Cobalt in PDB 3gao: Crystal Structure of the Guanine Riboswitch Bound to Xanthine.

The structure of Crystal Structure of the Guanine Riboswitch Bound to Xanthine., PDB code: 3gao 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)	19.49 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	131.351, 35.099, 42.248, 90.00, 90.38, 90.00
R / Rfree (%)	21 / 24.6

The structure of Crystal Structure of the Guanine Riboswitch Bound to Xanthine. also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of the Guanine Riboswitch Bound to Xanthine. (pdb code 3gao). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 13 binding sites of Cobalt where determined in the Crystal Structure of the Guanine Riboswitch Bound to Xanthine., PDB code: 3gao:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 13 in the Crystal Structure of the Guanine Riboswitch Bound to Xanthine.


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 the Guanine Riboswitch Bound to Xanthine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:17.9 occ:1.00 CO A:NCO101 0.0 17.9 1.0 N2 A:NCO101 2.0 15.1 1.0 N1 A:NCO101 2.0 14.6 1.0 N3 A:NCO101 2.0 14.2 1.0 N4 A:NCO101 2.0 16.9 1.0 N6 A:NCO101 2.0 14.1 1.0 N5 A:NCO101 2.0 16.2 1.0 O A:HOH492 3.8 42.0 1.0 O A:HOH402 3.9 22.2 1.0 OP1 A:U67 4.0 11.6 1.0 O A:HOH484 4.1 27.6 1.0 O A:HOH478 4.2 35.5 1.0 OP1 A:C28 4.3 18.7 1.0 O3' A:A66 4.3 11.9 1.0 OP2 A:C28 4.4 19.5 1.0 P A:C28 4.8 22.1 1.0 P A:U67 4.8 12.1 1.0 O2' A:A66 4.9 14.6 1.0

Cobalt binding site 2 out of 13 in the Crystal Structure of the Guanine Riboswitch Bound to Xanthine.


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 the Guanine Riboswitch Bound to Xanthine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:25.7 occ:1.00 CO A:NCO102 0.0 25.7 1.0 N3 A:NCO102 2.0 25.9 1.0 N4 A:NCO102 2.0 25.7 1.0 N1 A:NCO102 2.0 25.3 1.0 N2 A:NCO102 2.0 26.2 1.0 N5 A:NCO102 2.0 26.2 1.0 N6 A:NCO102 2.0 24.0 1.0 O A:HOH366 3.7 21.0 1.0 OP1 A:G38 3.9 13.8 1.0 O A:HOH405 3.9 31.1 1.0 O A:HOH449 4.0 21.9 1.0 O A:HOH346 4.0 24.5 1.0 OP1 A:G56 4.1 14.6 1.0 O A:HOH423 4.2 29.7 1.0 OP2 A:G56 4.7 12.4 1.0 O A:HOH412 4.7 36.5 1.0 P A:G56 4.9 13.3 1.0 P A:G38 5.0 13.4 1.0 C5' A:C39 5.0 17.2 1.0

Cobalt binding site 3 out of 13 in the Crystal Structure of the Guanine Riboswitch Bound to Xanthine.


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 the Guanine Riboswitch Bound to Xanthine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:16.5 occ:1.00 CO A:NCO103 0.0 16.5 1.0 N1 A:NCO103 2.0 13.2 1.0 N3 A:NCO103 2.0 14.0 1.0 N6 A:NCO103 2.0 12.7 1.0 N2 A:NCO103 2.0 13.0 1.0 N4 A:NCO103 2.0 14.2 1.0 N5 A:NCO103 2.0 12.4 1.0 O A:HOH370 4.0 23.9 1.0 O4 A:U69 4.0 16.2 1.0 O A:HOH351 4.0 29.4 1.0 O6 A:G56 4.0 11.4 1.0 O A:HOH374 4.1 22.0 1.0 OP2 A:C39 4.1 16.1 1.0 O A:HOH385 4.1 32.2 1.0 O A:HOH342 4.2 25.3 1.0 O A:HOH319 4.2 13.7 1.0 O A:HOH308 4.2 15.9 1.0 OP1 A:C39 4.5 16.6 1.0 N7 A:G56 4.6 13.4 1.0 O6 A:G68 4.8 11.8 1.0 P A:C39 4.8 15.5 1.0 C6 A:G56 4.9 10.9 1.0

Cobalt binding site 4 out of 13 in the Crystal Structure of the Guanine Riboswitch Bound to Xanthine.


