Magnesium in PDB 2qbz: Structure of the M-Box Riboswitch Aptamer Domain

The structure of Structure of the M-Box Riboswitch Aptamer Domain, PDB code: 2qbz was solved by C.E.Dann Iii, W.C.Winkler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.67 / 2.60
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	48.655, 101.081, 285.765, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.6

The structure of Structure of the M-Box Riboswitch Aptamer Domain also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Magnesium atom in the Structure of the M-Box Riboswitch Aptamer Domain (pdb code 2qbz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of the M-Box Riboswitch Aptamer Domain, PDB code: 2qbz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Structure of the M-Box Riboswitch Aptamer Domain


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 M-Box Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg201 b:16.7 occ:1.00 OP2 X:C102 2.2 20.3 1.0 O X:HOH306 2.2 17.5 1.0 OP2 X:A103 2.2 22.5 1.0 OP2 X:G100 2.2 17.0 1.0 O X:HOH305 2.2 15.3 1.0 O4 X:U104 2.2 22.4 1.0 C4 X:U104 3.2 20.9 1.0 P X:A103 3.5 25.9 1.0 P X:C102 3.5 21.9 1.0 P X:G100 3.6 20.4 1.0 C5 X:U104 3.7 19.9 1.0 O X:HOH428 3.8 17.6 1.0 OP1 X:A103 4.0 25.2 1.0 O5' X:G100 4.1 19.4 1.0 O X:HOH405 4.1 21.2 1.0 O5' X:C102 4.2 20.2 1.0 N7 X:G100 4.2 20.8 1.0 OP1 X:C102 4.2 24.5 1.0 C8 X:G100 4.3 20.4 1.0 O3' X:C102 4.4 20.5 1.0 N3 X:U104 4.4 20.3 1.0 C5' X:C102 4.5 21.8 1.0 C5' X:A101 4.5 17.7 1.0 O3' X:C99 4.6 20.5 1.0 C3' X:A101 4.6 19.4 1.0 OP1 X:G100 4.6 14.5 1.0 O5' X:A103 4.6 26.1 1.0 C3' X:C99 4.6 21.7 1.0 O3' X:A101 4.6 19.5 1.0 OP2 X:C99 4.7 21.6 1.0 C3' X:C102 4.8 22.1 1.0 O5' X:A101 4.9 18.5 1.0 O5' X:C99 4.9 20.8 1.0

Magnesium binding site 2 out of 6 in the Structure of the M-Box Riboswitch Aptamer Domain


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 M-Box Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg202 b:15.5 occ:1.00 O X:HOH307 2.1 13.9 1.0 O X:HOH309 2.1 10.1 1.0 OP1 X:G100 2.1 14.5 1.0 O X:HOH308 2.2 14.7 1.0 O X:HOH310 2.2 15.8 1.0 OP1 X:U23 2.2 12.2 1.0 P X:U23 3.2 8.9 1.0 P X:G100 3.5 20.4 1.0 OP2 X:U23 3.6 10.0 1.0 O3' X:C99 3.7 20.5 1.0 O3' X:G22 3.8 14.1 1.0 K X:K304 3.9 38.0 1.0 C5' X:G100 4.1 20.8 1.0 O5' X:G100 4.3 19.4 1.0 OP1 X:G22 4.4 6.0 1.0 OP1 X:G157 4.4 12.7 1.0 O X:HOH405 4.5 21.2 1.0 OP2 X:G157 4.6 18.0 1.0 O5' X:U23 4.6 8.8 1.0 OP2 X:G100 4.7 17.0 1.0 O X:HOH347 4.7 34.5 1.0 C3' X:G22 5.0 12.2 1.0 P X:G157 5.0 17.6 1.0

Magnesium binding site 3 out of 6 in the Structure of the M-Box Riboswitch Aptamer Domain


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 M-Box Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg203 b:20.2 occ:1.00 O X:HOH311 2.1 22.8 1.0 O X:HOH312 2.2 20.0 1.0 OP2 X:U24 2.2 12.4 1.0 OP1 X:A25 2.2 15.0 1.0 O X:HOH314 2.2 20.9 1.0 O X:HOH313 2.2 19.9 1.0 P X:A25 3.5 15.7 1.0 P X:U24 3.5 11.2 1.0 O X:HOH391 3.6 45.7 1.0 O X:HOH417 3.6 31.4 1.0 N7 X:G26 3.7 21.5 1.0 O6 X:G26 3.8 22.4 1.0 O3' X:U24 3.8 13.1 1.0 OP1 X:U24 4.0 12.6 1.0 O X:HOH418 4.1 14.3 1.0 N3 X:C160 4.1 19.6 1.0 O5' X:A25 4.2 14.9 1.0 C5' X:U24 4.3 10.4 1.0 C3' X:U24 4.4 10.6 1.0 C5 X:G26 4.4 21.6 1.0 C6 X:G26 4.4 22.3 1.0 O5' X:U24 4.5 9.1 1.0 N7 X:A25 4.5 19.7 1.0 N4 X:C160 4.6 21.3 1.0 C2' X:U23 4.6 10.5 1.0 O3' X:U23 4.6 11.6 1.0 OP2 X:A25 4.7 16.4 1.0 O X:HOH331 4.7 23.4 1.0 C8 X:A25 4.7 19.4 1.0 O4 X:U159 4.7 21.9 1.0 C8 X:G26 4.7 20.8 1.0 C4' X:U24 4.8 10.6 1.0 O4 X:U161 4.8 31.6 1.0 C3' X:U23 4.8 10.8 1.0 C4 X:C160 4.9 20.9 1.0

