Cobalt in PDB 3g4m: Crystal Structure of Guanine Riboswitch Bound to 2- Aminopurine

The structure of Crystal Structure of Guanine Riboswitch Bound to 2- Aminopurine, PDB code: 3g4m 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)	19.92 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.430, 35.160, 42.240, 90.00, 91.18, 90.00
R / Rfree (%)	22.9 / 27.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of Guanine Riboswitch Bound to 2- Aminopurine (pdb code 3g4m). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 11 binding sites of Cobalt where determined in the Crystal Structure of Guanine Riboswitch Bound to 2- Aminopurine, PDB code: 3g4m:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 11 in the Crystal Structure of Guanine Riboswitch Bound to 2- Aminopurine


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 2- Aminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:27.6 occ:1.00 CO A:NCO101 0.0 27.6 1.0 N5 A:NCO101 2.0 27.4 1.0 N4 A:NCO101 2.0 28.4 1.0 N6 A:NCO101 2.0 26.4 1.0 N3 A:NCO101 2.0 27.0 1.0 N2 A:NCO101 2.0 27.3 1.0 N1 A:NCO101 2.0 27.2 1.0 O A:HOH542 3.7 31.5 1.0 OP1 A:U67 3.9 24.0 1.0 O3' A:A66 4.3 26.1 1.0 P A:U67 4.7 24.1 1.0 O A:HOH509 4.9 33.0 1.0 O2' A:A66 4.9 27.1 1.0

Cobalt binding site 2 out of 11 in the Crystal Structure of Guanine Riboswitch Bound to 2- Aminopurine


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 2- Aminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:47.7 occ:1.00 CO A:NCO102 0.0 47.7 1.0 N2 A:NCO102 2.0 46.9 1.0 N4 A:NCO102 2.0 45.6 1.0 N6 A:NCO102 2.0 46.2 1.0 N3 A:NCO102 2.0 45.5 1.0 N1 A:NCO102 2.0 45.2 1.0 N5 A:NCO102 2.0 46.5 1.0 O A:HOH510 3.7 26.7 1.0 O A:HOH554 4.0 32.1 1.0 OP1 A:G56 4.1 29.7 1.0 OP1 A:G38 4.2 18.6 1.0 OP2 A:G56 4.7 27.3 1.0 P A:G56 4.9 29.0 1.0

Cobalt binding site 3 out of 11 in the Crystal Structure of Guanine Riboswitch Bound to 2- Aminopurine


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 2- Aminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:27.7 occ:1.00 CO A:NCO103 0.0 27.7 1.0 N1 A:NCO103 2.0 22.4 1.0 N2 A:NCO103 2.0 19.9 1.0 N4 A:NCO103 2.0 22.6 1.0 N3 A:NCO103 2.0 23.0 1.0 N5 A:NCO103 2.0 24.8 1.0 N6 A:NCO103 2.0 23.6 1.0 O A:HOH506 3.4 36.4 1.0 O A:HOH514 3.5 39.1 1.0 OP2 A:C39 3.7 27.8 1.0 O4 A:U69 3.9 21.9 1.0 O6 A:G56 4.2 31.4 1.0 O A:HOH508 4.2 27.9 1.0 N7 A:G56 4.5 29.7 1.0 O6 A:G68 4.7 25.4 1.0 C6 A:G56 5.0 32.1 1.0 N7 A:G55 5.0 23.8 1.0

Cobalt binding site 4 out of 11 in the Crystal Structure of Guanine Riboswitch Bound to 2- Aminopurine


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 2- Aminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co104 b:28.3 occ:1.00 CO A:NCO104 0.0 28.3 1.0 N6 A:NCO104 2.0 22.3 1.0 N3 A:NCO104 2.0 24.3 1.0 N4 A:NCO104 2.0 25.7 1.0 N5 A:NCO104 2.0 23.1 1.0 N1 A:NCO104 2.0 23.3 1.0 N2 A:NCO104 2.0 25.5 1.0 O A:HOH503 3.5 25.0 1.0 O A:HOH501 3.7 5.2 1.0 O6 A:G32 3.8 22.0 1.0 O6 A:G31 3.9 22.4 1.0 OP2 A:A66 4.0 30.6 1.0 N7 A:G31 4.3 15.8 1.0 O A:HOH523 4.4 21.3 1.0 O A:HOH525 4.6 27.9 1.0 C6 A:G31 4.8 18.2 1.0 C6 A:G32 4.8 19.0 1.0 C5 A:G31 4.9 16.4 1.0

Cobalt binding site 5 out of 11 in the Crystal Structure of Guanine Riboswitch Bound to 2- Aminopurine


