Cobalt in PDB 3ger: Guanine Riboswitch Bound to 6-Chloroguanine

The structure of Guanine Riboswitch Bound to 6-Chloroguanine, PDB code: 3ger 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)	19.93 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.100, 35.120, 41.810, 90.00, 90.03, 90.00
R / Rfree (%)	21.6 / 23.4

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

Chlorine

(Cl)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cobalt atom in the Guanine Riboswitch Bound to 6-Chloroguanine (pdb code 3ger). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 12 binding sites of Cobalt where determined in the Guanine Riboswitch Bound to 6-Chloroguanine, PDB code: 3ger:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 12 in the Guanine Riboswitch 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 Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:22.1 occ:1.00 CO A:NCO101 0.0 22.1 1.0 N1 A:NCO101 2.0 21.2 1.0 N2 A:NCO101 2.0 22.6 1.0 N3 A:NCO101 2.0 21.2 1.0 N5 A:NCO101 2.0 20.0 1.0 N4 A:NCO101 2.0 22.6 1.0 N6 A:NCO101 2.0 21.6 1.0 O A:HOH501 3.7 42.2 1.0 O A:HOH360 3.9 24.3 1.0 O A:HOH361 3.9 30.5 1.0 O A:HOH350 4.0 28.7 1.0 OP1 A:U67 4.1 13.2 1.0 O A:HOH393 4.3 31.4 1.0 O3' A:A66 4.4 13.1 1.0 O A:HOH529 4.8 46.7 1.0 P A:U67 4.9 12.6 1.0

Cobalt binding site 2 out of 12 in the Guanine Riboswitch 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 Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:33.7 occ:1.00 CO A:NCO102 0.0 33.7 1.0 N4 A:NCO102 2.0 33.2 1.0 N3 A:NCO102 2.0 33.3 1.0 N6 A:NCO102 2.0 33.0 1.0 N2 A:NCO102 2.0 33.1 1.0 N1 A:NCO102 2.0 32.5 1.0 N5 A:NCO102 2.0 32.8 1.0 O A:HOH388 3.7 26.3 1.0 O A:HOH439 3.8 33.6 1.0 OP1 A:G56 3.9 27.5 1.0 OP1 A:G38 4.0 14.3 1.0 O A:HOH331 4.0 25.4 1.0 O A:HOH411 4.2 34.2 1.0 O A:HOH496 4.3 32.2 1.0 P A:G56 4.9 25.8 1.0 C5' A:C39 4.9 21.2 1.0 OP2 A:G56 5.0 26.9 1.0 OP2 A:G38 5.0 14.9 1.0

Cobalt binding site 3 out of 12 in the Guanine Riboswitch 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 Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:25.2 occ:1.00 CO A:NCO103 0.0 25.2 1.0 N4 A:NCO103 2.0 26.6 1.0 N3 A:NCO103 2.0 25.3 1.0 N6 A:NCO103 2.0 25.9 1.0 N2 A:NCO103 2.0 25.4 1.0 N1 A:NCO103 2.0 24.6 1.0 N5 A:NCO103 2.0 25.9 1.0 O A:HOH465 3.8 32.8 1.0 O4 A:U69 4.0 16.2 1.0 O A:HOH434 4.0 30.9 1.0 O A:HOH456 4.0 41.1 1.0 O6 A:G56 4.0 18.3 1.0 O A:HOH487 4.2 36.0 1.0 O A:HOH414 4.3 35.3 1.0 O A:HOH315 4.3 19.5 1.0 OP2 A:C39 4.3 18.6 1.0 O A:HOH425 4.3 27.4 1.0 N7 A:G56 4.6 18.8 1.0 O6 A:G68 4.7 13.8 1.0 OP1 A:C39 4.8 17.1 1.0 C6 A:G56 4.9 18.8 1.0

Cobalt binding site 4 out of 12 in the Guanine Riboswitch 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 Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co104 b:18.0 occ:1.00 CO A:NCO104 0.0 18.0 1.0 N1 A:NCO104 2.0 18.6 1.0 N6 A:NCO104 2.0 18.1 1.0 N2 A:NCO104 2.0 18.6 1.0 N5 A:NCO104 2.0 17.2 1.0 N3 A:NCO104 2.0 16.9 1.0 N4 A:NCO104 2.0 15.4 1.0 OP2 A:A66 3.8 20.2 1.0 O A:HOH304 3.9 17.6 1.0 O6 A:G32 4.0 15.8 1.0 O A:HOH319 4.0 21.0 1.0 O6 A:G31 4.1 13.1 1.0 O A:HOH340 4.2 19.8 1.0 O A:HOH327 4.2 22.1 1.0 O A:HOH306 4.2 16.3 1.0 O A:HOH310 4.2 19.3 1.0 O A:HOH332 4.3 18.8 1.0 N7 A:G31 4.4 14.2 1.0 O A:HOH307 4.8 17.5 1.0 C6 A:G31 4.9 13.4 1.0 O4 A:U30 5.0 12.9 1.0

