Cobalt in PDB 4fep: Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine

The structure of Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine, PDB code: 4fep 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)	40.00 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.071, 35.252, 41.855, 90.00, 91.40, 90.00
R / Rfree (%)	17.9 / 22.9

The binding sites of Cobalt atom in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine (pdb code 4fep). 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 A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine, PDB code: 4fep:
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 A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


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/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:14.8 occ:1.00 CO B:NCO102 0.0 14.8 1.0 N1 B:NCO102 2.0 16.4 1.0 N2 B:NCO102 2.0 17.6 1.0 N3 B:NCO102 2.0 15.3 1.0 N4 B:NCO102 2.0 18.4 1.0 N6 B:NCO102 2.0 16.4 1.0 N5 B:NCO102 2.0 15.1 1.0 O B:HOH850 3.5 31.2 1.0 O B:HOH856 3.8 30.3 1.0 O B:HOH677 3.8 15.9 1.0 O B:HOH655 3.9 18.9 1.0 O B:HOH681 4.0 20.2 1.0 O B:HOH982 4.0 1.0 1.0 OP1 B:U67 4.1 11.7 1.0 O B:HOH1031 4.3 0.1 1.0 O3' B:A66 4.4 11.1 1.0 O B:HOH836 4.5 40.7 1.0 O B:HOH744 4.6 20.6 1.0 P B:U67 4.9 10.9 1.0 O2' B:A66 5.0 10.7 1.0

Cobalt binding site 2 out of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


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/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co103 b:25.3 occ:1.00 CO B:NCO103 0.0 25.3 1.0 N4 B:NCO103 2.0 26.2 1.0 N3 B:NCO103 2.0 24.9 1.0 N2 B:NCO103 2.0 24.9 1.0 N6 B:NCO103 2.0 24.9 1.0 N5 B:NCO103 2.0 26.3 1.0 N1 B:NCO103 2.0 24.8 1.0 O B:HOH1025 3.8 32.2 1.0 O B:HOH848 3.8 36.4 1.0 O B:HOH658 3.9 23.6 1.0 O B:HOH927 3.9 23.6 1.0 O B:HOH756 3.9 32.4 1.0 OP1 B:G38 4.1 11.8 1.0 OP1 B:G56 4.2 18.5 1.0 O B:HOH912 4.5 48.8 1.0 O B:HOH998 4.7 0.1 1.0 O B:HOH746 4.8 34.2 1.0 OP2 B:G56 4.9 18.6 1.0 O B:HOH771 4.9 30.2 1.0 O B:HOH811 4.9 33.2 1.0

Cobalt binding site 3 out of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


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/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co104 b:15.5 occ:1.00 CO B:NCO104 0.0 15.5 1.0 N6 B:NCO104 2.0 18.0 1.0 N3 B:NCO104 2.0 16.8 1.0 N1 B:NCO104 2.0 18.2 1.0 N4 B:NCO104 2.0 19.8 1.0 N2 B:NCO104 2.0 17.3 1.0 N5 B:NCO104 2.0 15.5 1.0 O B:HOH1135 3.6 57.4 1.0 O4 B:U69 4.0 8.9 1.0 O B:HOH720 4.1 25.3 1.0 O B:HOH763 4.1 32.1 1.0 O6 B:G56 4.1 14.0 1.0 O B:HOH698 4.2 25.6 1.0 O B:HOH697 4.3 27.2 1.0 O B:HOH617 4.4 17.5 1.0 O B:HOH726 4.4 20.6 1.0 OP2 B:C39 4.4 15.1 1.0 O B:HOH683 4.4 19.4 1.0 OP1 B:C39 4.5 14.2 1.0 N7 B:G56 4.7 13.7 1.0 O6 B:G68 4.9 10.1 1.0 C6 B:G56 5.0 13.1 1.0

Cobalt binding site 4 out of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


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/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co105 b:11.7 occ:1.00 CO B:NCO105 0.0 11.7 1.0 N6 B:NCO105 2.0 12.7 1.0 N5 B:NCO105 2.0 14.4 1.0 N1 B:NCO105 2.0 14.4 1.0 N2 B:NCO105 2.0 12.1 1.0 N3 B:NCO105 2.0 11.2 1.0 N4 B:NCO105 2.0 9.2 1.0 O B:HOH607 3.9 14.7 1.0 OP2 B:A66 3.9 17.3 1.0 O6 B:G32 4.0 11.2 1.0 O B:HOH643 4.1 19.2 1.0 O6 B:G31 4.1 8.6 1.0 O B:HOH638 4.1 16.4 1.0 O B:HOH727 4.2 24.8 1.0 O B:HOH641 4.2 19.4 1.0 O B:HOH624 4.3 18.8 1.0 O B:HOH646 4.3 13.5 1.0 O B:HOH610 4.3 18.3 1.0 N7 B:G31 4.4 10.7 1.0 C6 B:G31 4.9 10.2 1.0 O B:HOH950 4.9 37.2 1.0

