Cobalt in PDB 3fo6: Crystal Structure of Guanine Riboswitch Bound to 6-O- Methylguanine

The structure of Crystal Structure of Guanine Riboswitch Bound to 6-O- Methylguanine, PDB code: 3fo6 was solved by S.D.Gilbert, F.E.Reyes, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.70 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.180, 35.270, 42.120, 90.00, 90.45, 90.00
R / Rfree (%)	23.1 / 26.3

The binding sites of Cobalt atom in the Crystal Structure of Guanine Riboswitch Bound to 6-O- Methylguanine (pdb code 3fo6). 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 Guanine Riboswitch Bound to 6-O- Methylguanine, PDB code: 3fo6:
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 Guanine Riboswitch Bound to 6-O- Methylguanine


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 Guanine Riboswitch Bound to 6-O- Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:26.5 occ:1.00 CO A:NCO101 0.0 26.5 1.0 N1 A:NCO101 2.0 24.1 1.0 N2 A:NCO101 2.0 25.9 1.0 N4 A:NCO101 2.0 27.6 1.0 N6 A:NCO101 2.0 26.3 1.0 N5 A:NCO101 2.0 24.4 1.0 N3 A:NCO101 2.0 26.2 1.0 O A:HOH386 3.6 36.9 1.0 O A:HOH359 4.0 28.5 1.0 OP1 A:U67 4.1 18.4 1.0 O A:HOH460 4.2 72.1 1.0 O A:HOH518 4.3 37.4 1.0 O A:HOH497 4.3 78.9 1.0 O3' A:A66 4.4 17.6 1.0 P A:U67 4.9 17.5 1.0

Cobalt binding site 2 out of 9 in the Crystal Structure of Guanine Riboswitch Bound to 6-O- Methylguanine


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 Guanine Riboswitch Bound to 6-O- Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:35.7 occ:1.00 CO A:NCO102 0.0 35.7 1.0 N4 A:NCO102 2.0 32.9 1.0 N2 A:NCO102 2.0 33.6 1.0 N3 A:NCO102 2.0 31.6 1.0 N6 A:NCO102 2.0 32.9 1.0 N1 A:NCO102 2.0 32.7 1.0 N5 A:NCO102 2.0 33.0 1.0 O A:HOH470 3.6 43.8 1.0 OP1 A:G56 3.8 32.6 1.0 O A:HOH347 3.8 29.5 1.0 O A:HOH452 3.9 39.4 1.0 OP1 A:G38 4.0 18.9 1.0 O A:HOH381 4.2 27.8 1.0 O A:HOH416 4.6 42.1 1.0 P A:G56 4.9 31.0 1.0

Cobalt binding site 3 out of 9 in the Crystal Structure of Guanine Riboswitch Bound to 6-O- Methylguanine


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 Guanine Riboswitch Bound to 6-O- Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:33.1 occ:1.00 CO A:NCO103 0.0 33.1 1.0 N3 A:NCO103 2.0 30.2 1.0 N4 A:NCO103 2.0 33.2 1.0 N2 A:NCO103 2.0 33.8 1.0 N1 A:NCO103 2.0 32.2 1.0 N6 A:NCO103 2.0 33.9 1.0 N5 A:NCO103 2.0 32.4 1.0 O A:HOH457 3.5 38.2 1.0 O A:HOH442 3.9 40.2 1.0 O A:HOH315 4.0 23.1 1.0 O4 A:U69 4.0 21.3 1.0 O A:HOH462 4.0 45.3 1.0 O6 A:G56 4.0 28.6 1.0 O A:HOH401 4.2 25.5 1.0 OP2 A:C39 4.4 27.4 1.0 N7 A:G56 4.5 26.1 1.0 O A:HOH443 4.6 33.1 1.0 O6 A:G68 4.8 18.7 1.0 C6 A:G56 4.9 27.0 1.0 O A:HOH519 4.9 78.9 1.0 OP1 A:C39 4.9 26.7 1.0

Cobalt binding site 4 out of 9 in the Crystal Structure of Guanine Riboswitch Bound to 6-O- Methylguanine


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 Guanine Riboswitch Bound to 6-O- Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co104 b:26.3 occ:1.00 CO A:NCO104 0.0 26.3 1.0 N2 A:NCO104 2.0 23.1 1.0 N5 A:NCO104 2.0 22.9 1.0 N6 A:NCO104 2.0 23.7 1.0 N1 A:NCO104 2.0 24.2 1.0 N3 A:NCO104 2.0 22.9 1.0 N4 A:NCO104 2.0 20.7 1.0 OP2 A:A66 3.9 28.1 1.0 O A:HOH303 3.9 19.1 1.0 O6 A:G32 4.0 20.5 1.0 O A:HOH345 4.0 23.6 1.0 O6 A:G31 4.0 19.7 1.0 O A:HOH307 4.2 18.6 1.0 O A:HOH349 4.2 30.0 1.0 O A:HOH310 4.3 19.0 1.0 O A:HOH333 4.3 26.1 1.0 O A:HOH380 4.3 23.7 1.0 N7 A:G31 4.4 18.3 1.0 C6 A:G31 4.8 20.1 1.0 O A:HOH304 4.9 20.4 1.0 C6 A:G32 5.0 20.4 1.0 C5 A:G31 5.0 18.5 1.0

