Cobalt in PDB 6uc7: Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine

The structure of Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine, PDB code: 6uc7 was solved by M.M.Matyjasik, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.74 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.107, 35.082, 41.606, 90.00, 90.99, 90.00
R / Rfree (%)	n/a / 20.9

The binding sites of Cobalt atom in the Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine (pdb code 6uc7). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine, PDB code: 6uc7:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:30.8 occ:1.00 CO B:NCO101 0.0 30.8 1.0 N2 B:NCO101 2.0 26.6 1.0 N4 B:NCO101 2.0 26.4 1.0 N6 B:NCO101 2.0 24.5 1.0 N1 B:NCO101 2.0 23.7 1.0 N5 B:NCO101 2.0 23.3 1.0 N3 B:NCO101 2.0 29.8 1.0 O B:HOH214 3.5 23.7 1.0 O B:HOH340 3.7 40.2 1.0 O B:HOH253 3.8 42.4 1.0 O B:HOH355 3.8 29.0 1.0 OP1 B:G38 3.9 15.9 1.0 OP1 B:G56 3.9 29.1 1.0 O B:HOH277 4.0 22.8 1.0 O B:HOH329 4.0 20.7 1.0 O B:HOH397 4.9 35.5 1.0 P B:G56 4.9 23.3 1.0 P B:G38 4.9 13.6 1.0 O B:HOH307 4.9 29.7 1.0 OP2 B:G38 5.0 13.9 1.0 OP2 B:G56 5.0 24.8 1.0

Cobalt binding site 2 out of 8 in the Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:20.7 occ:1.00 CO B:NCO102 0.0 20.7 1.0 N4 B:NCO102 2.0 18.9 1.0 N1 B:NCO102 2.0 23.0 1.0 N3 B:NCO102 2.0 20.9 1.0 N6 B:NCO102 2.0 29.7 1.0 N5 B:NCO102 2.0 25.0 1.0 N2 B:NCO102 2.0 22.4 1.0 O4 B:U69 3.9 17.4 1.0 O B:HOH258 3.9 24.7 1.0 O B:HOH232 4.0 25.2 1.0 O B:HOH369 4.0 25.2 1.0 O6 B:G56 4.1 19.1 1.0 O B:HOH230 4.2 19.2 1.0 O B:HOH351 4.3 22.8 1.0 O B:HOH266 4.5 25.4 1.0 OP1 B:C39 4.5 17.6 1.0 O6 B:G68 4.5 16.3 1.0 OP2 B:C39 4.5 19.2 1.0 N7 B:G56 4.5 18.9 1.0 C6 B:G56 4.9 18.7 1.0

Cobalt binding site 3 out of 8 in the Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co103 b:14.5 occ:1.00 CO B:NCO103 0.0 14.5 1.0 N3 B:NCO103 2.0 15.7 1.0 N1 B:NCO103 2.0 16.6 1.0 N6 B:NCO103 2.0 19.9 1.0 N5 B:NCO103 2.0 15.4 1.0 N4 B:NCO103 2.0 15.9 1.0 N2 B:NCO103 2.0 11.7 1.0 OP2 B:A66 3.7 20.1 1.0 O B:HOH298 3.9 17.3 1.0 O6 B:G32 3.9 17.3 1.0 O6 B:G31 4.1 12.3 1.0 O B:HOH401 4.2 19.6 1.0 O B:HOH312 4.2 17.6 1.0 O B:HOH299 4.2 16.2 1.0 O B:HOH243 4.2 18.1 1.0 O B:HOH316 4.2 18.7 1.0 O B:HOH284 4.2 18.2 1.0 O B:HOH385 4.3 24.1 1.0 N7 B:G31 4.3 15.3 1.0 O B:HOH226 4.7 17.8 1.0 C6 B:G31 4.9 15.3 1.0 C6 B:G32 4.9 14.6 1.0 C5 B:G31 5.0 13.9 1.0 O2' B:A65 5.0 17.4 1.0

