Cobalt in PDB 6vmy: Structure of the B. Subtilis Cobalamin Riboswitch

The structure of Structure of the B. Subtilis Cobalamin Riboswitch, PDB code: 6vmy was solved by C.W.Chan, A.Mondragon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.21 / 3.25
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	118.282, 118.282, 261.547, 90.00, 90.00, 120.00
R / Rfree (%)	26.3 / 27.9

The structure of Structure of the B. Subtilis Cobalamin Riboswitch also contains other interesting chemical elements:

Magnesium

(Mg)

12 atoms

The binding sites of Cobalt atom in the Structure of the B. Subtilis Cobalamin Riboswitch (pdb code 6vmy). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Structure of the B. Subtilis Cobalamin Riboswitch, PDB code: 6vmy:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co405 b:0.4 occ:1.00 CO A:NCO405 0.0 0.4 1.0 N2 A:NCO405 2.0 0.3 1.0 N4 A:NCO405 2.0 1.0 1.0 N3 A:NCO405 2.0 0.4 1.0 N6 A:NCO405 2.0 0.1 1.0 N1 A:NCO405 2.0 0.5 1.0 N5 A:NCO405 2.0 0.4 1.0 O6 A:G212 4.2 0.3 1.0 O4 A:U213 4.4 0.7 1.0 OP2 A:U311 4.7 99.4 1.0

Cobalt binding site 2 out of 8 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co406 b:1.0 occ:1.00 CO A:NCO406 0.0 1.0 1.0 N6 A:NCO406 2.0 0.7 1.0 N2 A:NCO406 2.0 0.6 1.0 N3 A:NCO406 2.0 0.0 1.0 N5 A:NCO406 2.0 0.4 1.0 N4 A:NCO406 2.0 0.5 1.0 N1 A:NCO406 2.0 0.1 1.0 OP2 A:C271 4.1 0.4 1.0 O6 A:G268 4.2 0.4 1.0 N2 A:NCO408 4.3 0.0 1.0 N4 A:C274 4.4 0.4 1.0 OP2 A:C272 4.6 0.7 1.0 N3 A:NCO408 5.0 0.6 1.0

Cobalt binding site 3 out of 8 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co407 b:0.9 occ:1.00 CO A:NCO407 0.0 0.9 1.0 N4 A:NCO407 2.0 0.1 1.0 N2 A:NCO407 2.0 1.0 1.0 N6 A:NCO407 2.0 0.5 1.0 N1 A:NCO407 2.0 0.6 1.0 N3 A:NCO407 2.0 0.3 1.0 N5 A:NCO407 2.0 0.2 1.0 O6 A:G224 4.3 0.6 1.0 N7 A:G222 4.5 0.3 1.0 O6 A:G222 4.9 0.7 1.0

Cobalt binding site 4 out of 8 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co408 b:0.1 occ:1.00 CO A:NCO408 0.0 0.1 1.0 N2 A:NCO408 2.0 0.0 1.0 N4 A:NCO408 2.0 0.1 1.0 N1 A:NCO408 2.0 0.8 1.0 N5 A:NCO408 2.0 0.9 1.0 N3 A:NCO408 2.0 0.6 1.0 N6 A:NCO408 2.0 0.5 1.0 OP2 A:G267 3.7 0.1 1.0 OP1 A:C270 3.8 0.7 1.0 N6 A:NCO406 4.7 0.7 1.0 N7 A:G267 4.9 0.4 1.0 N3 A:NCO406 4.9 0.0 1.0 P A:G267 5.0 0.6 1.0 C8 A:G267 5.0 0.2 1.0

Cobalt binding site 5 out of 8 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co409 b:0.7 occ:1.00 CO A:NCO409 0.0 0.7 1.0 N2 A:NCO409 2.0 0.8 1.0 N4 A:NCO409 2.0 0.7 1.0 N6 A:NCO409 2.0 0.2 1.0 N3 A:NCO409 2.0 0.2 1.0 N1 A:NCO409 2.0 0.7 1.0 N5 A:NCO409 2.0 0.9 1.0 O4 A:U219 4.3 0.2 1.0 N7 A:G217 4.4 0.9 1.0 O6 A:G218 4.6 0.5 1.0 OP2 A:C230 4.6 0.9 1.0 OP1 A:C230 4.9 1.0 1.0 N7 A:G218 5.0 0.8 1.0