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 2- Aminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co105 b:56.6 occ:1.00 CO A:NCO105 0.0 56.6 1.0 N6 A:NCO105 2.0 54.4 1.0 N4 A:NCO105 2.0 55.3 1.0 N5 A:NCO105 2.0 54.3 1.0 N2 A:NCO105 2.0 53.7 1.0 N1 A:NCO105 2.0 53.5 1.0 N3 A:NCO105 2.0 55.2 1.0 O6 A:G38 4.0 22.0 1.0 O A:HOH539 4.0 59.2 1.0 N7 A:G38 4.1 24.4 1.0 OP2 A:G37 4.3 23.5 1.0 N7 A:G37 4.5 21.1 1.0 C6 A:G38 4.8 21.7 1.0 C5 A:G38 4.8 23.3 1.0

Cobalt binding site 6 out of 11 in the Crystal Structure of Guanine Riboswitch Bound to 2- Aminopurine


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 2- Aminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co107 b:0.5 occ:1.00 CO A:NCO107 0.0 0.5 1.0 N3 A:NCO107 2.0 0.1 1.0 N6 A:NCO107 2.0 0.2 1.0 N5 A:NCO107 2.0 0.3 1.0 N2 A:NCO107 2.0 0.9 1.0 N1 A:NCO107 2.0 1.0 1.0 N4 A:NCO107 2.0 0.2 1.0 OP1 A:C54 3.6 31.5 1.0 O A:HOH562 3.6 29.3 1.0 OP1 A:C53 4.2 44.4 1.0 OP2 A:C41 4.2 20.1 1.0 C5' A:C54 4.8 27.5 1.0 OP2 A:C53 4.9 43.4 1.0 P A:C53 4.9 44.2 1.0 P A:C54 5.0 31.4 1.0

Cobalt binding site 7 out of 11 in the Crystal Structure of Guanine Riboswitch Bound to 2- Aminopurine


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 2- Aminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co108 b:85.5 occ:1.00 CO A:NCO108 0.0 85.5 1.0 N2 A:NCO108 2.0 84.2 1.0 N5 A:NCO108 2.0 84.2 1.0 N6 A:NCO108 2.0 83.8 1.0 N1 A:NCO108 2.0 84.2 1.0 N4 A:NCO108 2.0 83.3 1.0 N3 A:NCO108 2.0 83.5 1.0 O4 A:U47 4.0 52.7 1.0 O A:HOH553 4.2 48.2 1.0 O6 A:G46 4.4 34.2 1.0 OP2 A:C50 4.9 51.8 1.0 OP2 A:U51 4.9 48.9 1.0

Cobalt binding site 8 out of 11 in the Crystal Structure of Guanine Riboswitch Bound to 2- Aminopurine


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 2- Aminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co109 b:0.5 occ:1.00 CO A:NCO109 0.0 0.5 1.0 N4 A:NCO109 2.0 0.3 1.0 N6 A:NCO109 2.0 1.0 1.0 N3 A:NCO109 2.0 0.1 1.0 N1 A:NCO109 2.0 0.1 1.0 N2 A:NCO109 2.0 0.1 1.0 N5 A:NCO109 2.0 0.2 1.0 OP2 A:C71 4.0 27.2 1.0 OP1 A:A24 4.4 35.6 1.0 O A:HOH507 4.4 20.2 1.0 O A:HOH522 4.7 29.6 1.0

Cobalt binding site 9 out of 11 in the Crystal Structure of Guanine Riboswitch Bound to 2- Aminopurine


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 2- Aminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co110 b:0.2 occ:1.00 CO A:NCO110 0.0 0.2 1.0 N5 A:NCO110 2.0 0.9 1.0 N4 A:NCO110 2.0 0.9 1.0 N2 A:NCO110 2.0 0.9 1.0 N6 A:NCO110 2.0 0.0 1.0 N3 A:NCO110 2.0 0.8 1.0 N1 A:NCO110 2.0 0.0 1.0 OP2 A:U22 3.7 40.4 1.0 OP1 A:A21 3.9 43.9 1.0 O A:HOH531 4.5 32.3 1.0 P A:U22 5.0 39.8 1.0

Cobalt binding site 10 out of 11 in the Crystal Structure of Guanine Riboswitch Bound to 2- Aminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Crystal Structure of Guanine Riboswitch Bound to 2- Aminopurine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co111 b:0.5 occ:1.00 CO A:NCO111 0.0 0.5 1.0 N2 A:NCO111 2.0 0.1 1.0 N6 A:NCO111 2.0 0.2 1.0 N4 A:NCO111 2.0 0.1 1.0 N5 A:NCO111 2.0 0.2 1.0 N3 A:NCO111 2.0 0.1 1.0 N1 A:NCO111 2.0 0.2 1.0 O A:HOH543 3.9 46.9 1.0 OP2 A:A33 4.5 26.2 1.0 OP2 A:G32 4.5 15.9 1.0 OP2 A:A65 4.9 36.8 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