Cobalt binding site 5 out of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


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/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co106 b:37.9 occ:1.00 CO B:NCO106 0.0 37.9 1.0 N5 B:NCO106 2.0 39.0 1.0 N1 B:NCO106 2.0 37.6 1.0 N2 B:NCO106 2.0 38.0 1.0 N6 B:NCO106 2.0 37.8 1.0 N4 B:NCO106 2.0 38.4 1.0 N3 B:NCO106 2.0 38.0 1.0 O B:HOH1132 3.7 41.7 1.0 O B:HOH715 3.8 33.3 1.0 OP2 B:G37 4.0 11.3 1.0 O B:HOH629 4.0 19.9 1.0 O B:HOH827 4.2 33.3 1.0 O6 B:G38 4.3 8.1 1.0 O B:HOH694 4.4 25.4 1.0 N7 B:G38 4.4 8.6 1.0 O B:HOH886 4.5 33.6 1.0 O B:HOH967 4.6 29.0 1.0 N7 B:G37 4.6 11.0 1.0 O B:HOH703 5.0 28.6 1.0

Cobalt binding site 6 out of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


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/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co107 b:29.0 occ:1.00 CO B:NCO107 0.0 29.0 1.0 N1 B:NCO107 2.0 29.1 1.0 N6 B:NCO107 2.0 28.6 1.0 N5 B:NCO107 2.0 28.0 1.0 N2 B:NCO107 2.0 28.8 1.0 N3 B:NCO107 2.0 28.7 1.0 N4 B:NCO107 2.0 28.1 1.0 O B:HOH674 3.7 27.3 1.0 O B:HOH614 3.9 19.6 1.0 O B:HOH881 3.9 43.1 1.0 OP1 B:C54 4.0 23.2 1.0 O B:HOH1023 4.0 41.0 1.0 OP2 B:C41 4.1 14.2 1.0 O B:HOH858 4.3 31.5 1.0 O B:HOH602 4.4 14.1 1.0 OP2 B:G42 4.5 10.8 1.0 O5' B:C54 4.7 19.6 1.0 O B:HOH883 4.8 43.9 1.0 P B:C54 4.9 22.4 1.0

Cobalt binding site 7 out of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


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/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co108 b:26.7 occ:1.00 CO B:NCO108 0.0 26.7 1.0 N4 B:NCO108 2.0 27.9 1.0 N2 B:NCO108 2.0 26.4 1.0 N3 B:NCO108 2.0 27.2 1.0 N5 B:NCO108 2.0 26.9 1.0 N1 B:NCO108 2.0 26.3 1.0 N6 B:NCO108 2.0 25.9 1.0 O B:HOH676 3.4 96.1 1.0 O B:HOH1004 3.7 50.5 1.0 O B:HOH1059 3.8 41.5 1.0 O B:HOH1157 3.9 46.4 1.0 O B:HOH859 3.9 36.9 1.0 O4 B:U47 4.2 18.2 1.0 O B:HOH894 4.2 28.6 1.0 O6 B:G46 4.2 14.6 1.0 N7 B:G46 4.5 15.8 1.0 O B:HOH806 4.5 29.7 1.0 O B:HOH721 4.5 24.3 1.0 O B:HOH776 4.8 25.1 1.0 O B:HOH754 4.8 27.9 1.0

Cobalt binding site 8 out of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


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 A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co109 b:0.5 occ:1.00 CO B:NCO109 0.0 0.5 1.0 N1 B:NCO109 2.0 0.3 1.0 N6 B:NCO109 2.0 0.2 1.0 N5 B:NCO109 2.0 0.2 1.0 N3 B:NCO109 2.0 0.2 1.0 N4 B:NCO109 2.0 0.2 1.0 N2 B:NCO109 2.0 0.3 1.0 OP1 B:A21 3.7 23.4 1.0 OP2 B:U22 3.9 21.1 1.0 O B:HOH1166 4.5 65.3 1.0 O B:HOH1130 4.5 62.0 1.0 P B:A21 4.8 24.5 1.0 O B:HOH951 4.9 61.8 1.0 O B:HOH817 5.0 32.6 1.0

Cobalt binding site 9 out of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


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 A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co110 b:15.8 occ:0.64 CO B:NCO110 0.0 15.8 0.6 N5 B:NCO110 2.0 16.2 0.6 N2 B:NCO110 2.0 17.1 0.6 N1 B:NCO110 2.0 18.1 0.6 N3 B:NCO110 2.0 18.2 0.6 N6 B:NCO110 2.0 15.9 0.6 N4 B:NCO110 2.0 15.9 0.6 O B:HOH875 4.0 48.1 1.0 OP1 B:G72 4.2 12.1 1.0 O B:HOH888 4.2 36.1 1.0 OP1 B:A73 4.2 23.0 1.0 O B:HOH1078 4.4 61.6 1.0 O B:HOH675 4.5 22.2 1.0 OP2 B:A73 4.9 26.5 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