Magnesium 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:

Cobalt

(Co)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Structure of the B. Subtilis Cobalamin Riboswitch (pdb code 6vmy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Structure of the B. Subtilis Cobalamin Riboswitch, PDB code: 6vmy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:63.2 occ:1.00 N7 A:G244 3.3 99.4 1.0 O6 A:G244 3.9 95.6 1.0 C5 A:G244 4.2 98.4 1.0 C8 A:G244 4.3 0.7 1.0 C6 A:G244 4.4 96.7 1.0 OP1 A:G232 4.5 0.5 1.0 O6 A:G245 4.7 89.3 1.0 N7 A:G245 4.8 92.7 1.0

Magnesium binding site 2 out of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:88.1 occ:1.00 N6 A:A324 3.8 0.8 1.0 N7 A:A324 4.0 0.6 1.0 C5 A:C323 4.3 0.4 1.0 N4 A:C323 4.3 0.4 1.0 N6 A:A349 4.4 0.5 1.0 O6 A:G325 4.5 0.2 1.0 C4 A:C323 4.5 1.0 1.0 C5 A:A324 4.7 0.5 1.0 C6 A:A324 4.7 0.1 1.0

Magnesium binding site 3 out of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:83.7 occ:1.00 N4 A:C343 3.7 0.6 1.0 N6 A:A344 4.3 0.3 1.0 C4 A:C343 4.5 0.6 1.0 C5 A:C343 4.6 0.6 1.0 O6 A:G345 4.8 0.3 1.0

Magnesium binding site 4 out of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:0.3 occ:1.00 N7 A:A258 3.8 95.2 1.0 C5 A:A258 3.9 94.2 1.0 C6 A:A258 4.1 94.3 1.0 N6 A:A258 4.1 95.9 1.0 C8 A:A258 4.4 94.8 1.0 C4 A:A258 4.6 93.8 1.0 N1 A:A258 4.9 93.7 1.0 N9 A:A258 4.9 93.2 1.0

Magnesium binding site 5 out of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg413 b:95.5 occ:1.00 O A:HOH523 2.2 95.6 1.0 O A:HOH544 2.2 97.0 1.0 O A:HOH518 2.2 94.4 1.0 O A:HOH517 2.2 97.8 1.0 O A:HOH547 2.2 95.4 1.0 O A:HOH527 2.2 93.4 1.0 N7 A:G262 4.1 0.3 1.0 O6 A:G263 4.5 0.8 1.0 O6 A:G262 4.6 0.1 1.0 C5 A:C261 4.8 0.9 1.0 N7 A:G263 4.9 0.2 1.0 C5 A:G262 4.9 0.8 1.0 C8 A:G262 5.0 0.5 1.0

Magnesium binding site 6 out of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg414 b:91.1 occ:1.00 O A:HOH505 2.2 90.7 1.0 O A:HOH519 2.2 91.7 1.0 O A:HOH510 2.2 91.7 1.0 O A:HOH504 2.2 91.4 1.0 O A:HOH529 2.2 90.6 1.0 O A:HOH530 2.2 93.3 1.0 OP2 A:A258 3.4 0.3 1.0 O6 A:G253 4.1 0.6 1.0 O6 A:G252 4.3 0.4 1.0 C8 A:A257 4.3 0.9 1.0 OP2 A:G259 4.3 91.7 1.0 C2' A:A257 4.3 0.6 1.0 N7 A:G252 4.5 0.7 1.0 N4 A:C260 4.6 0.0 1.0 C3' A:A257 4.8 0.8 1.0 P A:A258 4.8 99.8 1.0 N7 A:A257 4.9 0.8 1.0 N4 A:C251 4.9 0.3 1.0 N9 A:A257 4.9 0.2 1.0 C6 A:G252 5.0 0.8 1.0 O A:HOH539 5.0 97.9 1.0

Magnesium binding site 7 out of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg415 b:97.4 occ:1.00 O A:HOH515 2.2 97.1 1.0 O A:HOH511 2.2 97.5 1.0 O A:HOH507 2.2 97.4 1.0 O A:HOH533 2.2 96.2 1.0 O A:HOH512 2.2 98.1 1.0 O A:HOH539 2.2 97.9 1.0 OP2 A:G252 3.7 0.2 1.0 O2' A:U254 4.2 0.3 1.0 OP2 A:A255 4.2 0.5 1.0 OP2 A:G253 4.4 0.4 1.0 P A:G252 4.5 0.9 1.0 O3' A:U254 4.5 0.1 1.0 O5' A:G252 4.7 0.9 1.0 O A:HOH530 4.7 93.3 1.0 OP1 A:G252 4.7 0.2 1.0 C2' A:U254 4.8 0.0 1.0 P A:A255 5.0 0.2 1.0

Magnesium binding site 8 out of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg416 b:0.2 occ:1.00 O A:HOH506 2.2 0.5 1.0 O A:HOH508 2.2 0.1 1.0 O A:HOH501 2.2 0.1 1.0 O A:HOH520 2.2 0.9 1.0 O A:HOH528 2.2 0.9 1.0 O A:HOH534 2.2 0.5 1.0 OP2 A:A303 3.2 83.2 1.0 N7 A:A248 3.9 89.3 1.0 P A:A303 4.4 85.5 1.0 C8 A:A248 4.7 90.1 1.0 OP1 A:A303 4.7 86.4 1.0 N6 A:A248 4.9 91.2 1.0 C5 A:A248 5.0 89.3 1.0

Magnesium binding site 9 out of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg417 b:0.7 occ:1.00 O A:HOH531 2.2 0.0 1.0 O A:HOH514 2.2 0.6 1.0 O A:HOH538 2.2 0.6 1.0 O A:HOH521 2.2 0.2 1.0 O A:HOH545 2.2 0.3 1.0 N7 A:G224 3.9 0.4 1.0 OP2 A:U223 4.4 0.5 1.0 C8 A:G224 4.6 0.6 1.0 OP2 A:G224 4.7 0.3 1.0

Magnesium binding site 10 out of 12 in the Structure of the B. Subtilis Cobalamin Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the B. Subtilis Cobalamin Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg418 b:0.1 occ:1.00 O A:HOH503 2.2 0.7 1.0 O A:HOH509 2.2 0.2 1.0 O A:HOH502 2.2 0.2 1.0 O A:HOH513 2.2 0.8 1.0 O A:HOH543 2.2 0.5 1.0 O A:HOH532 2.2 0.6 1.0 OP1 A:U335 3.6 0.5 1.0 OP2 A:G336 3.7 0.1 1.0 OP2 A:C337 4.0 0.1 1.0 OP2 A:C334 4.2 0.1 1.0 OP2 A:U335 4.3 0.7 1.0 P A:U335 4.5 0.2 1.0 P A:G336 4.9 0.0 1.0 O5' A:C334 5.0 0.5 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.