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 the Guanine Riboswitch Bound to Xanthine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co104 b:17.0 occ:1.00 CO A:NCO104 0.0 17.0 1.0 N1 A:NCO104 2.0 15.0 1.0 N3 A:NCO104 2.0 13.7 1.0 N5 A:NCO104 2.0 16.0 1.0 N2 A:NCO104 2.0 15.3 1.0 N4 A:NCO104 2.0 14.1 1.0 N6 A:NCO104 2.0 14.8 1.0 OP2 A:A66 3.8 17.9 1.0 O A:HOH321 3.9 19.9 1.0 O6 A:G32 3.9 12.0 1.0 O A:HOH303 4.0 16.3 1.0 O6 A:G31 4.0 7.5 1.0 O A:HOH302 4.1 17.7 1.0 O A:HOH326 4.2 17.5 1.0 O A:HOH336 4.3 19.2 1.0 O A:HOH345 4.3 20.3 1.0 O A:HOH341 4.3 28.1 1.0 N7 A:G31 4.4 12.4 1.0 C6 A:G31 4.8 10.2 1.0 O A:HOH324 4.9 16.8 1.0 C6 A:G32 5.0 11.9 1.0 C5 A:G31 5.0 11.5 1.0

Cobalt binding site 5 out of 13 in the Crystal Structure of the Guanine Riboswitch Bound to Xanthine.


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 the Guanine Riboswitch Bound to Xanthine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co105 b:24.5 occ:1.00 CO A:NCO105 0.0 24.5 1.0 N6 A:NCO105 2.0 20.9 1.0 N5 A:NCO105 2.0 20.9 1.0 N1 A:NCO105 2.0 20.9 1.0 N4 A:NCO105 2.0 20.3 1.0 N3 A:NCO105 2.0 20.2 1.0 N2 A:NCO105 2.0 19.5 1.0 O A:HOH508 3.6 34.8 1.0 O A:HOH407 3.7 42.6 1.0 O A:HOH490 3.9 26.8 1.0 O A:HOH475 4.0 36.6 1.0 O6 A:G38 4.0 13.9 1.0 OP2 A:G37 4.0 16.8 1.0 O A:HOH452 4.1 27.1 1.0 O A:HOH376 4.1 25.9 1.0 N7 A:G38 4.2 12.8 1.0 N7 A:G37 4.3 11.8 1.0 O A:HOH491 4.3 31.1 1.0 O A:HOH438 4.7 35.2 1.0 C6 A:G38 4.8 13.5 1.0 C5 A:G38 4.9 12.3 1.0 C8 A:G37 4.9 11.3 1.0

Cobalt binding site 6 out of 13 in the Crystal Structure of the Guanine Riboswitch Bound to Xanthine.


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 the Guanine Riboswitch Bound to Xanthine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co106 b:57.0 occ:1.00 CO A:NCO106 0.0 57.0 1.0 N4 A:NCO106 2.0 52.7 1.0 N2 A:NCO106 2.0 53.2 1.0 N5 A:NCO106 2.0 53.6 1.0 N3 A:NCO106 2.0 53.1 1.0 N1 A:NCO106 2.0 53.1 1.0 N6 A:NCO106 2.0 54.4 1.0 O A:HOH427 3.5 36.1 1.0 O A:HOH492 3.9 42.0 1.0 OP1 A:C26 4.0 26.4 1.0 OP1 A:G27 4.3 29.3 1.0 OP1 A:G68 4.3 13.2 1.0 O A:HOH477 4.9 35.6 1.0

Cobalt binding site 7 out of 13 in the Crystal Structure of the Guanine Riboswitch Bound to Xanthine.


