Cobalt in PDB 2eeu: Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine

The structure of Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine, PDB code: 2eeu was solved by S.D.Gilbert, C.E.Love, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.91 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.990, 35.240, 42.130, 90.00, 90.42, 90.00
R / Rfree (%)	23.2 / 27.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cobalt atom in the Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine (pdb code 2eeu). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 12 binding sites of Cobalt where determined in the Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine, PDB code: 2eeu:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 12 in the Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:24.8 occ:1.00 CO A:NCO101 0.0 24.8 1.0 N2 A:NCO101 2.0 20.0 1.0 N1 A:NCO101 2.0 20.0 1.0 N4 A:NCO101 2.0 23.8 1.0 N3 A:NCO101 2.0 22.0 1.0 N5 A:NCO101 2.0 21.4 1.0 N6 A:NCO101 2.0 22.0 1.0 O A:HOH236 3.7 52.9 1.0 O A:HOH307 3.7 41.5 1.0 OP1 A:U67 4.1 18.2 1.0 O A:HOH269 4.1 33.8 1.0 O A:HOH311 4.2 45.2 1.0 O3' A:A66 4.2 20.7 1.0 OP1 A:C28 4.5 34.2 1.0 OP2 A:C28 4.5 38.9 1.0 OP2 A:G68 4.8 46.0 1.0 P A:U67 4.9 19.3 1.0 P A:C28 5.0 37.8 1.0 OP1 A:G27 5.0 48.9 1.0

Cobalt binding site 2 out of 12 in the Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:33.7 occ:1.00 CO A:NCO102 0.0 33.7 1.0 N2 A:NCO102 2.0 33.9 1.0 N3 A:NCO102 2.0 33.6 1.0 N4 A:NCO102 2.0 32.7 1.0 N6 A:NCO102 2.0 33.0 1.0 N5 A:NCO102 2.0 34.1 1.0 N1 A:NCO102 2.0 31.4 1.0 O A:HOH274 3.8 26.0 1.0 O A:HOH242 3.8 27.4 1.0 OP1 A:G38 3.9 17.2 1.0 O A:HOH138 3.9 25.5 1.0 OP1 A:G56 4.0 27.7 1.0 O A:HOH204 4.1 23.1 1.0 OP2 A:G56 4.8 27.8 1.0 P A:G56 5.0 28.9 1.0 C5' A:C39 5.0 24.9 1.0

Cobalt binding site 3 out of 12 in the Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:26.5 occ:1.00 CO A:NCO103 0.0 26.5 1.0 N1 A:NCO103 2.0 21.1 1.0 N6 A:NCO103 2.0 23.8 1.0 N3 A:NCO103 2.0 23.5 1.0 N2 A:NCO103 2.0 23.2 1.0 N4 A:NCO103 2.0 23.6 1.0 N5 A:NCO103 2.0 24.3 1.0 O A:HOH271 3.7 27.4 1.0 O A:HOH148 3.8 32.5 1.0 O6 A:G56 4.0 19.1 1.0 O4 A:U69 4.1 21.2 1.0 O A:HOH166 4.1 22.1 1.0 OP2 A:C39 4.2 22.5 1.0 O A:HOH253 4.2 33.8 1.0 O A:HOH154 4.2 28.3 1.0 O A:HOH128 4.2 17.4 1.0 N7 A:G56 4.5 21.8 1.0 OP1 A:C39 4.6 21.7 1.0 C6 A:G56 4.9 21.0 1.0 O6 A:G68 4.9 17.1 1.0 P A:C39 4.9 23.0 1.0

Cobalt binding site 4 out of 12 in the Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co104 b:24.2 occ:1.00 CO A:NCO104 0.0 24.2 1.0 N2 A:NCO104 2.0 21.3 1.0 N6 A:NCO104 2.0 19.5 1.0 N3 A:NCO104 2.0 20.8 1.0 N5 A:NCO104 2.0 20.0 1.0 N1 A:NCO104 2.0 20.7 1.0 N4 A:NCO104 2.0 19.0 1.0 O A:HOH146 3.8 21.2 1.0 O6 A:G32 3.9 21.2 1.0 O A:HOH115 3.9 12.6 1.0 OP2 A:A66 4.0 29.1 1.0 O A:HOH216 4.1 28.4 1.0 O A:HOH147 4.1 14.9 1.0 O6 A:G31 4.2 13.2 1.0 O A:HOH149 4.3 30.6 1.0 O A:HOH117 4.3 16.8 1.0 O A:HOH161 4.4 29.2 1.0 N7 A:G31 4.4 18.9 1.0 O A:HOH133 4.7 20.0 1.0 O5' A:A66 4.9 32.9 1.0 C6 A:G32 4.9 20.0 1.0 O2' A:A65 5.0 28.3 1.0 C6 A:G31 5.0 18.7 1.0

