Cobalt in PDB 3gog: Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine

The structure of Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine, PDB code: 3gog 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)	19.97 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.510, 35.120, 41.760, 90.00, 90.57, 90.00
R / Rfree (%)	22 / 25.6

The structure of Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Cobalt atom in the Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine (pdb code 3gog). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine, PDB code: 3gog:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:33.0 occ:1.00 CO A:NCO101 0.0 33.0 1.0 N2 A:NCO101 2.0 29.7 1.0 N1 A:NCO101 2.0 29.5 1.0 N3 A:NCO101 2.0 29.5 1.0 N4 A:NCO101 2.0 30.7 1.0 N5 A:NCO101 2.0 30.1 1.0 N6 A:NCO101 2.0 30.9 1.0 O A:HOH322 3.7 33.9 1.0 O A:HOH435 3.8 42.3 1.0 OP1 A:U67 3.9 25.2 1.0 O A:HOH358 4.0 29.3 1.0 O3' A:A66 4.2 24.6 1.0 O A:HOH315 4.4 35.3 1.0 O A:HOH349 4.5 71.2 1.0 P A:U67 4.7 25.3 1.0 O2' A:A66 5.0 29.4 1.0

Cobalt binding site 2 out of 8 in the Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:67.1 occ:1.00 CO A:NCO102 0.0 67.1 1.0 N2 A:NCO102 2.0 66.6 1.0 N4 A:NCO102 2.0 66.5 1.0 N3 A:NCO102 2.0 66.4 1.0 N6 A:NCO102 2.0 66.3 1.0 N1 A:NCO102 2.0 66.4 1.0 N5 A:NCO102 2.0 66.4 1.0 O A:HOH312 3.6 33.4 1.0 O A:HOH428 3.6 42.3 1.0 OP1 A:G56 3.7 37.6 1.0 O A:HOH464 3.8 47.9 1.0 OP1 A:G38 3.8 26.0 1.0 O A:HOH530 4.0 43.4 1.0 O A:HOH381 4.7 34.5 1.0 P A:G56 4.8 36.6 1.0 OP2 A:G56 4.8 36.5 1.0 C5' A:C39 4.9 30.4 1.0 P A:G38 5.0 27.9 1.0

Cobalt binding site 3 out of 8 in the Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:37.8 occ:1.00 CO A:NCO103 0.0 37.8 1.0 N3 A:NCO103 2.0 35.5 1.0 N4 A:NCO103 2.0 37.7 1.0 N6 A:NCO103 2.0 36.6 1.0 N1 A:NCO103 2.0 36.1 1.0 N5 A:NCO103 2.0 35.7 1.0 N2 A:NCO103 2.0 36.0 1.0 O A:HOH341 3.4 32.2 1.0 O4 A:U69 3.7 25.1 1.0 O A:HOH415 3.8 46.5 1.0 O6 A:G56 3.9 31.7 1.0 O A:HOH307 4.0 24.4 1.0 O A:HOH481 4.0 46.7 1.0 O A:HOH348 4.2 27.3 1.0 O A:HOH371 4.2 48.4 1.0 N7 A:G56 4.4 31.5 1.0 OP2 A:C39 4.4 29.8 1.0 O6 A:G68 4.5 25.1 1.0 C6 A:G56 4.7 32.1 1.0 OP1 A:C39 4.9 30.0 1.0 C5 A:G56 4.9 31.3 1.0 C4 A:U69 4.9 27.1 1.0 O6 A:G57 5.0 27.9 1.0

Cobalt binding site 4 out of 8 in the Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co104 b:31.2 occ:1.00 CO A:NCO104 0.0 31.2 1.0 N6 A:NCO104 2.0 28.6 1.0 N3 A:NCO104 2.0 28.2 1.0 N5 A:NCO104 2.0 28.4 1.0 N4 A:NCO104 2.0 27.5 1.0 N2 A:NCO104 2.0 28.4 1.0 N1 A:NCO104 2.0 28.5 1.0 O A:HOH306 3.7 25.1 1.0 O A:HOH334 3.8 27.5 1.0 OP2 A:A66 3.8 26.6 1.0 O6 A:G32 3.8 26.9 1.0 O A:HOH302 4.0 26.3 1.0 O6 A:G31 4.0 27.4 1.0 O A:HOH469 4.2 40.9 1.0 O A:HOH480 4.2 38.6 1.0 O A:HOH311 4.2 33.0 1.0 N7 A:G31 4.3 27.8 1.0 O A:HOH329 4.4 25.6 1.0 C6 A:G31 4.8 27.9 1.0 O A:HOH368 4.9 58.0 1.0 C6 A:G32 4.9 28.1 1.0 C5 A:G31 5.0 27.2 1.0