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 the Guanine Riboswitch Bound to Xanthine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co107 b:78.7 occ:1.00 CO A:NCO107 0.0 78.7 1.0 N4 A:NCO107 2.0 77.0 1.0 N1 A:NCO107 2.0 77.0 1.0 N6 A:NCO107 2.0 77.0 1.0 N2 A:NCO107 2.0 76.9 1.0 N3 A:NCO107 2.0 77.0 1.0 N5 A:NCO107 2.0 77.4 1.0 OP2 A:C41 3.6 15.4 1.0 O A:HOH520 3.8 46.6 1.0 OP1 A:C54 3.8 30.4 1.0 O A:HOH312 4.2 17.1 1.0 O A:HOH386 4.6 34.5 1.0 OP1 A:C53 4.7 26.7 1.0 P A:C41 4.7 16.2 1.0 O A:HOH380 4.7 21.6 1.0 OP2 A:G42 4.8 15.1 1.0 OP1 A:C41 4.8 15.3 1.0 OP2 A:C53 5.0 26.9 1.0 O A:HOH311 5.0 20.8 1.0

Cobalt binding site 8 out of 13 in the Crystal Structure of the Guanine Riboswitch Bound to Xanthine.


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 the Guanine Riboswitch Bound to Xanthine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co108 b:59.9 occ:1.00 CO A:NCO108 0.0 59.9 1.0 N1 A:NCO108 2.0 58.5 1.0 N2 A:NCO108 2.0 58.4 1.0 N3 A:NCO108 2.0 57.0 1.0 N5 A:NCO108 2.0 58.4 1.0 N4 A:NCO108 2.0 57.3 1.0 N6 A:NCO108 2.0 58.4 1.0 O4 A:U47 3.6 26.8 1.0 O A:HOH497 4.0 41.7 1.0 O A:HOH527 4.3 35.2 1.0 OP2 A:U51 4.3 33.4 1.0 C4 A:U47 4.6 26.6 1.0 OP1 A:C50 4.7 32.8 1.0 OP2 A:C50 4.8 32.4 1.0 O6 A:G46 4.8 19.5 1.0

Cobalt binding site 9 out of 13 in the Crystal Structure of the Guanine Riboswitch Bound to Xanthine.


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 the Guanine Riboswitch Bound to Xanthine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co109 b:35.8 occ:1.00 CO A:NCO109 0.0 35.8 1.0 N6 A:NCO109 2.0 36.8 1.0 N5 A:NCO109 2.0 36.8 1.0 N3 A:NCO109 2.0 37.5 1.0 N4 A:NCO109 2.0 37.4 1.0 N1 A:NCO109 2.0 36.4 1.0 N2 A:NCO109 2.0 36.9 1.0 O A:HOH344 3.7 32.5 1.0 O A:HOH418 3.8 24.7 1.0 OP2 A:C71 4.0 15.7 1.0 OP1 A:A24 4.1 21.0 1.0 O A:HOH446 4.1 28.8 1.0 O A:HOH454 4.2 32.7 1.0 O A:HOH430 4.8 25.6 1.0

Cobalt binding site 10 out of 13 in the Crystal Structure of the Guanine Riboswitch Bound to Xanthine.


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 the Guanine Riboswitch Bound to Xanthine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co110 b:89.5 occ:1.00 CO A:NCO110 0.0 89.5 1.0 N5 A:NCO110 2.0 88.6 1.0 N3 A:NCO110 2.0 88.5 1.0 N6 A:NCO110 2.0 88.5 1.0 N4 A:NCO110 2.0 88.7 1.0 N1 A:NCO110 2.0 88.4 1.0 N2 A:NCO110 2.0 88.7 1.0 OP1 A:A21 3.5 23.6 1.0 OP2 A:U22 4.3 21.1 1.0 P A:A21 4.6 24.4 1.0 OP2 A:A21 4.6 23.2 1.0 O A:HOH511 4.6 42.7 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