Cobalt binding site 5 out of 12 in the Guanine Riboswitch 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 Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co105 b:54.8 occ:1.00 CO A:NCO105 0.0 54.8 1.0 N5 A:NCO105 2.0 54.2 1.0 N4 A:NCO105 2.0 54.4 1.0 N1 A:NCO105 2.0 54.2 1.0 N6 A:NCO105 2.0 54.1 1.0 N2 A:NCO105 2.0 54.1 1.0 N3 A:NCO105 2.0 54.4 1.0 O A:HOH514 3.7 31.1 1.0 O A:HOH474 3.9 35.9 1.0 O A:HOH343 4.0 28.1 1.0 OP2 A:G37 4.0 14.3 1.0 O6 A:G38 4.2 12.6 1.0 O A:HOH378 4.3 25.8 1.0 N7 A:G38 4.3 14.6 1.0 O A:HOH534 4.4 43.2 1.0 N7 A:G37 4.5 13.9 1.0 O A:HOH513 4.7 42.2 1.0 C6 A:G38 5.0 14.2 1.0

Cobalt binding site 6 out of 12 in the Guanine Riboswitch 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 Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co106 b:69.1 occ:1.00 CO A:NCO106 0.0 69.1 1.0 N1 A:NCO106 2.0 67.3 1.0 N6 A:NCO106 2.0 67.3 1.0 N3 A:NCO106 2.0 67.7 1.0 N5 A:NCO106 2.0 67.4 1.0 N2 A:NCO106 2.0 67.2 1.0 N4 A:NCO106 2.0 67.2 1.0 O A:HOH361 3.5 30.5 1.0 OP1 A:C26 3.7 26.2 1.0 O A:HOH498 3.7 32.8 1.0 O A:HOH477 3.9 31.7 1.0 OP1 A:G68 4.7 15.5 1.0 OP1 A:G27 4.8 23.6 1.0 O A:HOH529 4.9 46.7 1.0 OP2 A:G27 4.9 24.4 1.0

Cobalt binding site 7 out of 12 in the Guanine Riboswitch 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 Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co107 b:68.3 occ:1.00 CO A:NCO107 0.0 68.3 1.0 N5 A:NCO107 2.0 68.2 1.0 N4 A:NCO107 2.0 68.0 1.0 N1 A:NCO107 2.0 68.2 1.0 N6 A:NCO107 2.0 68.1 1.0 N3 A:NCO107 2.0 68.2 1.0 N2 A:NCO107 2.0 68.1 1.0 OP1 A:C54 3.8 29.6 1.0 OP2 A:C41 3.8 16.7 1.0 O A:HOH406 4.1 35.5 1.0 O A:HOH313 4.3 21.1 1.0 O A:HOH303 4.4 16.1 1.0 O A:HOH377 4.5 27.5 1.0 OP1 A:C53 4.6 29.0 1.0 C5' A:C54 4.8 26.2 1.0 OP2 A:G42 4.8 16.6 1.0 P A:C41 5.0 15.5 1.0 P A:C54 5.0 27.9 1.0

Cobalt binding site 8 out of 12 in the Guanine Riboswitch 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 Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co108 b:46.1 occ:1.00 CO A:NCO108 0.0 46.1 1.0 N1 A:NCO108 2.0 45.6 1.0 N4 A:NCO108 2.0 45.6 1.0 N6 A:NCO108 2.0 45.8 1.0 N3 A:NCO108 2.0 45.7 1.0 N2 A:NCO108 2.0 45.9 1.0 N5 A:NCO108 2.0 45.5 1.0 O4 A:U47 3.7 29.3 1.0 OP2 A:U51 4.0 35.5 1.0 O A:HOH495 4.3 39.9 1.0 OP2 A:C50 4.3 35.0 1.0 C4 A:U47 4.7 28.6 1.0 OP1 A:C50 4.7 35.4 1.0 O6 A:G46 4.8 23.6 1.0 P A:C50 4.9 35.0 1.0

Cobalt binding site 9 out of 12 in the Guanine Riboswitch Bound to 6-Chloroguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Guanine Riboswitch Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co109 b:50.7 occ:1.00 CO A:NCO109 0.0 50.7 1.0 N4 A:NCO109 2.0 50.1 1.0 N1 A:NCO109 2.0 49.9 1.0 N6 A:NCO109 2.0 49.9 1.0 N5 A:NCO109 2.0 50.1 1.0 N2 A:NCO109 2.0 49.9 1.0 N3 A:NCO109 2.0 50.2 1.0 O A:HOH363 3.9 26.5 1.0 OP1 A:A24 4.0 23.6 1.0 O A:HOH444 4.1 32.9 1.0 OP2 A:C71 4.1 16.7 1.0 O A:HOH454 4.3 36.0 1.0 O A:HOH427 4.7 65.5 1.0 O A:HOH349 4.9 21.4 1.0

Cobalt binding site 10 out of 12 in the Guanine Riboswitch Bound to 6-Chloroguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Guanine Riboswitch Bound to 6-Chloroguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co110 b:93.0 occ:1.00 CO A:NCO110 0.0 93.0 1.0 N3 A:NCO110 2.0 92.4 1.0 N6 A:NCO110 2.0 92.4 1.0 N1 A:NCO110 2.0 92.5 1.0 N4 A:NCO110 2.0 92.4 1.0 N2 A:NCO110 2.0 92.4 1.0 N5 A:NCO110 2.0 92.5 1.0 OP1 A:A21 3.8 28.1 1.0 OP2 A:U22 4.0 25.1 1.0 O A:HOH518 4.5 43.2 1.0 O A:HOH416 4.7 46.7 1.0 O A:HOH497 4.9 37.8 1.0 P A:A21 5.0 28.4 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