Cobalt binding site 4 out of 8 in the Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co104 b:17.7 occ:1.00 CO B:NCO104 0.0 17.7 1.0 N6 B:NCO104 2.0 18.1 1.0 N4 B:NCO104 2.0 22.4 1.0 N2 B:NCO104 2.0 16.0 1.0 N1 B:NCO104 2.0 21.1 1.0 N3 B:NCO104 2.0 16.6 1.0 N5 B:NCO104 2.0 22.7 1.0 O B:HOH327 3.8 29.6 1.0 O B:HOH291 3.8 21.1 1.0 O B:HOH237 3.9 21.4 1.0 O B:HOH310 4.0 18.7 1.0 OP1 B:U67 4.1 16.0 1.0 O B:HOH367 4.3 25.4 1.0 O3' B:A66 4.3 14.0 1.0 O B:HOH392 4.3 31.9 1.0 P B:U67 4.9 14.0 1.0 O2' B:A66 5.0 14.4 1.0

Cobalt binding site 5 out of 8 in the Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co105 b:54.9 occ:1.00 CO B:NCO105 0.0 54.9 1.0 N4 B:NCO105 2.0 38.7 1.0 N3 B:NCO105 2.0 35.4 1.0 N2 B:NCO105 2.0 27.9 1.0 N5 B:NCO105 2.0 40.2 1.0 N1 B:NCO105 2.0 33.8 1.0 N6 B:NCO105 2.0 32.5 1.0 OP2 B:C41 3.8 18.9 1.0 OP1 B:C54 4.1 29.2 1.0 O B:HOH257 4.2 34.7 1.0 O B:HOH293 4.3 23.8 1.0 O B:HOH391 4.4 31.2 1.0 O B:HOH250 4.4 16.3 1.0 OP1 B:C53 4.5 30.4 1.0 OP2 B:G42 4.6 20.6 1.0 O5' B:C54 4.8 24.1 1.0 P B:C41 4.9 17.1 1.0 OP2 B:C53 4.9 32.4 1.0

Cobalt binding site 6 out of 8 in the Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co106 b:52.9 occ:1.00 CO B:NCO106 0.0 52.9 1.0 N1 B:NCO106 2.0 46.6 1.0 N5 B:NCO106 2.0 43.0 1.0 N2 B:NCO106 2.0 30.4 1.0 N4 B:NCO106 2.0 41.3 1.0 N3 B:NCO106 2.0 37.6 1.0 N6 B:NCO106 2.0 28.0 1.0 OP1 B:G72 4.1 15.6 1.0 OP2 B:A73 4.5 41.8 1.0 O B:HOH360 4.8 38.0 1.0

Cobalt binding site 7 out of 8 in the Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co107 b:57.1 occ:1.00 CO B:NCO107 0.0 57.1 1.0 N5 B:NCO107 2.0 44.4 1.0 N2 B:NCO107 2.0 50.7 1.0 N3 B:NCO107 2.0 46.6 1.0 N6 B:NCO107 2.0 45.0 1.0 N1 B:NCO107 2.0 47.9 1.0 N4 B:NCO107 2.0 51.4 1.0 O4 B:U47 3.9 35.9 1.0 O6 B:G46 4.4 28.9 1.0 OP2 B:C50 4.8 44.0 1.0 C4 B:U47 4.8 32.2 1.0 OP2 B:U51 5.0 40.2 1.0

Cobalt binding site 8 out of 8 in the Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Structure of Guanine Riboswitch Bound to N2-Acetyl Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co108 b:50.1 occ:1.00 CO B:NCO108 0.0 50.1 1.0 N2 B:NCO108 2.0 38.1 1.0 N1 B:NCO108 2.0 30.8 1.0 N3 B:NCO108 2.0 35.2 1.0 N6 B:NCO108 2.0 39.2 1.0 N5 B:NCO108 2.0 35.2 1.0 N4 B:NCO108 2.0 38.9 1.0 O6 B:G38 4.0 17.0 1.0 OP2 B:G37 4.0 17.1 1.0 O B:HOH332 4.1 27.0 1.0 O B:HOH239 4.2 26.7 1.0 N7 B:G38 4.3 15.4 1.0 N7 B:G37 4.4 15.1 1.0 O B:HOH301 4.4 25.4 1.0 O B:HOH261 4.6 26.2 1.0 O B:HOH388 4.8 34.3 1.0 C6 B:G38 4.9 17.5 1.0 C8 B:G37 5.0 18.2 1.0

M.M.Matyjasik, S.D.Hall, R.T.Batey. High Affinity Binding of N2-Modified Guanine Derivatives Significantly Disrupts the Ligand Binding Pocket of the Guanine Riboswitch. Molecules V. 25 2020.
ISSN: ESSN 1420-3049
PubMed: 32414072
DOI: 10.3390/MOLECULES25102295