Cobalt in PDB 2g9c: Modified Pyrimidines Specifically Bind the Purine Riboswitch

The structure of Modified Pyrimidines Specifically Bind the Purine Riboswitch, PDB code: 2g9c was solved by S.D.Gilbert, S.J.Mediatore, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	131.990, 35.100, 41.800, 90.00, 90.43, 90.00
R / Rfree (%)	19.5 / 24.2

Pages:

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

Binding sites:

The binding sites of Cobalt atom in the Modified Pyrimidines Specifically Bind the Purine Riboswitch (pdb code 2g9c). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 12 binding sites of Cobalt where determined in the Modified Pyrimidines Specifically Bind the Purine Riboswitch, PDB code: 2g9c:
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 Modified Pyrimidines Specifically Bind the Purine Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Modified Pyrimidines Specifically Bind the Purine Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:17.6 occ:1.00 CO A:NCO101 0.0 17.6 1.0 N1 A:NCO101 1.9 19.0 1.0 N2 A:NCO101 1.9 19.8 1.0 N5 A:NCO101 2.0 17.1 1.0 N6 A:NCO101 2.0 18.9 1.0 N4 A:NCO101 2.0 20.4 1.0 N3 A:NCO101 2.0 18.7 1.0 O A:HOH516 3.7 40.2 1.0 O A:HOH362 3.9 25.7 1.0 O A:HOH592 3.9 19.5 1.0 O A:HOH326 4.0 20.3 1.0 OP1 A:U67 4.1 11.7 1.0 O3' A:A66 4.3 13.0 1.0 O A:HOH368 4.4 47.6 1.0 P A:U67 4.9 11.9 1.0 O2' A:A66 5.0 13.4 1.0 O A:HOH505 5.0 37.6 1.0

Cobalt binding site 2 out of 12 in the Modified Pyrimidines Specifically Bind the Purine Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Modified Pyrimidines Specifically Bind the Purine Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:21.5 occ:1.00 CO A:NCO102 0.0 21.5 1.0 N3 A:NCO102 1.9 22.4 1.0 N4 A:NCO102 1.9 22.4 1.0 N2 A:NCO102 2.0 23.1 1.0 N6 A:NCO102 2.0 22.1 1.0 N5 A:NCO102 2.0 23.0 1.0 N1 A:NCO102 2.0 21.9 1.0 O A:HOH361 3.8 28.3 1.0 OP1 A:G38 3.9 13.7 1.0 O A:HOH391 3.9 25.9 1.0 O A:HOH325 4.0 23.8 1.0 OP1 A:G56 4.1 24.0 1.0 O A:HOH616 4.1 38.2 1.0 O A:HOH342 4.1 27.6 1.0 C5' A:C39 4.8 22.1 1.0 O A:HOH606 4.8 36.8 1.0 OP2 A:G56 4.9 24.2 1.0 P A:G38 4.9 12.2 1.0 O A:HOH371 5.0 27.2 1.0 OP2 A:G38 5.0 12.4 1.0

Cobalt binding site 3 out of 12 in the Modified Pyrimidines Specifically Bind the Purine Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Modified Pyrimidines Specifically Bind the Purine Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:19.5 occ:1.00 CO A:NCO103 0.0 19.5 1.0 N3 A:NCO103 1.9 20.8 1.0 N6 A:NCO103 1.9 22.0 1.0 N1 A:NCO103 2.0 19.5 1.0 N2 A:NCO103 2.0 21.2 1.0 N4 A:NCO103 2.0 22.5 1.0 N5 A:NCO103 2.0 21.9 1.0 O A:HOH388 3.9 23.7 1.0 O A:HOH442 3.9 27.9 1.0 O4 A:U69 4.0 16.1 1.0 O A:HOH412 4.0 36.1 1.0 O6 A:G56 4.1 15.9 1.0 O A:HOH434 4.1 27.8 1.0 O A:HOH320 4.2 18.0 1.0 O A:HOH463 4.2 23.9 1.0 O A:HOH374 4.3 24.4 1.0 OP2 A:C39 4.4 19.6 1.0 OP1 A:C39 4.5 16.9 1.0 N7 A:G56 4.6 15.6 1.0 O6 A:G68 4.8 12.7 1.0 O A:HOH632 4.9 69.2 1.0 P A:C39 5.0 15.1 1.0 C6 A:G56 5.0 16.5 1.0

