Magnesium in PDB 1y26: A-Riboswitch-Adenine Complex

The structure of A-Riboswitch-Adenine Complex, PDB code: 1y26 was solved by A.Serganov, Y.R.Yuan, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	49.655, 155.036, 25.185, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 29.7

The binding sites of Magnesium atom in the A-Riboswitch-Adenine Complex (pdb code 1y26). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the A-Riboswitch-Adenine Complex, PDB code: 1y26:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the A-Riboswitch-Adenine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A-Riboswitch-Adenine Complex within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg101 b:52.1 occ:1.00 O X:HOH267 2.2 50.5 1.0 O X:HOH269 2.2 49.2 1.0 O X:HOH270 2.2 48.7 1.0 O X:HOH272 2.2 52.7 1.0 O X:HOH268 2.2 50.7 1.0 O X:HOH271 2.2 49.2 1.0 O4 X:U47 4.1 51.0 1.0 OP2 X:A45 4.1 62.5 1.0 N7 X:G46 4.3 55.0 1.0 O X:HOH225 4.4 36.1 1.0 O6 X:G46 4.5 54.8 1.0 O X:HOH226 4.8 34.6 1.0 C4 X:U47 4.8 51.4 1.0 C5 X:U47 4.9 52.8 1.0

Magnesium binding site 2 out of 5 in the A-Riboswitch-Adenine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A-Riboswitch-Adenine Complex within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg102 b:60.8 occ:1.00 OP1 X:A24 2.1 54.1 1.0 O X:HOH276 2.2 58.4 1.0 O X:HOH275 2.2 57.8 1.0 O X:HOH277 2.2 60.2 1.0 O X:HOH273 2.2 57.9 1.0 O X:HOH274 2.2 60.1 1.0 P X:A24 3.5 52.5 1.0 O X:HOH216 4.1 43.3 1.0 OP2 X:A24 4.3 52.4 1.0 N7 X:A24 4.3 54.9 1.0 O5' X:A24 4.3 52.8 1.0 C8 X:A24 4.4 54.8 1.0 O6 X:G72 4.4 52.9 1.0 N7 X:G72 4.4 53.4 1.0 O3' X:A23 4.5 53.7 1.0 C5 X:U71 4.9 54.4 1.0

Magnesium binding site 3 out of 5 in the A-Riboswitch-Adenine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A-Riboswitch-Adenine Complex within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg103 b:62.9 occ:1.00 O X:HOH278 2.2 62.8 1.0 O X:HOH279 2.2 60.4 1.0 O X:HOH280 2.2 63.0 1.0 O X:HOH283 2.2 61.7 1.0 O X:HOH282 2.2 61.7 1.0 O X:HOH281 2.2 63.9 1.0 O X:HOH207 4.2 43.4 1.0 OP1 X:G44 4.2 60.3 1.0 C5' X:G44 4.8 58.4 1.0

Magnesium binding site 4 out of 5 in the A-Riboswitch-Adenine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A-Riboswitch-Adenine Complex within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg104 b:62.5 occ:1.00 O X:HOH287 2.2 61.1 1.0 O X:HOH284 2.2 61.7 1.0 O X:HOH285 2.2 62.4 1.0 O X:HOH289 2.2 60.3 1.0 O X:HOH286 2.2 63.3 1.0 O X:HOH288 2.2 62.3 1.0 N7 X:G43 4.2 58.3 1.0 O6 X:G43 4.4 58.1 1.0 N7 X:G44 4.5 55.7 1.0 O6 X:G44 4.7 56.6 1.0 O X:HOH235 4.9 40.7 1.0 C5 X:G43 4.9 56.7 1.0

Magnesium binding site 5 out of 5 in the A-Riboswitch-Adenine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of A-Riboswitch-Adenine Complex within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg105 b:64.1 occ:1.00 O X:HOH291 2.2 62.7 1.0 O X:HOH292 2.2 62.7 1.0 O X:HOH293 2.2 63.4 1.0 O X:HOH294 2.2 63.3 1.0 O X:HOH290 2.2 60.4 1.0 OP2 X:A23 2.4 53.0 1.0 P X:A23 3.7 55.2 1.0 O3' X:U22 3.8 56.6 1.0 O X:HOH231 4.0 51.1 1.0 N7 X:A21 4.3 49.2 1.0 N6 X:A21 4.3 51.1 1.0 O X:HOH224 4.5 38.3 1.0 OP1 X:A23 4.6 56.6 1.0 O2' X:U22 4.6 56.5 1.0 O5' X:A23 4.8 56.7 1.0 C5 X:A21 4.9 49.8 1.0 C3' X:U22 5.0 55.3 1.0

A.Serganov, Y.R.Yuan, O.Pikovskaya, A.Polonskaia, L.Malinina, A.T.Phan, C.Hobartner, R.Micura, R.R.Breaker, D.J.Patel. Structural Basis For Discriminative Regulation of Gene Expression By Adenine- and Guanine-Sensing Mrnas Chem.Biol. V. 11 1729 2004.
ISSN: ISSN 1074-5521
PubMed: 15610857
DOI: 10.1016/J.CHEMBIOL.2004.11.018