Cobalt binding site 6 out of 8 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co410 b:0.7 occ:1.00 CO A:NCO410 0.0 0.7 1.0 N3 A:NCO410 2.0 0.9 1.0 N2 A:NCO410 2.0 1.0 1.0 N6 A:NCO410 2.0 0.9 1.0 N5 A:NCO410 2.0 0.6 1.0 N1 A:NCO410 2.0 1.0 1.0 N4 A:NCO410 2.0 0.0 1.0

Cobalt binding site 7 out of 8 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co411 b:0.1 occ:1.00 CO A:NCO411 0.0 0.1 1.0 N4 A:NCO411 2.0 0.6 1.0 N6 A:NCO411 2.0 0.2 1.0 N2 A:NCO411 2.0 0.7 1.0 N1 A:NCO411 2.0 0.1 1.0 N5 A:NCO411 2.0 0.9 1.0 N3 A:NCO411 2.0 0.4 1.0 O2' A:A231 3.8 0.2 1.0 OP1 A:G305 4.2 96.3 1.0 N0A A:B1Z412 4.5 80.8 1.0 C6 A:U307 4.5 0.6 1.0 OP2 A:G305 4.5 99.5 1.0 N7 A:A308 4.6 92.6 1.0 C4' A:A231 4.6 0.3 1.0 P A:G305 4.7 96.2 1.0 C1' A:U307 4.8 0.1 1.0 O4' A:U307 4.8 0.9 1.0 N1 A:U307 4.9 0.1 1.0 C2' A:A231 4.9 0.9 1.0 O4' A:G305 4.9 0.4 1.0 O3' A:A231 4.9 0.7 1.0 O5' A:G305 4.9 96.3 1.0 C4' A:G305 5.0 0.0 1.0 C5' A:A306 5.0 1.0 1.0

Cobalt binding site 8 out of 8 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Co412 b:87.0 occ:1.00 CO A:B1Z412 0.0 87.0 1.0 N21 A:B1Z412 1.9 84.9 1.0 N24 A:B1Z412 1.9 87.8 1.0 N22 A:B1Z412 1.9 87.2 1.0 N23 A:B1Z412 1.9 88.0 1.0 C5A A:B1Z412 2.1 86.7 1.0 N3B A:B1Z412 2.2 95.0 1.0 C9 A:B1Z412 2.9 87.5 1.0 C19 A:B1Z412 2.9 87.5 1.0 C1 A:B1Z412 2.9 85.6 1.0 C4 A:B1Z412 2.9 84.4 1.0 C11 A:B1Z412 2.9 88.8 1.0 C6 A:B1Z412 3.0 86.0 1.0 C16 A:B1Z412 3.0 90.0 1.0 C14 A:B1Z412 3.0 91.6 1.0 C4A A:B1Z412 3.1 86.2 1.0 C2B A:B1Z412 3.2 98.1 1.0 C10 A:B1Z412 3.3 87.3 1.0 C5 A:B1Z412 3.3 84.1 1.0 C9B A:B1Z412 3.3 97.4 1.0 C15 A:B1Z412 3.4 91.6 1.0 C20 A:B1Z412 3.5 86.5 1.0 O6A A:B1Z412 3.8 84.8 1.0 C4B A:B1Z412 3.8 97.2 1.0 C18 A:B1Z412 4.1 88.8 1.0 C2 A:B1Z412 4.1 85.0 1.0 C3 A:B1Z412 4.2 86.0 1.0 C8 A:B1Z412 4.2 88.3 1.0 C7 A:B1Z412 4.2 87.5 1.0 C17 A:B1Z412 4.2 90.9 1.0 C12 A:B1Z412 4.2 91.7 1.0 C13 A:B1Z412 4.3 92.7 1.0 N1B A:B1Z412 4.4 0.2 1.0 C3A A:B1Z412 4.4 87.3 1.0 C8B A:B1Z412 4.5 99.3 1.0 C26 A:B1Z412 4.6 84.8 1.0 C35 A:B1Z412 4.8 83.5 1.0 O8A A:B1Z412 4.8 88.5 1.0 C37 A:B1Z412 4.9 88.0 1.0 C53 A:B1Z412 4.9 92.5 1.0 C41 A:B1Z412 5.0 89.8 1.0 C54 A:B1Z412 5.0 91.9 1.0

C.W.Chan, A.Mondragon. Crystal Structure of An Atypical Cobalamin Riboswitch Reveals Rna Structural Adaptability As Basis For Promiscuous Ligand Binding To Be Published.