Cobalt in PDB 4fel: Crystal Structure of the U25A/A46G Mutant of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine

The structure of Crystal Structure of the U25A/A46G Mutant of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine, PDB code: 4fel 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 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.698, 35.193, 41.569, 90.00, 90.42, 90.00
R / Rfree (%)	18.9 / 22.9

The binding sites of Cobalt atom in the Crystal Structure of the U25A/A46G Mutant of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine (pdb code 4fel). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 9 binding sites of Cobalt where determined in the Crystal Structure of the U25A/A46G Mutant of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine, PDB code: 4fel:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cobalt binding site 1 out of 9 in the Crystal Structure of the U25A/A46G Mutant of the 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 U25A/A46G Mutant of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co103 b:19.9 occ:1.00 CO B:NCO103 0.0 19.9 1.0 N1 B:NCO103 1.9 18.7 1.0 N2 B:NCO103 2.0 22.5 1.0 N4 B:NCO103 2.0 19.8 1.0 N6 B:NCO103 2.0 19.3 1.0 N3 B:NCO103 2.0 19.9 1.0 N5 B:NCO103 2.0 18.2 1.0 O B:HOH362 3.8 25.6 1.0 O B:HOH313 4.0 22.0 1.0 O B:HOH429 4.1 32.5 1.0 O B:HOH544 4.1 33.7 1.0 OP1 B:U67 4.1 14.3 1.0 O B:HOH673 4.4 45.7 1.0 O3' B:A66 4.4 14.2 1.0 O B:HOH472 4.5 32.7 1.0 P B:U67 5.0 13.1 1.0

Cobalt binding site 2 out of 9 in the Crystal Structure of the U25A/A46G Mutant of the 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 U25A/A46G Mutant of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co104 b:28.4 occ:1.00 CO B:NCO104 0.0 28.4 1.0 N3 B:NCO104 2.0 28.4 1.0 N4 B:NCO104 2.0 27.6 1.0 N6 B:NCO104 2.0 28.3 1.0 N2 B:NCO104 2.0 28.5 1.0 N5 B:NCO104 2.0 29.0 1.0 N1 B:NCO104 2.0 26.4 1.0 O B:HOH317 3.7 34.0 1.0 O B:HOH333 3.9 29.9 1.0 OP1 B:G38 4.0 16.6 1.0 OP1 B:G56 4.1 26.5 1.0 O B:HOH271 4.1 38.4 1.0 O B:HOH641 4.2 32.5 1.0 O B:HOH368 4.4 43.3 1.0 O B:HOH754 4.7 35.4 1.0 O B:HOH268 5.0 32.9 1.0

Cobalt binding site 3 out of 9 in the Crystal Structure of the U25A/A46G Mutant of the 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 U25A/A46G Mutant of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co105 b:18.7 occ:1.00 CO B:NCO105 0.0 18.7 1.0 N6 B:NCO105 2.0 22.5 1.0 N4 B:NCO105 2.0 24.5 1.0 N2 B:NCO105 2.0 24.1 1.0 N3 B:NCO105 2.0 21.3 1.0 N1 B:NCO105 2.0 21.0 1.0 N5 B:NCO105 2.0 21.8 1.0 O B:HOH467 3.8 40.1 1.0 O B:HOH308 3.9 31.1 1.0 O B:HOH434 3.9 52.7 1.0 O4 B:U69 3.9 14.2 1.0 O6 B:G56 4.1 14.8 1.0 O B:HOH224 4.2 24.3 1.0 O B:HOH519 4.3 34.8 1.0 O B:HOH250 4.5 34.5 1.0 OP2 B:C39 4.5 16.3 1.0 O B:HOH693 4.5 47.9 1.0 O B:HOH348 4.6 47.4 1.0 N7 B:G56 4.6 18.8 1.0 OP1 B:C39 4.7 16.2 1.0 O6 B:G68 4.9 14.8 1.0 C6 B:G56 5.0 15.4 1.0

Cobalt binding site 4 out of 9 in the Crystal Structure of the U25A/A46G Mutant of the 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 U25A/A46G Mutant of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co106 b:16.1 occ:1.00 CO B:NCO106 0.0 16.1 1.0 N6 B:NCO106 2.0 16.9 1.0 N2 B:NCO106 2.0 17.1 1.0 N5 B:NCO106 2.0 16.2 1.0 N3 B:NCO106 2.0 17.5 1.0 N4 B:NCO106 2.0 16.2 1.0 N1 B:NCO106 2.0 16.6 1.0 O B:HOH214 3.9 21.0 1.0 OP2 B:A66 3.9 18.1 1.0 O6 B:G32 4.0 15.5 1.0 O B:HOH231 4.1 21.6 1.0 O6 B:G31 4.2 13.0 1.0 O B:HOH459 4.2 35.7 1.0 O B:HOH276 4.3 27.0 1.0 O B:HOH254 4.3 24.7 1.0 O B:HOH212 4.3 14.5 1.0 O B:HOH307 4.3 28.0 1.0 O B:HOH227 4.3 17.6 1.0 N7 B:G31 4.4 10.5 1.0 O B:HOH681 4.4 37.9 1.0 C6 B:G31 5.0 12.3 1.0 O4 B:U30 5.0 10.4 1.0

