Cobalt in PDB 3v7e: Crystal Structure of Ybxf Bound to the Sam-I Riboswitch Aptamer

The structure of Crystal Structure of Ybxf Bound to the Sam-I Riboswitch Aptamer, PDB code: 3v7e was solved by N.J.Baird, J.Zhang, T.Hamma, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.54 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	191.762, 54.305, 106.366, 90.00, 116.56, 90.00
R / Rfree (%)	21.8 / 27.4

The structure of Crystal Structure of Ybxf Bound to the Sam-I Riboswitch Aptamer also contains other interesting chemical elements:

Magnesium

(Mg)

22 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of Ybxf Bound to the Sam-I Riboswitch Aptamer (pdb code 3v7e). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 18 binding sites of Cobalt where determined in the Crystal Structure of Ybxf Bound to the Sam-I Riboswitch Aptamer, PDB code: 3v7e:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 18 in the Crystal Structure of Ybxf Bound to the Sam-I Riboswitch Aptamer


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 Ybxf Bound to the Sam-I Riboswitch Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Co901 b:84.5 occ:1.00 CO C:NCO901 0.0 84.5 1.0 N6 C:NCO901 2.0 78.3 1.0 N3 C:NCO901 2.0 76.8 1.0 N5 C:NCO901 2.0 77.6 1.0 N2 C:NCO901 2.0 81.0 1.0 N1 C:NCO901 2.0 77.9 1.0 N4 C:NCO901 2.0 73.8 1.0 O4 C:U120 3.9 38.8 1.0 O4 C:U5 3.9 48.4 1.0 O4 C:U4 4.2 60.6 1.0 O6 C:G121 4.7 52.2 1.0 C4 C:U120 4.8 34.3 1.0

Cobalt binding site 2 out of 18 in the Crystal Structure of Ybxf Bound to the Sam-I Riboswitch Aptamer


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 Ybxf Bound to the Sam-I Riboswitch Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Co902 b:78.1 occ:1.00 CO C:NCO902 0.0 78.1 1.0 N6 C:NCO902 2.0 64.6 1.0 N2 C:NCO902 2.0 68.0 1.0 N4 C:NCO902 2.0 64.7 1.0 N5 C:NCO902 2.0 68.3 1.0 N3 C:NCO902 2.0 65.4 1.0 N1 C:NCO902 2.0 66.9 1.0 OP2 C:U26 3.9 56.4 1.0 C5 C:U26 4.0 56.6 1.0 N7 C:G28 4.3 45.2 1.0 O6 C:G27 4.4 53.0 1.0 OP2 C:C25 4.5 53.9 1.0 N7 C:G27 4.6 45.5 1.0 O6 C:G28 4.6 34.6 1.0 C6 C:U26 4.7 57.5 1.0 C4 C:U26 4.7 51.2 1.0 O4 C:U26 4.8 51.2 1.0

Cobalt binding site 3 out of 18 in the Crystal Structure of Ybxf Bound to the Sam-I Riboswitch Aptamer


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 Ybxf Bound to the Sam-I Riboswitch Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Co903 b:0.6 occ:1.00 CO C:NCO903 0.0 0.6 1.0 N6 C:NCO903 2.0 0.6 1.0 N5 C:NCO903 2.0 0.7 1.0 N2 C:NCO903 2.0 0.1 1.0 N4 C:NCO903 2.0 0.8 1.0 N3 C:NCO903 2.0 0.5 1.0 N1 C:NCO903 2.0 0.4 1.0 O6 C:G73 3.6 0.9 1.0 O4 C:U61 4.0 99.8 1.0 N7 C:G60 4.1 0.1 1.0 O6 C:G60 4.5 95.4 1.0 N1 C:NCO909 4.5 0.9 1.0 N6 C:A74 4.6 0.8 1.0 N4 C:C59 4.7 0.3 1.0 C6 C:G73 4.7 0.7 1.0 C5 C:C59 4.9 0.2 1.0 C5 C:G60 5.0 100.0 1.0