Cobalt binding site 5 out of 9 in the Crystal Structure of Guanine Riboswitch Bound to 6-O- Methylguanine


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 Guanine Riboswitch Bound to 6-O- Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co105 b:57.3 occ:1.00 CO A:NCO105 0.0 57.3 1.0 N1 A:NCO105 2.0 56.1 1.0 N2 A:NCO105 2.0 55.7 1.0 N4 A:NCO105 2.0 56.9 1.0 N5 A:NCO105 2.0 56.5 1.0 N6 A:NCO105 2.0 56.0 1.0 N3 A:NCO105 2.0 57.3 1.0 O A:HOH495 3.4 66.4 1.0 O A:HOH499 3.5 78.9 1.0 O A:HOH360 3.6 35.5 1.0 O A:HOH512 3.6 67.3 1.0 O A:HOH342 4.1 27.6 1.0 OP2 A:G37 4.2 21.7 1.0 O A:HOH371 4.2 31.0 1.0 O A:HOH399 4.3 43.9 1.0 O6 A:G38 4.3 20.8 1.0 N7 A:G38 4.5 21.1 1.0 O A:HOH356 4.6 47.1 1.0 O A:HOH424 4.7 21.4 1.0 N7 A:G37 4.7 21.5 1.0 O A:HOH436 4.8 30.8 1.0

Cobalt binding site 6 out of 9 in the Crystal Structure of Guanine Riboswitch Bound to 6-O- Methylguanine


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 Guanine Riboswitch Bound to 6-O- Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co107 b:69.6 occ:1.00 CO A:NCO107 0.0 69.6 1.0 N6 A:NCO107 2.0 69.1 1.0 N4 A:NCO107 2.0 69.0 1.0 N3 A:NCO107 2.0 69.8 1.0 N1 A:NCO107 2.0 69.8 1.0 N2 A:NCO107 2.0 69.2 1.0 N5 A:NCO107 2.0 69.5 1.0 OP1 A:C54 3.9 35.8 1.0 O A:HOH340 4.1 33.1 1.0 OP2 A:C41 4.2 21.2 1.0 O A:HOH312 4.2 32.0 1.0 O A:HOH314 4.5 17.8 1.0 O A:HOH362 4.5 28.5 1.0 OP1 A:C53 4.8 35.1 1.0 OP2 A:G42 4.9 21.4 1.0

Cobalt binding site 7 out of 9 in the Crystal Structure of Guanine Riboswitch Bound to 6-O- Methylguanine


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 Guanine Riboswitch Bound to 6-O- Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co108 b:61.8 occ:1.00 CO A:NCO108 0.0 61.8 1.0 N5 A:NCO108 2.0 61.5 1.0 N4 A:NCO108 2.0 60.9 1.0 N2 A:NCO108 2.0 61.6 1.0 N3 A:NCO108 2.0 61.8 1.0 N1 A:NCO108 2.0 61.5 1.0 N6 A:NCO108 2.0 61.4 1.0 O A:HOH420 3.8 41.5 1.0 O4 A:U47 4.0 39.2 1.0 O6 A:G46 4.2 31.9 1.0 N7 A:G46 4.6 32.1 1.0 C4 A:U47 5.0 37.5 1.0 O A:HOH379 5.0 39.2 1.0

Cobalt binding site 8 out of 9 in the Crystal Structure of Guanine Riboswitch Bound to 6-O- Methylguanine


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 Guanine Riboswitch Bound to 6-O- Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co109 b:88.9 occ:1.00 CO A:NCO109 0.0 88.9 1.0 N3 A:NCO109 2.0 88.2 1.0 N1 A:NCO109 2.0 88.2 1.0 N2 A:NCO109 2.0 88.1 1.0 N4 A:NCO109 2.0 88.5 1.0 N6 A:NCO109 2.0 88.2 1.0 N5 A:NCO109 2.0 88.1 1.0 O A:HOH387 3.8 49.8 1.0 OP1 A:A24 3.8 32.3 1.0 OP2 A:C71 4.0 24.4 1.0 O A:HOH465 4.3 45.5 1.0

Cobalt binding site 9 out of 9 in the Crystal Structure of Guanine Riboswitch Bound to 6-O- Methylguanine


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 Guanine Riboswitch Bound to 6-O- Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co112 b:34.3 occ:1.00 CO A:NCO112 0.0 34.3 1.0 N4 A:NCO112 2.0 41.8 0.6 N3 A:NCO112 2.0 42.6 0.6 N5 A:NCO112 2.0 42.7 0.6 N6 A:NCO112 2.0 42.6 0.6 N2 A:NCO112 2.0 41.8 0.6 N1 A:NCO112 2.0 42.3 0.6 OP1 A:G72 4.1 16.7 1.0 OP2 A:A73 4.9 31.9 1.0

S.D.Gilbert, F.E.Reyes, A.L.Edwards, R.T.Batey. Adaptive Ligand Binding By the Purine Riboswitch in the Recognition of Guanine and Adenine Analogs. Structure V. 17 857 2009.
ISSN: ISSN 0969-2126
PubMed: 19523903
DOI: 10.1016/J.STR.2009.04.009