Cobalt in PDB 5c7w: 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine.

The structure of 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine., PDB code: 5c7w was solved by A.R.Hernandez, Y.Shao, S.Hoshika, Z.Yang, S.A.Shelke, J.Herrou, H.-J.Kim, M.-J.Kim, J.A.Piccirilli, S.A.Benner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.92 / 3.22
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	52.180, 52.180, 274.500, 90.00, 90.00, 120.00
R / Rfree (%)	22.8 / 28

The binding sites of Cobalt atom in the 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine. (pdb code 5c7w). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine., PDB code: 5c7w:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine. within 5.0Å range: probe atom residue distance (Å) B Occ C:Co101 b:0.9 occ:1.00 CO C:NCO101 0.0 0.9 1.0 N3 C:NCO101 2.0 0.8 1.0 N6 C:NCO101 2.0 97.8 1.0 N1 C:NCO101 2.0 91.0 1.0 N2 C:NCO101 2.0 94.9 1.0 N4 C:NCO101 2.0 0.8 1.0 N5 C:NCO101 2.0 0.5 1.0 O4 C:U69 4.0 94.8 1.0 N7 C:G56 4.3 0.5 1.0 O6 C:G57 4.4 97.1 1.0 O6 C:G56 4.4 0.9 1.0 O6 C:G68 4.9 78.2 1.0

Cobalt binding site 2 out of 8 in the 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine. within 5.0Å range: probe atom residue distance (Å) B Occ C:Co102 b:0.5 occ:1.00 CO C:NCO102 0.0 0.5 1.0 N6 C:NCO102 2.0 0.1 1.0 N3 C:NCO102 2.0 0.3 1.0 N1 C:NCO102 2.0 92.6 1.0 N4 C:NCO102 2.0 0.4 1.0 N2 C:NCO102 2.0 0.5 1.0 N5 C:NCO102 2.0 0.2 1.0 N7 C:G38 4.4 93.2 1.0 OP2 C:G37 4.5 0.0 1.0 O6 C:G38 4.7 96.9 1.0 N7 C:G37 4.8 99.3 1.0

Cobalt binding site 3 out of 8 in the 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine. within 5.0Å range: probe atom residue distance (Å) B Occ C:Co103 b:0.1 occ:1.00 CO C:NCO103 0.0 0.1 1.0 N6 C:NCO103 2.0 89.1 1.0 N2 C:NCO103 2.0 91.4 1.0 N1 C:NCO103 2.0 96.6 1.0 N3 C:NCO103 2.0 98.7 1.0 N5 C:NCO103 2.0 0.9 1.0 N4 C:NCO103 2.0 89.3 1.0 O6 C:G32 4.0 0.5 1.0 OP2 C:A66 4.0 96.3 1.0 O6 C:G31 4.1 0.9 1.0 N7 C:G31 4.4 0.7 1.0 O4 C:U30 4.8 1.0 1.0 C5 C:U30 4.8 0.1 1.0 C6 C:G31 4.9 0.3 1.0 C6 C:G32 4.9 0.1 1.0 N7 C:G32 5.0 1.0 1.0

Cobalt binding site 4 out of 8 in the 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine. within 5.0Å range: probe atom residue distance (Å) B Occ C:Co104 b:0.3 occ:1.00 CO C:NCO104 0.0 0.3 1.0 N2 C:NCO104 2.0 0.7 1.0 N1 C:NCO104 2.0 0.7 1.0 N3 C:NCO104 2.0 0.5 1.0 N4 C:NCO104 2.0 0.8 1.0 N6 C:NCO104 2.0 0.5 1.0 N5 C:NCO104 2.0 0.9 1.0 N7 C:G62 4.1 0.8 1.0 O6 C:G62 4.4 0.4 1.0 OP2 C:C61 4.5 80.5 1.0 C5 C:G62 5.0 98.7 1.0

Cobalt binding site 5 out of 8 in the 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine. within 5.0Å range: probe atom residue distance (Å) B Occ C:Co105 b:0.8 occ:1.00 CO C:NCO105 0.0 0.8 1.0 N3 C:NCO105 2.0 0.1 1.0 N1 C:NCO105 2.0 0.2 1.0 N2 C:NCO105 2.0 0.3 1.0 N5 C:NCO105 2.0 0.3 1.0 N6 C:NCO105 2.0 0.2 1.0 N4 C:NCO105 2.0 0.8 1.0 O6 C:G46 4.3 0.0 1.0 O4 C:U47 4.3 0.7 1.0 OP2 C:U51 4.7 0.5 1.0 N7 C:G46 5.0 0.9 1.0

Cobalt binding site 6 out of 8 in the 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine. within 5.0Å range: probe atom residue distance (Å) B Occ C:Co106 b:0.9 occ:1.00 CO C:NCO106 0.0 0.9 1.0 N3 C:NCO106 2.0 0.3 1.0 N6 C:NCO106 2.0 0.2 1.0 N4 C:NCO106 2.0 0.1 1.0 N1 C:NCO106 2.0 0.3 1.0 N2 C:NCO106 2.0 0.2 1.0 N5 C:NCO106 2.0 1.0 1.0 OP2 C:A21 3.6 0.6 1.0 OP1 C:A21 3.8 1.0 1.0 P C:A21 4.2 0.4 1.0 OP2 C:U22 4.7 0.1 1.0 O5' C:A21 5.0 0.2 1.0

Cobalt binding site 7 out of 8 in the 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine. within 5.0Å range: probe atom residue distance (Å) B Occ C:Co107 b:0.4 occ:1.00 CO C:NCO107 0.0 0.4 1.0 N6 C:NCO107 2.0 0.1 1.0 N3 C:NCO107 2.0 0.1 1.0 N1 C:NCO107 2.0 0.8 1.0 N5 C:NCO107 2.0 0.6 1.0 N2 C:NCO107 2.0 0.9 1.0 N4 C:NCO107 2.0 0.6 1.0 OP2 C:U47 4.4 0.1 1.0 OP1 C:G46 5.0 0.2 1.0

Cobalt binding site 8 out of 8 in the 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of 5'-Monophosphate Z:P Guanine Riboswitch Bound to Hypoxanthine. within 5.0Å range: probe atom residue distance (Å) B Occ C:Co108 b:0.1 occ:1.00 CO C:NCO108 0.0 0.1 1.0 N3 C:NCO108 2.0 0.3 1.0 N6 C:NCO108 2.0 0.7 1.0 N2 C:NCO108 2.0 94.8 1.0 N5 C:NCO108 2.0 0.4 1.0 N4 C:NCO108 2.0 0.2 1.0 N1 C:NCO108 2.0 0.9 1.0 OP1 C:U69 4.5 91.6 1.0 OP1 C:C26 5.0 0.7 1.0

A.R.Hernandez, Y.Shao, S.Hoshika, Z.Yang, S.A.Shelke, J.Herrou, H.J.Kim, M.J.Kim, J.A.Piccirilli, S.A.Benner. A Crystal Structure of A Functional Rna Molecule Containing An Artificial Nucleobase Pair. Angew.Chem.Int.Ed.Engl. V. 54 9853 2015.
ISSN: ESSN 1521-3773
PubMed: 26223188
DOI: 10.1002/ANIE.201504731