Cobalt binding site 4 out of 18 in the Crystal Structure of Ybxf Bound to the Sam-I Riboswitch Aptamer


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 Ybxf Bound to the Sam-I Riboswitch Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Co904 b:0.3 occ:1.00 CO C:NCO904 0.0 0.3 1.0 N1 C:NCO904 2.0 91.8 1.0 N4 C:NCO904 2.0 96.5 1.0 N6 C:NCO904 2.0 95.6 1.0 N5 C:NCO904 2.0 95.9 1.0 N2 C:NCO904 2.0 97.3 1.0 N3 C:NCO904 2.0 98.2 1.0 N7 C:G87 4.3 55.9 1.0 N1 C:A45 4.5 46.7 1.0 N6 C:A45 4.5 32.6 1.0 N7 C:G88 4.6 59.3 1.0 O6 C:G88 4.6 59.3 1.0 N1 C:A46 4.7 54.0 1.0 C2 C:A46 4.9 59.6 1.0 O6 C:G87 5.0 60.7 1.0

Cobalt binding site 5 out of 18 in the Crystal Structure of Ybxf Bound to the Sam-I Riboswitch Aptamer


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 Ybxf Bound to the Sam-I Riboswitch Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Co905 b:0.6 occ:1.00 CO C:NCO905 0.0 0.6 1.0 N1 C:NCO905 2.0 0.3 1.0 N5 C:NCO905 2.0 0.0 1.0 N4 C:NCO905 2.0 0.2 1.0 N3 C:NCO905 2.0 0.4 1.0 N2 C:NCO905 2.0 0.8 1.0 N6 C:NCO905 2.0 1.0 1.0 OP2 C:A10 3.0 59.9 1.0 OP2 C:U96 3.1 40.7 1.0 P C:U96 3.9 37.9 1.0 OP1 C:U96 3.9 18.0 1.0 OP1 C:A94 4.0 68.8 1.0 P C:A10 4.1 54.2 1.0 N7 C:G11 4.1 48.4 1.0 O5' C:A10 4.2 54.0 1.0 O6 C:G11 4.2 51.3 1.0 O3' C:U95 4.4 45.7 1.0 C8 C:A10 4.4 48.4 1.0 N7 C:A10 4.5 52.4 1.0 OP1 C:A10 4.7 45.4 1.0 C5 C:G11 4.9 45.2 1.0 C6 C:G11 4.9 43.1 1.0

Cobalt binding site 6 out of 18 in the Crystal Structure of Ybxf Bound to the Sam-I Riboswitch Aptamer


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 Ybxf Bound to the Sam-I Riboswitch Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Co906 b:0.4 occ:1.00 CO C:NCO906 0.0 0.4 1.0 N5 C:NCO906 2.0 96.8 1.0 N3 C:NCO906 2.0 96.8 1.0 N6 C:NCO906 2.0 99.7 1.0 N4 C:NCO906 2.0 96.0 1.0 N2 C:NCO906 2.0 96.0 1.0 N1 C:NCO906 2.0 92.5 1.0 N7 C:G114 4.3 46.8 1.0 O6 C:G114 4.5 64.3 1.0 C5 C:U113 4.7 37.8 1.0 N6 C:A115 4.9 59.1 1.0 O4 C:U113 4.9 43.5 1.0

Cobalt binding site 7 out of 18 in the Crystal Structure of Ybxf Bound to the Sam-I Riboswitch Aptamer