Cobalt binding site 5 out of 9 in the Crystal Structure of the U25A/A46G Mutant of the 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 U25A/A46G Mutant of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co107 b:46.1 occ:1.00 CO B:NCO107 0.0 46.1 1.0 N1 B:NCO107 2.0 46.2 1.0 N6 B:NCO107 2.0 46.3 1.0 N5 B:NCO107 2.0 47.0 1.0 N4 B:NCO107 2.0 46.4 1.0 N3 B:NCO107 2.0 46.1 1.0 N2 B:NCO107 2.0 46.4 1.0 O B:HOH478 3.6 36.6 1.0 O B:HOH318 3.7 37.2 1.0 OP2 B:G37 4.0 15.2 1.0 O B:HOH258 4.2 28.0 1.0 O6 B:G38 4.2 11.2 1.0 O B:HOH381 4.2 30.3 1.0 N7 B:G38 4.3 13.3 1.0 O B:HOH711 4.3 50.0 1.0 N7 B:G37 4.5 13.6 1.0 O B:HOH642 4.7 41.7 1.0 O B:HOH491 4.7 30.5 1.0 O B:HOH605 5.0 52.6 1.0

Cobalt binding site 6 out of 9 in the Crystal Structure of the U25A/A46G Mutant of the 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 U25A/A46G Mutant of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co108 b:68.2 occ:1.00 CO B:NCO108 0.0 68.2 1.0 N2 B:NCO108 2.0 66.5 1.0 N6 B:NCO108 2.0 67.4 1.0 N5 B:NCO108 2.0 67.9 1.0 N4 B:NCO108 2.0 67.7 1.0 N1 B:NCO108 2.0 67.5 1.0 N3 B:NCO108 2.0 67.7 1.0 O B:HOH415 3.6 18.1 1.0 O B:HOH623 3.6 37.2 1.0 O B:HOH640 4.2 41.9 1.0 OP2 B:C41 4.2 16.4 1.0 OP1 B:C54 4.4 22.1 1.0 OP1 B:C53 4.4 23.1 1.0 O B:HOH343 4.4 39.2 1.0 O B:HOH597 4.6 52.3 1.0 O B:HOH705 4.6 37.2 1.0 O B:HOH686 4.7 38.9 1.0 O B:HOH785 4.7 55.2 1.0 O5' B:C54 4.7 20.6 1.0 O B:HOH349 4.9 33.7 1.0 OP1 B:C41 5.0 17.4 1.0

Cobalt binding site 7 out of 9 in the Crystal Structure of the U25A/A46G Mutant of the 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 U25A/A46G Mutant of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co109 b:25.4 occ:1.00 CO B:NCO109 0.0 25.4 1.0 N5 B:NCO109 2.0 27.2 1.0 N2 B:NCO109 2.0 26.6 1.0 N6 B:NCO109 2.0 25.4 1.0 N4 B:NCO109 2.0 26.0 1.0 N1 B:NCO109 2.0 26.7 1.0 N3 B:NCO109 2.0 28.1 1.0 O B:HOH395 3.7 37.6 1.0 O B:HOH496 4.1 39.0 1.0 O6 B:G46 4.2 17.2 1.0 O B:HOH367 4.2 34.6 1.0 O4 B:U47 4.3 21.4 1.0 O B:HOH632 4.3 42.5 1.0 O B:HOH226 4.3 24.3 1.0 N7 B:G46 4.5 16.5 1.0 O B:HOH593 4.5 55.4 1.0 O B:HOH330 4.6 36.2 1.0 O B:HOH290 4.8 29.2 1.0 O B:HOH479 4.9 38.5 1.0

Cobalt binding site 8 out of 9 in the Crystal Structure of the U25A/A46G Mutant of the 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 8 of Crystal Structure of the U25A/A46G Mutant of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co110 b:0.0 occ:1.00 CO B:NCO110 0.0 0.0 1.0 N1 B:NCO110 2.0 0.7 1.0 N4 B:NCO110 2.0 0.6 1.0 N5 B:NCO110 2.0 0.7 1.0 N2 B:NCO110 2.0 0.6 1.0 N6 B:NCO110 2.0 0.7 1.0 N3 B:NCO110 2.0 0.6 1.0 O B:HOH422 3.7 26.1 1.0 OP1 B:A21 3.9 22.5 1.0 OP2 B:U22 3.9 19.3 1.0 O B:HOH559 3.9 53.2 1.0 O B:HOH396 4.3 34.5 1.0 O B:HOH730 4.4 53.1 1.0 O B:HOH685 4.7 41.3 1.0 OP1 B:U22 4.8 21.1 1.0 P B:U22 4.9 21.1 1.0

Cobalt binding site 9 out of 9 in the Crystal Structure of the U25A/A46G Mutant of the 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 9 of Crystal Structure of the U25A/A46G Mutant of the Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co111 b:25.2 occ:0.64 CO B:NCO111 0.0 25.2 0.6 N1 B:NCO111 2.0 26.5 0.6 N2 B:NCO111 2.0 26.6 0.6 N6 B:NCO111 2.0 26.3 0.6 N4 B:NCO111 2.0 24.2 0.6 N5 B:NCO111 2.0 25.5 0.6 N3 B:NCO111 2.0 26.5 0.6 O B:HOH542 3.5 53.7 1.0 OP1 B:G72 4.2 11.9 1.0 O B:HOH461 4.3 48.4 1.0 O B:HOH778 4.4 54.6 1.0 OP2 B:A73 4.8 21.9 1.0 O B:HOH684 4.8 51.0 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