Cobalt in PDB 3ges: Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine

The structure of Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine, PDB code: 3ges was solved by S.D.Gilbert, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.44 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.940, 35.040, 42.190, 90.00, 89.61, 90.00
R / Rfree (%)	23.8 / 28.3

The binding sites of Cobalt atom in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine (pdb code 3ges). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine, PDB code: 3ges:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant 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 the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:28.3 occ:1.00 CO A:NCO101 0.0 28.3 1.0 N4 A:NCO101 2.0 27.3 1.0 N2 A:NCO101 2.0 22.8 1.0 N6 A:NCO101 2.0 25.1 1.0 N1 A:NCO101 2.0 24.0 1.0 N5 A:NCO101 2.0 25.6 1.0 N3 A:NCO101 2.0 25.8 1.0 O A:HOH410 3.7 40.6 1.0 OP1 A:U67 4.2 19.4 1.0 O3' A:A66 4.4 20.3 1.0 OP2 A:C28 4.6 52.1 1.0 OP1 A:G27 4.8 55.6 1.0 OP1 A:C28 4.8 48.5 1.0 O2' A:A66 4.9 28.5 1.0 P A:U67 5.0 20.7 1.0

Cobalt binding site 2 out of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant 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 the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:45.0 occ:1.00 CO A:NCO102 0.0 45.0 1.0 N2 A:NCO102 2.0 46.9 1.0 N5 A:NCO102 2.0 45.5 1.0 N4 A:NCO102 2.0 45.6 1.0 N6 A:NCO102 2.0 45.5 1.0 N3 A:NCO102 2.0 45.3 1.0 N1 A:NCO102 2.0 44.5 1.0 OP1 A:G56 3.9 34.1 1.0 OP1 A:G38 4.0 20.2 1.0 O A:HOH333 4.0 27.7 1.0 OP2 A:G56 4.7 32.1 1.0 O A:HOH336 4.8 33.4 1.0 C5' A:C39 4.8 30.2 1.0 P A:G56 4.8 32.0 1.0 O A:HOH360 4.9 34.5 1.0

Cobalt binding site 3 out of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant 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 the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:35.5 occ:1.00 CO A:NCO103 0.0 35.5 1.0 N1 A:NCO103 2.0 33.0 1.0 N3 A:NCO103 2.0 32.6 1.0 N2 A:NCO103 2.0 33.7 1.0 N6 A:NCO103 2.0 35.6 1.0 N4 A:NCO103 2.0 34.5 1.0 N5 A:NCO103 2.0 34.3 1.0 O6 A:G56 3.9 30.7 1.0 O4 A:U69 3.9 24.5 1.0 O A:HOH339 4.4 24.7 1.0 N7 A:G56 4.4 28.5 1.0 OP2 A:C39 4.5 28.6 1.0 OP1 A:C39 4.7 26.3 1.0 C6 A:G56 4.7 30.4 1.0 O6 A:G68 4.9 17.2 1.0 C5 A:G56 5.0 29.2 1.0

Cobalt binding site 4 out of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant 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 the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co104 b:33.0 occ:1.00 CO A:NCO104 0.0 33.0 1.0 N3 A:NCO104 2.0 30.2 1.0 N1 A:NCO104 2.0 28.6 1.0 N6 A:NCO104 2.0 29.5 1.0 N5 A:NCO104 2.0 31.3 1.0 N2 A:NCO104 2.0 30.0 1.0 N4 A:NCO104 2.0 28.0 1.0 O A:HOH305 3.7 23.5 1.0 O6 A:G32 3.9 22.7 1.0 OP2 A:A66 3.9 31.5 1.0 O A:HOH328 4.0 29.2 1.0 O A:HOH312 4.1 16.3 1.0 O A:HOH300 4.1 20.2 1.0 O6 A:G31 4.2 20.1 1.0 N7 A:G31 4.4 22.6 1.0 O A:HOH316 4.6 18.2 1.0 O A:HOH322 4.8 21.6 1.0 C6 A:G32 4.9 22.8 1.0 C6 A:G31 4.9 22.1 1.0 O A:HOH330 4.9 35.4 1.0

Cobalt binding site 5 out of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant 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 the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co105 b:80.3 occ:1.00 CO A:NCO105 0.0 80.3 1.0 N6 A:NCO105 2.0 80.4 1.0 N2 A:NCO105 2.0 80.9 1.0 N3 A:NCO105 2.0 80.6 1.0 N1 A:NCO105 2.0 81.2 1.0 N5 A:NCO105 2.0 80.0 1.0 N4 A:NCO105 2.0 80.5 1.0 O A:HOH396 3.6 62.1 1.0 O A:HOH365 3.9 67.4 1.0 OP2 A:G37 3.9 28.7 1.0 O6 A:G38 4.3 28.5 1.0 N7 A:G38 4.3 25.8 1.0 O A:HOH398 4.4 37.1 1.0 O A:HOH311 4.4 36.0 1.0 O A:HOH320 4.5 31.5 1.0 N7 A:G37 4.7 23.4 1.0

Cobalt binding site 6 out of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant 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 the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co108 b:76.5 occ:1.00 CO A:NCO108 0.0 76.5 1.0 N3 A:NCO108 2.0 76.3 1.0 N5 A:NCO108 2.0 76.4 1.0 N4 A:NCO108 2.0 76.0 1.0 N2 A:NCO108 2.0 75.9 1.0 N1 A:NCO108 2.0 76.0 1.0 N6 A:NCO108 2.0 76.0 1.0 O A:HOH382 3.2 40.3 1.0 O4 A:U47 3.7 45.2 1.0 O6 A:G46 4.3 35.1 1.0 C4 A:U47 4.6 43.4 1.0 N7 A:G46 4.7 39.2 1.0 OP2 A:C50 4.9 46.6 1.0

Cobalt binding site 7 out of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant 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 the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co109 b:88.7 occ:1.00 CO A:NCO109 0.0 88.7 1.0 N1 A:NCO109 2.0 88.6 1.0 N4 A:NCO109 2.0 88.4 1.0 N6 A:NCO109 2.0 88.5 1.0 N5 A:NCO109 2.0 88.6 1.0 N2 A:NCO109 2.0 88.1 1.0 N3 A:NCO109 2.0 88.0 1.0 O A:HOH307 3.9 51.8 1.0 OP2 A:C71 4.0 28.0 1.0 OP1 A:A24 4.0 37.0 1.0

Cobalt binding site 8 out of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant 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 the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co112 b:50.2 occ:0.64 CO A:NCO112 0.0 50.2 0.6 N2 A:NCO112 2.0 49.3 0.6 N6 A:NCO112 2.0 49.5 0.6 N3 A:NCO112 2.0 49.6 0.6 N4 A:NCO112 2.0 48.7 0.6 N1 A:NCO112 2.0 49.8 0.6 N5 A:NCO112 2.0 49.4 0.6 O A:HOH353 3.1 51.2 1.0 OP1 A:G72 4.0 20.5 1.0 O A:HOH413 4.3 63.0 1.0 OP2 A:A73 5.0 35.7 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