Cobalt in PDB 4rum: Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt

The structure of Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt, PDB code: 4rum was solved by A.Ramesh, W.C.Winkler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.87 / 2.64
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	95.790, 95.790, 229.986, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.1

The structure of Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt also contains other interesting chemical elements:

Strontium	(Sr)	1 atom
Magnesium	(Mg)	2 atoms
Potassium	(K)	7 atoms

The binding sites of Cobalt atom in the Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt (pdb code 4rum). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt, PDB code: 4rum:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt


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 Nico Transition-Metal Riboswitch Bound to Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co108 b:12.2 occ:1.00 O A:HOH202 1.9 8.7 1.0 O A:HOH203 2.0 10.3 1.0 O A:HOH201 2.0 11.6 1.0 N7 A:G87 2.0 15.1 1.0 N7 A:G47 2.2 11.2 1.0 O2' A:G46 2.3 16.1 1.0 C8 A:G87 2.9 14.9 1.0 C8 A:G47 3.0 12.0 1.0 C2' A:G46 3.2 15.3 1.0 C5 A:G87 3.2 14.3 1.0 C5 A:G47 3.3 10.8 1.0 O2' A:G86 3.6 18.3 1.0 O6 A:G87 3.8 13.1 1.0 O6 A:G47 3.9 12.0 1.0 C6 A:G87 3.9 12.8 1.0 C6 A:G47 4.0 10.9 1.0 C1' A:G46 4.0 15.9 1.0 N9 A:G87 4.1 14.6 1.0 O A:HOH278 4.2 16.4 1.0 OP2 A:G47 4.2 17.3 1.0 N9 A:G47 4.3 10.0 1.0 C4 A:G87 4.3 15.8 1.0 O A:HOH239 4.3 20.2 1.0 OP2 A:G87 4.3 13.5 1.0 N1 A:A61 4.4 11.6 1.0 C4 A:G47 4.4 12.0 1.0 C3' A:G46 4.5 15.9 1.0 O3' A:G86 4.6 14.8 1.0 O3' A:G46 4.7 17.2 1.0 N9 A:G46 4.8 17.1 1.0 C2' A:G86 4.9 13.9 1.0 C5 A:C48 4.9 10.5 1.0 C2 A:A61 4.9 11.5 1.0 O A:HOH233 4.9 16.1 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt


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 Nico Transition-Metal Riboswitch Bound to Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co109 b:15.5 occ:1.00 O A:HOH216 1.9 17.7 1.0 N7 A:G88 2.0 15.7 1.0 O A:HOH214 2.0 21.9 1.0 N7 A:G46 2.1 14.4 1.0 O A:HOH217 2.1 12.0 1.0 O2' A:G87 2.1 15.8 1.0 C8 A:G88 2.8 19.4 1.0 C8 A:G46 3.0 16.6 1.0 C2' A:G87 3.1 15.0 1.0 C5 A:G88 3.2 17.0 1.0 C5 A:G46 3.2 15.6 1.0 O6 A:G46 3.6 15.1 1.0 O A:HOH215 3.7 23.6 1.0 O6 A:G88 3.8 20.1 1.0 C6 A:G46 3.8 15.2 1.0 O2' A:G45 3.8 16.2 1.0 C6 A:G88 3.9 19.1 1.0 C1' A:G87 3.9 14.8 1.0 N9 A:G88 4.1 18.4 1.0 OP2 A:G46 4.2 13.4 1.0 N9 A:G46 4.2 17.1 1.0 C4 A:G88 4.2 17.6 1.0 N1 A:A17 4.3 16.5 1.0 C4 A:G46 4.3 15.9 1.0 C3' A:G87 4.4 14.9 1.0 O3' A:G45 4.4 19.7 1.0 O A:HOH233 4.5 16.1 1.0 O3' A:G87 4.5 19.0 1.0 C2 A:A17 4.6 15.5 1.0 N9 A:G87 4.7 14.6 1.0 P A:G46 4.9 16.8 1.0 C2' A:G45 4.9 14.0 1.0 O4' A:G87 5.0 17.3 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt


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 Nico Transition-Metal Riboswitch Bound to Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co110 b:23.2 occ:1.00 O A:HOH208 1.9 9.3 1.0 N7 A:A14 1.9 17.1 1.0 O A:HOH213 2.0 17.3 1.0 O A:HOH212 2.0 19.5 1.0 O A:HOH220 2.1 21.1 1.0 N7 A:G45 2.2 14.1 1.0 C8 A:A14 2.8 18.5 1.0 C5 A:A14 3.0 16.1 1.0 C5 A:G45 3.1 12.1 1.0 C8 A:G45 3.2 13.6 1.0 O6 A:G45 3.2 17.2 1.0 C6 A:G45 3.5 13.6 1.0 N6 A:A14 3.5 15.7 1.0 C6 A:A14 3.7 17.2 1.0 N9 A:A14 4.0 19.2 1.0 C4 A:A14 4.1 15.2 1.0 OP2 A:A14 4.3 25.1 1.0 C4 A:G45 4.3 11.7 1.0 N9 A:G45 4.3 13.8 1.0 OP2 A:G45 4.3 10.0 1.0 O A:HOH249 4.4 18.3 1.0 N7 A:G13 4.8 18.8 1.0 N1 A:G45 4.9 13.6 1.0 C5 A:C44 4.9 11.2 1.0 O5' A:A14 5.0 21.3 1.0 N1 A:A14 5.0 15.6 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt


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 Nico Transition-Metal Riboswitch Bound to Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co111 b:14.0 occ:1.00 O A:HOH206 2.2 12.7 1.0 O A:HOH207 2.3 14.2 1.0 O A:HOH211 2.4 15.8 1.0 O A:HOH236 2.5 18.4 1.0 O A:HOH210 2.5 12.9 1.0 O6 A:G18 2.6 15.7 1.0 N7 A:G18 2.9 14.3 1.0 C6 A:G18 3.3 14.2 1.0 C5 A:G18 3.4 12.2 1.0 N2 A:G45 4.0 15.9 1.0 C8 A:G18 4.1 15.5 1.0 OP2 A:A17 4.2 21.7 1.0 O A:HOH259 4.2 14.2 1.0 OP1 A:C16 4.4 19.5 1.0 O6 A:G19 4.6 10.7 1.0 N7 A:A17 4.6 17.9 1.0 N4 A:C44 4.6 11.0 1.0 N1 A:A41 4.7 22.4 1.0 N1 A:G18 4.7 14.2 1.0 C4 A:G18 4.7 12.2 1.0 N7 A:G19 4.7 10.3 1.0 C2 A:G45 4.8 16.4 1.0 C2 A:A41 4.9 21.9 1.0 C8 A:A17 5.0 18.2 1.0

K.Furukawa, A.Ramesh, Z.Zhou, Z.Weinberg, T.Vallery, W.C.Winkler, R.R.Breaker. Bacterial Riboswitches Cooperatively Bind Ni(2+) or Co(2+) Ions and Control Expression of Heavy Metal Transporters. Mol.Cell V. 57 1088 2015.
ISSN: ISSN 1097-2765
PubMed: 25794617
DOI: 10.1016/J.MOLCEL.2015.02.009