Cobalt binding site 4 out of 12 in the Modified Pyrimidines Specifically Bind the Purine Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Modified Pyrimidines Specifically Bind the Purine Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co104 b:14.5 occ:1.00 CO A:NCO104 0.0 14.5 1.0 N1 A:NCO104 2.0 16.8 1.0 N2 A:NCO104 2.0 16.2 1.0 N5 A:NCO104 2.0 17.0 1.0 N6 A:NCO104 2.0 16.7 1.0 N3 A:NCO104 2.0 18.3 1.0 N4 A:NCO104 2.0 15.2 1.0 OP2 A:A66 3.8 19.7 1.0 O A:HOH304 3.9 18.4 1.0 O6 A:G32 4.0 13.4 1.0 O A:HOH346 4.0 22.6 1.0 O6 A:G31 4.2 13.9 1.0 O A:HOH340 4.2 20.2 1.0 O A:HOH305 4.2 13.9 1.0 O A:HOH319 4.2 17.2 1.0 O A:HOH306 4.2 16.4 1.0 O A:HOH336 4.3 19.4 1.0 N7 A:G31 4.4 12.8 1.0 O A:HOH309 4.8 18.1 1.0 C6 A:G31 4.9 14.0 1.0 O4 A:U30 5.0 11.7 1.0 O A:HOH370 5.0 24.8 1.0

Cobalt binding site 5 out of 12 in the Modified Pyrimidines Specifically Bind the Purine Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Modified Pyrimidines Specifically Bind the Purine Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co105 b:30.2 occ:1.00 CO A:NCO105 0.0 30.2 1.0 N1 A:NCO105 2.0 30.9 1.0 N5 A:NCO105 2.0 31.4 1.0 N4 A:NCO105 2.0 31.0 1.0 N6 A:NCO105 2.0 30.9 1.0 N2 A:NCO105 2.0 29.7 1.0 N3 A:NCO105 2.0 30.4 1.0 O A:HOH424 3.8 25.8 1.0 O A:HOH327 3.9 23.0 1.0 O A:HOH468 4.0 31.4 1.0 OP2 A:G37 4.0 13.1 1.0 O6 A:G38 4.1 12.6 1.0 O A:HOH415 4.2 24.6 1.0 N7 A:G38 4.3 11.4 1.0 N7 A:G37 4.3 13.4 1.0 O A:HOH357 4.4 25.6 1.0 O A:HOH547 4.5 25.4 1.0 O A:HOH499 4.5 35.2 1.0 O A:HOH590 4.6 58.2 1.0 O A:HOH609 4.9 42.7 1.0 C8 A:G37 4.9 13.7 1.0 C6 A:G38 4.9 14.5 1.0

Cobalt binding site 6 out of 12 in the Modified Pyrimidines Specifically Bind the Purine Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Modified Pyrimidines Specifically Bind the Purine Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co106 b:63.8 occ:1.00 CO A:NCO106 0.0 63.8 1.0 N1 A:NCO106 2.0 60.3 1.0 N3 A:NCO106 2.0 61.1 1.0 N5 A:NCO106 2.0 60.6 1.0 N6 A:NCO106 2.0 60.4 1.0 N2 A:NCO106 2.0 60.0 1.0 N4 A:NCO106 2.0 60.1 1.0 O A:HOH362 3.4 25.7 1.0 OP1 A:C26 3.6 27.4 1.0 O A:HOH460 3.7 33.0 1.0 O A:HOH532 3.8 27.9 1.0 O A:HOH507 4.0 38.9 1.0 O A:HOH618 4.5 33.5 1.0 OP1 A:G27 4.6 22.8 1.0 OP1 A:G68 4.6 14.4 1.0 OP2 A:G27 4.8 25.0 1.0 P A:C26 4.9 24.0 1.0 C5' A:C26 5.0 23.3 1.0

