Cobalt in PDB 2b57: Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine

The structure of Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine, PDB code: 2b57 was solved by S.D.Gilbert, C.D.Stoddard, S.J.Wise, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.86 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	131.900, 34.800, 41.460, 90.00, 90.83, 90.00
R / Rfree (%)	22.8 / 28.9

The binding sites of Cobalt atom in the Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine (pdb code 2b57). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 9 binding sites of Cobalt where determined in the Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine, PDB code: 2b57:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cobalt binding site 1 out of 9 in the Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:31.9 occ:1.00 CO A:NCO101 0.0 31.9 1.0 N2 A:NCO101 2.0 24.6 1.0 N1 A:NCO101 2.0 25.0 1.0 N6 A:NCO101 2.0 27.5 1.0 N4 A:NCO101 2.0 31.1 1.0 N3 A:NCO101 2.0 27.9 1.0 N5 A:NCO101 2.0 28.8 1.0 O A:HOH314 3.9 36.9 1.0 O A:HOH363 3.9 37.7 1.0 OP1 A:U67 4.1 24.0 1.0 O3' A:A66 4.4 26.7 1.0 O A:HOH375 4.7 61.3 1.0 O A:HOH457 4.9 39.9 1.0 P A:U67 4.9 27.0 1.0 O2' A:A66 5.0 32.0 1.0

Cobalt binding site 2 out of 9 in the Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:75.0 occ:1.00 CO A:NCO102 0.0 75.0 1.0 N2 A:NCO102 2.0 74.6 1.0 N3 A:NCO102 2.0 74.2 1.0 N4 A:NCO102 2.0 74.0 1.0 N6 A:NCO102 2.0 74.0 1.0 N5 A:NCO102 2.0 73.9 1.0 N1 A:NCO102 2.0 73.7 1.0 O A:HOH453 3.5 41.5 1.0 O A:HOH400 3.7 34.9 1.0 OP1 A:G56 3.7 41.1 1.0 O A:HOH403 3.8 55.0 1.0 O A:HOH445 3.8 58.9 1.0 O A:HOH317 3.9 80.0 1.0 OP1 A:G38 4.1 24.8 1.0 O A:HOH418 4.1 47.7 1.0 O A:HOH442 4.3 43.1 1.0 OP2 A:G56 4.6 38.2 1.0 P A:G56 4.7 38.3 1.0

Cobalt binding site 3 out of 9 in the Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:36.5 occ:1.00 CO A:NCO103 0.0 36.5 1.0 N4 A:NCO103 2.0 35.2 1.0 N3 A:NCO103 2.0 33.1 1.0 N5 A:NCO103 2.0 36.5 1.0 N6 A:NCO103 2.0 36.3 1.0 N1 A:NCO103 2.0 36.6 1.0 N2 A:NCO103 2.0 34.1 1.0 O A:HOH481 3.7 79.3 1.0 O A:HOH349 3.8 45.3 1.0 O4 A:U69 3.8 24.0 1.0 O A:HOH335 4.0 47.8 1.0 O6 A:G56 4.1 27.5 1.0 O A:HOH360 4.1 36.7 1.0 O A:HOH329 4.1 39.0 1.0 O A:HOH467 4.3 60.9 1.0 N7 A:G56 4.4 27.1 1.0 OP2 A:C39 4.5 33.7 1.0 O A:HOH319 4.6 28.6 1.0 O6 A:G68 4.8 21.3 1.0 C6 A:G56 4.8 29.2 1.0 OP1 A:C39 4.9 27.1 1.0 C5 A:G56 5.0 27.1 1.0

Cobalt binding site 4 out of 9 in the Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co104 b:37.0 occ:1.00 CO A:NCO104 0.0 37.0 1.0 N3 A:NCO104 2.0 34.7 1.0 N1 A:NCO104 2.0 32.9 1.0 N4 A:NCO104 2.0 33.6 1.0 N6 A:NCO104 2.0 32.7 1.0 N5 A:NCO104 2.0 33.6 1.0 N2 A:NCO104 2.0 35.0 1.0 O A:HOH304 3.6 19.8 1.0 O6 A:G32 3.8 27.9 1.0 O6 A:G31 3.9 35.7 1.0 O A:HOH432 3.9 62.3 1.0 OP2 A:A66 4.0 33.5 1.0 O A:HOH318 4.0 36.2 1.0 O A:HOH333 4.2 33.9 1.0 N7 A:G31 4.2 30.4 1.0 O A:HOH365 4.5 44.2 1.0 O A:HOH447 4.5 46.4 1.0 O A:HOH377 4.6 19.5 1.0 C6 A:G31 4.7 32.4 1.0 C5 A:G31 4.8 30.3 1.0 C6 A:G32 4.8 27.8 1.0 O4 A:U30 4.9 29.1 1.0

