2 B:NCO110 2.0 17.6 0.6 O B:HOH763 4.0 47.6 1.0 OP1 B:A73 4.2 21.6 1.0 OP1 B:G72 4.2 13.4 1.0 O B:HOH540 4.4 38.8 1.0 O B:HOH428 4.4 38.2 1.0 O B:HOH406 4.5 35.0 1.0 O B:HOH261 4.6 22.3 1.0

C.D.Stoddard, J.Widmann, J.J.Trausch, J.G.Marcano-Velazquez, R.Knight, R.T.Batey. Nucleotides Adjacent to the Ligand-Binding Pocket Are Linked to Activity Tuning in the Purine Riboswitch. J.Mol.Biol. V. 425 1596 2013.
ISSN: ISSN 0022-2836
PubMed: 23485418
DOI: 10.1016/J.JMB.2013.02.023