Cobalt binding site 7 out of 12 in the Modified Pyrimidines Specifically Bind the Purine Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Modified Pyrimidines Specifically Bind the Purine Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co107 b:70.4 occ:1.00 CO A:NCO107 0.0 70.4 1.0 N5 A:NCO107 2.0 70.3 1.0 N3 A:NCO107 2.0 70.6 1.0 N4 A:NCO107 2.0 70.1 1.0 N6 A:NCO107 2.0 70.1 1.0 N1 A:NCO107 2.0 70.0 1.0 N2 A:NCO107 2.0 70.3 1.0 OP1 A:C54 3.5 32.5 1.0 OP2 A:C41 3.7 15.4 1.0 O A:HOH390 3.9 35.8 1.0 OP1 A:C53 4.4 28.4 1.0 O A:HOH312 4.4 16.4 1.0 O A:HOH546 4.5 58.9 1.0 C5' A:C54 4.6 26.1 1.0 O A:HOH329 4.7 21.0 1.0 P A:C54 4.7 28.4 1.0 OP2 A:C53 4.8 26.9 1.0 O A:HOH476 4.9 33.5 1.0 P A:C41 4.9 14.9 1.0 P A:C53 4.9 27.0 1.0

Cobalt binding site 8 out of 12 in the Modified Pyrimidines Specifically Bind the Purine Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Modified Pyrimidines Specifically Bind the Purine Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co108 b:44.5 occ:1.00 CO A:NCO108 0.0 44.5 1.0 N4 A:NCO108 2.0 44.2 1.0 N5 A:NCO108 2.0 43.6 1.0 N6 A:NCO108 2.0 44.3 1.0 N1 A:NCO108 2.0 43.6 1.0 N3 A:NCO108 2.0 43.6 1.0 N2 A:NCO108 2.0 44.4 1.0 O A:HOH648 3.4 58.4 1.0 O4 A:U47 3.7 29.6 1.0 OP2 A:U51 4.0 33.8 1.0 O A:HOH448 4.1 41.8 1.0 OP2 A:C50 4.3 36.0 1.0 OP1 A:C50 4.7 36.9 1.0 C4 A:U47 4.7 29.1 1.0 O6 A:G46 4.9 25.5 1.0 P A:C50 4.9 36.2 1.0

Cobalt binding site 9 out of 12 in the Modified Pyrimidines Specifically Bind the Purine Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Modified Pyrimidines Specifically Bind the Purine Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co109 b:40.7 occ:1.00 CO A:NCO109 0.0 40.7 1.0 N6 A:NCO109 2.0 40.6 1.0 N4 A:NCO109 2.0 40.8 1.0 N3 A:NCO109 2.0 41.1 1.0 N1 A:NCO109 2.0 40.5 1.0 N2 A:NCO109 2.0 40.7 1.0 N5 A:NCO109 2.0 40.9 1.0 O A:HOH383 3.7 27.4 1.0 O A:HOH360 3.9 31.9 1.0 OP2 A:C71 4.0 16.1 1.0 O A:HOH623 4.1 40.8 1.0 O A:HOH585 4.2 45.0 1.0 OP1 A:A24 4.2 23.0 1.0 O A:HOH652 4.5 40.3 1.0 O A:HOH334 4.6 19.7 1.0 O A:HOH465 5.0 31.7 1.0

Cobalt binding site 10 out of 12 in the Modified Pyrimidines Specifically Bind the Purine Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Modified Pyrimidines Specifically Bind the Purine Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co110 b:89.2 occ:1.00 CO A:NCO110 0.0 89.2 1.0 N6 A:NCO110 2.0 88.4 1.0 N5 A:NCO110 2.0 88.4 1.0 N4 A:NCO110 2.0 88.5 1.0 N2 A:NCO110 2.0 88.5 1.0 N3 A:NCO110 2.0 88.4 1.0 N1 A:NCO110 2.0 88.4 1.0 O A:HOH548 4.0 37.2 1.0 OP1 A:A21 4.2 29.0 1.0 OP2 A:U22 4.6 24.9 1.0 O A:HOH528 4.9 38.0 1.0

S.D.Gilbert, S.J.Mediatore, R.T.Batey. Modified Pyrimidines Specifically Bind the Purine Riboswitch. J.Am.Chem.Soc. V. 128 14214 2006.
ISSN: ISSN 0002-7863
PubMed: 17076468
DOI: 10.1021/JA063645T