Cobalt binding site 5 out of 9 in the Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co105 b:0.5 occ:1.00 CO A:NCO105 0.0 0.5 1.0 N2 A:NCO105 2.0 0.2 1.0 N3 A:NCO105 2.0 0.3 1.0 N4 A:NCO105 2.0 0.3 1.0 N5 A:NCO105 2.0 0.1 1.0 N6 A:NCO105 2.0 0.9 1.0 N1 A:NCO105 2.0 0.2 1.0 O A:HOH331 3.7 40.6 1.0 OP2 A:G37 4.1 34.5 1.0 N7 A:G38 4.2 31.7 1.0 O6 A:G38 4.4 34.9 1.0 O A:HOH370 4.5 43.3 1.0 N7 A:G37 4.6 28.1 1.0

Cobalt binding site 6 out of 9 in the Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co107 b:95.9 occ:1.00 CO A:NCO107 0.0 95.9 1.0 N4 A:NCO107 2.0 95.5 1.0 N3 A:NCO107 2.0 95.6 1.0 N1 A:NCO107 2.0 95.2 1.0 N2 A:NCO107 2.0 95.5 1.0 N6 A:NCO107 2.0 95.2 1.0 N5 A:NCO107 2.0 95.5 1.0 OP2 A:C41 3.6 31.0 1.0 O A:HOH474 4.0 40.1 1.0 OP1 A:C54 4.0 40.7 1.0 O A:HOH316 4.1 26.6 1.0 O A:HOH384 4.2 32.7 1.0 O A:HOH366 4.4 38.4 1.0 OP2 A:G42 4.6 29.5 1.0 OP1 A:C53 4.7 41.0 1.0 C5' A:C54 4.8 36.9 1.0 P A:C41 4.8 30.2 1.0

Cobalt binding site 7 out of 9 in the Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co108 b:64.0 occ:1.00 CO A:NCO108 0.0 64.0 1.0 N2 A:NCO108 2.0 63.0 1.0 N4 A:NCO108 2.0 63.3 1.0 N1 A:NCO108 2.0 62.3 1.0 N3 A:NCO108 2.0 63.1 1.0 N5 A:NCO108 2.0 63.2 1.0 N6 A:NCO108 2.0 63.2 1.0 O A:HOH411 3.4 50.1 1.0 O4 A:U47 3.6 47.6 1.0 O A:HOH471 3.6 54.0 1.0 OP2 A:U51 4.0 51.1 1.0 C4 A:U47 4.7 45.4 1.0 OP2 A:C50 4.7 53.8 1.0 OP1 A:C50 4.7 54.4 1.0 O6 A:G46 4.8 31.0 1.0 O A:HOH390 4.8 54.9 1.0

Cobalt binding site 8 out of 9 in the Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co109 b:78.7 occ:1.00 CO A:NCO109 0.0 78.7 1.0 N4 A:NCO109 2.0 78.8 1.0 N2 A:NCO109 2.0 78.0 1.0 N1 A:NCO109 2.0 78.3 1.0 N5 A:NCO109 2.0 78.2 1.0 N3 A:NCO109 2.0 78.5 1.0 N6 A:NCO109 2.0 78.6 1.0 O A:HOH301 3.7 31.6 1.0 OP2 A:C71 4.0 29.4 1.0 OP1 A:A24 4.0 36.4 1.0 O A:HOH368 4.1 46.8 1.0 O A:HOH325 4.6 23.5 1.0

Cobalt binding site 9 out of 9 in the Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Guanine Riboswitch C74U Mutant Bound to 2,6-Diaminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co112 b:57.8 occ:1.00 CO A:NCO112 0.0 57.8 1.0 N6 A:NCO112 2.0 56.1 1.0 N2 A:NCO112 2.0 55.8 1.0 N4 A:NCO112 2.0 55.6 1.0 N5 A:NCO112 2.0 56.3 1.0 N3 A:NCO112 2.0 55.5 1.0 N1 A:NCO112 2.0 56.3 1.0 O A:HOH422 3.5 47.8 1.0 OP1 A:G72 4.1 23.9 1.0 O A:HOH394 4.3 59.0 1.0

S.D.Gilbert, C.D.Stoddard, S.J.Wise, R.T.Batey. Thermodynamic and Kinetic Characterization of Ligand Binding to the Purine Riboswitch Aptamer Domain. J.Mol.Biol. V. 359 754 2006.
ISSN: ISSN 0022-2836
PubMed: 16650860
DOI: 10.1016/J.JMB.2006.04.003