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 Ybxf Bound to the Sam-I Riboswitch Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Co907 b:74.0 occ:1.00 CO C:NCO907 0.0 74.0 1.0 N2 C:NCO907 2.0 64.9 1.0 N4 C:NCO907 2.0 64.1 1.0 N6 C:NCO907 2.0 63.7 1.0 N5 C:NCO907 2.0 64.4 1.0 N1 C:NCO907 2.0 68.5 1.0 N3 C:NCO907 2.0 53.6 1.0 O6 C:G100 3.8 59.9 1.0 C5 C:U99 4.1 56.1 1.0 N1 C:A116 4.2 57.7 1.0 N7 C:G100 4.3 41.8 1.0 OP2 C:U99 4.3 43.6 1.0 O2' C:U96 4.4 61.8 1.0 O4 C:U99 4.4 55.2 1.0 O2 C:U96 4.5 30.8 1.0 C2 C:A117 4.5 34.1 1.0 OP2 C:C98 4.7 42.5 1.0 C6 C:G100 4.7 47.6 1.0 C4 C:U99 4.7 57.3 1.0 N6 C:A24 4.7 76.8 1.0 C2 C:A116 4.9 63.2 1.0 C5 C:G100 4.9 44.9 1.0 N3 C:A117 5.0 36.7 1.0 N6 C:A116 5.0 60.1 1.0 N4 C:C25 5.0 60.8 1.0

Cobalt binding site 8 out of 18 in the Crystal Structure of Ybxf Bound to the Sam-I Riboswitch Aptamer


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 Ybxf Bound to the Sam-I Riboswitch Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Co908 b:0.5 occ:1.00 CO C:NCO908 0.0 0.5 1.0 N1 C:NCO908 2.0 0.0 1.0 N3 C:NCO908 2.0 0.2 1.0 N4 C:NCO908 2.0 0.0 1.0 N6 C:NCO908 2.0 0.5 1.0 N2 C:NCO908 2.0 0.8 1.0 N5 C:NCO908 2.0 0.8 1.0 N7 C:G42 4.0 72.5 1.0 OP2 C:C41 4.3 65.5 1.0 O6 C:G42 4.4 68.8 1.0 O6 C:G43 4.5 52.0 1.0 OP2 C:G42 4.7 72.1 1.0 C5 C:G42 4.9 73.0 1.0 C8 C:G42 4.9 63.8 1.0

Cobalt binding site 9 out of 18 in the Crystal Structure of Ybxf Bound to the Sam-I Riboswitch Aptamer


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 Ybxf Bound to the Sam-I Riboswitch Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Co909 b:0.5 occ:1.00 CO C:NCO909 0.0 0.5 1.0 N6 C:NCO909 2.0 0.3 1.0 N4 C:NCO909 2.0 0.8 1.0 N3 C:NCO909 2.0 0.9 1.0 N5 C:NCO909 2.0 0.6 1.0 N2 C:NCO909 2.0 0.8 1.0 N1 C:NCO909 2.0 0.9 1.0 N1 C:NCO903 4.7 0.4 1.0 OP2 C:A57 4.8 75.9 1.0 N4 C:C59 4.9 0.3 1.0 OP2 C:G73 5.0 98.8 1.0

Cobalt binding site 10 out of 18 in the Crystal Structure of Ybxf Bound to the Sam-I Riboswitch Aptamer


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 Ybxf Bound to the Sam-I Riboswitch Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Co910 b:0.0 occ:1.00 CO C:NCO910 0.0 0.0 1.0 N5 C:NCO910 2.0 0.4 1.0 N1 C:NCO910 2.0 0.6 1.0 N6 C:NCO910 2.0 0.4 1.0 N3 C:NCO910 2.0 0.0 1.0 N2 C:NCO910 2.0 0.0 1.0 N4 C:NCO910 2.0 0.4 1.0 O2' C:A46 3.8 56.4 1.0 N6 C:A84 4.3 94.1 1.0 N7 C:A84 4.4 0.9 1.0 N3 C:A46 4.7 60.1 1.0 C2' C:A46 4.8 45.0 1.0 C2 C:A46 4.9 59.6 1.0 C4 C:A46 4.9 57.5 1.0

N.J.Baird, J.Zhang, T.Hamma, A.R.Ferre-D'amare. Ybxf and Ylxq Are Bacterial Homologs of L7AE and Bind K-Turns But Not K-Loops. Rna V. 18 759 2012.
ISSN: ISSN 1355-8382
PubMed: 22355167
DOI: 10.1261/RNA.031518.111