Cobalt binding site 5 out of 8 in the Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co105 b:76.1 occ:1.00 CO A:NCO105 0.0 76.1 1.0 N1 A:NCO105 2.0 75.5 1.0 N2 A:NCO105 2.0 75.5 1.0 N4 A:NCO105 2.0 75.7 1.0 N6 A:NCO105 2.0 75.0 1.0 N3 A:NCO105 2.0 75.8 1.0 N5 A:NCO105 2.0 75.5 1.0 O A:HOH324 3.7 41.0 1.0 O A:HOH547 3.8 66.3 1.0 O A:HOH408 3.9 61.1 1.0 O A:HOH413 4.0 38.2 1.0 O6 A:G38 4.1 26.0 1.0 OP2 A:G37 4.1 26.3 1.0 O A:HOH365 4.1 46.5 1.0 O A:HOH320 4.2 36.9 1.0 N7 A:G38 4.4 26.8 1.0 O A:HOH505 4.4 53.4 1.0 O A:HOH444 4.4 44.8 1.0 N7 A:G37 4.5 26.4 1.0 O A:HOH375 4.8 45.3 1.0 C6 A:G38 4.9 27.4 1.0

Cobalt binding site 6 out of 8 in the Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co107 b:93.1 occ:1.00 CO A:NCO107 0.0 93.1 1.0 N2 A:NCO107 2.0 92.8 1.0 N3 A:NCO107 2.0 93.0 1.0 N4 A:NCO107 2.0 93.0 1.0 N1 A:NCO107 2.0 92.9 1.0 N5 A:NCO107 2.0 92.9 1.0 N6 A:NCO107 2.0 93.0 1.0 O A:HOH404 3.7 40.9 1.0 OP2 A:C41 4.0 26.9 1.0 OP1 A:C54 4.0 38.3 1.0 OP1 A:C53 4.1 40.5 1.0 O A:HOH326 4.2 50.8 1.0 O A:HOH335 4.4 27.7 1.0 C5' A:C54 4.8 34.1 1.0 O A:HOH354 4.9 33.9 1.0 P A:C53 4.9 39.6 1.0 OP2 A:C53 4.9 40.7 1.0 O A:HOH467 5.0 39.7 1.0

Cobalt binding site 7 out of 8 in the Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co108 b:72.7 occ:1.00 CO A:NCO108 0.0 72.7 1.0 N3 A:NCO108 2.0 71.7 1.0 N4 A:NCO108 2.0 71.8 1.0 N2 A:NCO108 2.0 71.7 1.0 N5 A:NCO108 2.0 72.0 1.0 N6 A:NCO108 2.0 71.9 1.0 N1 A:NCO108 2.0 71.7 1.0 O4 A:U47 3.7 40.8 1.0 O A:HOH384 3.7 76.2 1.0 O A:HOH487 3.7 81.4 1.0 O6 A:G46 4.5 32.0 1.0 OP2 A:U51 4.6 46.7 1.0 C4 A:U47 4.7 40.2 1.0 OP1 A:C50 4.8 45.5 1.0 OP2 A:C50 4.8 44.3 1.0

Cobalt binding site 8 out of 8 in the Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Guanine Riboswitch A21G,U75C Mutant Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co112 b:59.9 occ:0.64 CO A:NCO112 0.0 59.9 0.6 N4 A:NCO112 2.0 58.9 0.6 N6 A:NCO112 2.0 59.1 0.6 N1 A:NCO112 2.0 58.9 0.6 N5 A:NCO112 2.0 58.7 0.6 N3 A:NCO112 2.0 58.9 0.6 N2 A:NCO112 2.0 58.9 0.6 O A:HOH366 3.9 42.0 1.0 OP1 A:G72 4.0 23.7 1.0 OP2 A:A73 4.9 35.8 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