Potassium 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:

Cobalt	(Co)	4 atoms
Strontium	(Sr)	1 atom
Magnesium	(Mg)	2 atoms

The binding sites of Potassium 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 Potassium atom.
In total 7 binding sites of Potassium where determined in the Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt, PDB code: 4rum:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in the Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K101 b:46.9 occ:1.00 O3' A:C51 3.2 17.9 1.0 OP1 A:G52 3.5 22.6 1.0 O2' A:C51 3.8 15.8 1.0 P A:G52 4.0 13.8 1.0 C3' A:C51 4.3 12.3 1.0 C4' A:C51 4.5 11.4 1.0 O5' A:G52 4.6 20.4 1.0 C2' A:C51 4.6 11.6 1.0

Potassium binding site 2 out of 7 in the Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K102 b:43.1 occ:1.00 O4 A:U49 2.6 15.6 1.0 O A:HOH209 2.6 16.3 1.0 O A:HOH218 2.7 17.6 1.0 O6 A:G58 2.9 10.2 1.0 O A:HOH234 3.0 16.0 1.0 C4 A:U49 3.6 9.8 1.0 N3 A:U49 3.8 9.7 1.0 C6 A:G58 4.0 9.4 1.0 O6 A:G59 4.6 10.5 1.0 N7 A:G58 4.6 10.3 1.0 C5 A:G58 4.7 9.6 1.0 C5 A:U49 4.9 9.0 1.0 O6 A:G50 4.9 12.5 1.0

Potassium binding site 3 out of 7 in the Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K103 b:54.6 occ:1.00 O A:HOH261 2.5 30.3 1.0 O2B A:GTP6 2.7 41.7 1.0 O A:HOH262 2.8 34.1 1.0 O A:HOH269 2.8 38.9 1.0 O1A A:GTP6 2.9 39.6 1.0 OP1 A:A91 3.9 37.0 1.0 PA A:GTP6 4.0 40.4 1.0 O2A A:GTP6 4.0 23.6 1.0 PB A:GTP6 4.1 38.1 1.0 O A:HOH271 4.1 37.8 1.0 O3A A:GTP6 4.4 41.4 1.0 O3B A:GTP6 4.8 33.6 1.0 OP2 A:G92 4.8 35.1 1.0 P A:A91 4.8 36.8 1.0 OP2 A:A91 4.9 37.6 1.0

Potassium binding site 4 out of 7 in the Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K104 b:73.5 occ:1.00 O4 A:U35 4.0 38.1 1.0 O4 A:U23 4.5 21.8 1.0 O6 A:G24 4.7 27.7 1.0 O6 A:G34 4.7 39.3 1.0 N7 A:G34 4.8 42.5 1.0

Potassium binding site 5 out of 7 in the Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:K105 b:50.5 occ:1.00 O A:HOH287 3.6 65.3 1.0 C5' A:C79 4.2 60.3 1.0 OP1 A:C79 4.7 62.9 1.0

Potassium binding site 6 out of 7 in the Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:K106 b:39.6 occ:1.00 O A:HOH274 2.6 35.2 1.0 O A:HOH275 2.6 11.9 1.0 O6 A:G86 2.8 23.6 1.0 O A:HOH273 2.9 29.4 1.0 C6 A:G86 3.9 13.8 1.0 OP2 A:U85 4.6 34.5 1.0 N7 A:G86 4.6 15.3 1.0 C5 A:G86 4.7 13.0 1.0 C5 A:U85 4.8 22.2 1.0 O4 A:U85 4.8 19.9 1.0 N1 A:G86 5.0 13.1 1.0

Potassium binding site 7 out of 7 in the Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of the Nico Transition-Metal Riboswitch Bound to Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:K107 b:74.1 occ:1.00 OP1 A:G13 4.2 41.9 1.0 OP1 A:C43 4.3 36.5 1.0 OP2 A:C44 4.7 19.4 1.0 OP2 A:A14 4.8 25.1 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