Cobalt binding site 5 out of 12 in the Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co105 b:36.5 occ:1.00 CO A:NCO105 0.0 36.5 1.0 N5 A:NCO105 2.0 34.1 1.0 N6 A:NCO105 2.0 35.1 1.0 N4 A:NCO105 2.0 35.2 1.0 N1 A:NCO105 2.0 35.6 1.0 N2 A:NCO105 2.0 33.9 1.0 N3 A:NCO105 2.0 34.1 1.0 O A:HOH220 3.9 37.8 1.0 O A:HOH260 3.9 29.6 1.0 O A:HOH209 3.9 51.4 1.0 O6 A:G38 4.1 21.0 1.0 OP2 A:G37 4.1 17.7 1.0 O A:HOH201 4.2 25.1 1.0 N7 A:G38 4.3 20.0 1.0 O A:HOH270 4.3 31.2 1.0 N7 A:G37 4.4 19.8 1.0 O A:HOH312 4.4 34.2 1.0 O A:HOH212 4.7 31.5 1.0 C6 A:G38 4.9 20.9 1.0 O A:HOH256 5.0 55.8 1.0 C5 A:G38 5.0 18.8 1.0 C8 A:G37 5.0 20.2 1.0

Cobalt binding site 6 out of 12 in the Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co106 b:0.7 occ:1.00 CO A:NCO106 0.0 0.7 1.0 N5 A:NCO106 2.0 0.6 1.0 N2 A:NCO106 2.0 0.3 1.0 N6 A:NCO106 2.0 0.5 1.0 N3 A:NCO106 2.0 0.3 1.0 N1 A:NCO106 2.0 0.5 1.0 N4 A:NCO106 2.0 0.4 1.0 O A:HOH319 3.8 35.6 1.0 O A:HOH210 3.8 29.9 1.0 OP1 A:C26 3.9 42.1 1.0 O A:HOH131 4.3 29.8 1.0 O A:HOH307 4.8 41.5 1.0

Cobalt binding site 7 out of 12 in the Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co107 b:94.9 occ:1.00 CO A:NCO107 0.0 94.9 1.0 N1 A:NCO107 2.0 94.2 1.0 N6 A:NCO107 2.0 94.1 1.0 N4 A:NCO107 2.0 93.8 1.0 N3 A:NCO107 2.0 94.3 1.0 N5 A:NCO107 2.0 94.1 1.0 N2 A:NCO107 2.0 94.2 1.0 OP2 A:C41 3.7 19.8 1.0 OP1 A:C54 4.0 35.3 1.0 O A:HOH139 4.5 21.1 1.0 OP1 A:C53 4.7 33.7 1.0 P A:C41 4.7 20.1 1.0 OP2 A:C53 4.7 30.7 1.0 OP1 A:C41 4.9 21.3 1.0 OP2 A:G42 5.0 23.6 1.0 O A:HOH218 5.0 35.9 1.0

Cobalt binding site 8 out of 12 in the Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co108 b:73.0 occ:1.00 CO A:NCO108 0.0 73.0 1.0 N2 A:NCO108 2.0 73.1 1.0 N6 A:NCO108 2.0 73.2 1.0 N1 A:NCO108 2.0 72.9 1.0 N4 A:NCO108 2.0 73.1 1.0 N5 A:NCO108 2.0 73.5 1.0 N3 A:NCO108 2.0 73.3 1.0 O A:HOH276 3.9 50.1 1.0 N7 A:G46 4.2 30.7 1.0 O A:HOH280 4.2 58.1 1.0 O6 A:G46 4.2 28.5 1.0 OP2 A:A45 4.3 42.6 1.0 O4 A:U47 4.5 35.1 1.0 C6 A:G46 5.0 31.1 1.0 C5 A:G46 5.0 29.5 1.0

Cobalt binding site 9 out of 12 in the Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co109 b:60.6 occ:1.00 CO A:NCO109 0.0 60.6 1.0 N3 A:NCO109 2.0 60.5 1.0 N1 A:NCO109 2.0 60.5 1.0 N6 A:NCO109 2.0 61.1 1.0 N5 A:NCO109 2.0 61.2 1.0 N2 A:NCO109 2.0 60.8 1.0 N4 A:NCO109 2.0 60.4 1.0 O A:HOH145 3.6 75.5 1.0 O A:HOH262 3.7 29.5 1.0 O A:HOH304 4.0 48.9 1.0 OP1 A:A24 4.0 32.6 1.0 OP2 A:C71 4.2 22.0 1.0 O A:HOH281 4.6 46.0 1.0

Cobalt binding site 10 out of 12 in the Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Guanine Riboswitch U22A, A52U Mutant Bound to Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co110 b:0.3 occ:1.00 CO A:NCO110 0.0 0.3 1.0 N4 A:NCO110 2.0 0.4 1.0 N2 A:NCO110 2.0 0.5 1.0 N1 A:NCO110 2.0 0.5 1.0 N5 A:NCO110 2.0 0.5 1.0 N6 A:NCO110 2.0 0.5 1.0 N3 A:NCO110 2.0 0.5 1.0 OP1 A:A21 3.7 27.0 1.0 O A:HOH315 4.0 50.7 1.0 OP2 A:A22 4.7 29.8 1.0 P A:A21 4.8 28.0 1.0 OP2 A:A21 4.9 25.2 1.0

S.D.Gilbert, C.E.Love, A.L.Edwards, R.T.Batey. Mutational Analysis of the Purine Riboswitch Aptamer Domain Biochemistry V. 46 13297 2007.
ISSN: ISSN 0006-2960
PubMed: 17960911
DOI: 10.1021/BI700410G