Magnesium binding site 4 out of 6 in the Structure of the M-Box Riboswitch Aptamer Domain


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 M-Box Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg204 b:23.3 occ:1.00 O X:HOH316 2.2 21.2 1.0 O X:HOH315 2.2 20.7 1.0 O X:HOH319 2.2 26.6 1.0 O X:HOH318 2.2 25.4 1.0 O X:HOH317 2.2 24.0 1.0 OP2 X:A72 2.2 18.3 1.0 P X:A72 3.6 20.5 1.0 N3 X:C69 4.0 21.2 1.0 O2 X:C69 4.0 25.6 1.0 O X:HOH337 4.2 33.6 1.0 OP1 X:A72 4.4 21.3 1.0 O3' X:A71 4.4 19.4 1.0 C2 X:C69 4.4 22.3 1.0 O6 X:G73 4.5 20.6 1.0 O5' X:A71 4.6 21.4 1.0 N7 X:G73 4.6 20.3 1.0 O5' X:A72 4.6 18.2 1.0 C3' X:A71 4.6 19.4 1.0 O X:HOH377 4.7 25.7 1.0 C6 X:G73 4.7 19.4 1.0 C5 X:G73 4.8 19.6 1.0 N7 X:A72 4.8 22.9 1.0 OP2 X:A71 4.9 19.9 1.0 C8 X:A72 5.0 21.0 1.0

Magnesium binding site 5 out of 6 in the Structure of the M-Box Riboswitch Aptamer Domain


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 M-Box Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg205 b:34.0 occ:1.00 OP2 X:A63 2.2 33.1 1.0 O X:HOH321 2.2 32.6 1.0 O X:HOH320 2.2 35.0 1.0 O X:HOH322 2.2 35.6 1.0 O X:HOH324 2.2 35.4 1.0 O X:HOH323 2.2 34.1 1.0 P X:A63 3.5 34.6 1.0 O4 X:U65 3.7 31.5 1.0 O6 X:G76 3.9 24.8 1.0 N3 X:C77 4.0 29.0 1.0 O5' X:A63 4.2 33.4 1.0 O2 X:C77 4.2 31.6 1.0 O2 X:C78 4.2 28.2 1.0 OP1 X:A63 4.2 34.0 1.0 O X:HOH350 4.3 41.9 1.0 N7 X:A63 4.4 41.9 1.0 N7 X:A64 4.5 39.3 1.0 C8 X:A63 4.5 41.7 1.0 O3' X:A62 4.6 33.3 1.0 C2 X:C77 4.6 29.0 1.0 C3' X:A62 4.6 33.8 1.0 C4 X:U65 4.6 32.1 1.0 C2 X:C78 4.7 28.6 1.0 C6 X:G76 4.7 25.2 1.0 N6 X:A64 4.8 38.6 1.0 C5' X:A62 4.8 31.6 1.0 OP2 X:A64 4.9 39.5 1.0 N1 X:G76 4.9 25.8 1.0 O X:HOH342 5.0 48.3 1.0

Magnesium binding site 6 out of 6 in the Structure of the M-Box Riboswitch Aptamer Domain


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 M-Box Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg206 b:36.5 occ:1.00 O X:HOH328 2.2 35.4 1.0 O X:HOH325 2.2 37.0 1.0 O X:HOH327 2.2 36.3 1.0 OP2 X:A80 2.2 32.4 1.0 O X:HOH326 2.2 36.4 1.0 O4 X:U81 2.2 33.5 1.0 C4 X:U81 2.9 32.6 1.0 C5 X:U81 3.0 32.4 1.0 P X:A80 3.3 32.7 1.0 O X:HOH376 3.3 37.5 1.0 OP1 X:A80 3.8 32.3 1.0 O5' X:A80 4.0 33.6 1.0 N3 X:U81 4.2 31.9 1.0 C6 X:U81 4.4 33.1 1.0 N6 X:A60 4.5 23.2 1.0 O3' X:A79 4.6 33.3 1.0 O6 X:G82 4.9 31.1 1.0 N1 X:A61 5.0 27.5 1.0

C.E.Dann Iii, C.A.Wakeman, C.L.Sieling, S.C.Baker, I.Irnov, W.C.Winkler. Structure and Mechanism of A Metal-Sensing Regulatory Rna Cell(Cambridge,Mass.) V. 130 878 2007.
ISSN: ISSN 0092-8674
PubMed: 17803910
DOI: 10.1016/J.CELL.2007.06.051