Magnesium in PDB 4yaz: 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp

The structure of 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp, PDB code: 4yaz was solved by A.M.Ren, D.J.Patel, R.K.Rajashankar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.50 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.623, 50.517, 78.657, 90.00, 90.92, 90.00
R / Rfree (%)	21.3 / 25

The structure of 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp also contains other interesting chemical elements:

Potassium

(K)

3 atoms

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

Magnesium binding site 1 out of 5 in the 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg101 b:27.7 occ:1.00 OP1 R:G44 2.0 14.8 1.0 O R:HOH281 2.0 25.3 1.0 O R:HOH259 2.1 13.9 1.0 O R:HOH232 2.1 33.4 1.0 O R:HOH216 2.1 26.2 1.0 OP2 R:C45 2.1 18.9 1.0 P R:G44 3.3 20.2 1.0 P R:C45 3.4 21.5 1.0 OP2 R:G44 3.7 20.1 1.0 O3' R:G44 4.0 17.5 1.0 O2' R:U16 4.0 14.2 1.0 OP1 R:C45 4.1 28.0 1.0 O R:HOH221 4.3 19.8 1.0 OP1 R:G66 4.3 20.3 1.0 O3' R:A43 4.3 21.7 1.0 O5' R:G44 4.3 23.4 1.0 C3' R:G44 4.3 14.6 1.0 C5' R:G44 4.4 20.7 1.0 O5' R:C45 4.6 33.0 1.0 OP2 R:G66 4.8 17.1 1.0 O R:HOH224 4.8 21.6 1.0 C4' R:G44 4.9 14.7 1.0 O3' R:U16 4.9 20.0 1.0 P R:G66 5.0 20.3 1.0

Magnesium binding site 2 out of 5 in the 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg102 b:47.3 occ:1.00 O R:HOH274 2.1 66.4 1.0 O R:HOH289 2.1 59.7 1.0 O2' R:G51 3.3 36.8 1.0 N3 R:G51 3.3 25.1 1.0 N2 R:G51 3.6 26.6 1.0 O2 R:C68 3.8 33.9 1.0 C2' R:G51 3.8 34.8 1.0 C2 R:G51 3.9 22.8 1.0 C1' R:G51 4.1 30.8 1.0 O4' R:G52 4.2 35.8 1.0 N2 R:G50 4.3 23.8 1.0 C4 R:G51 4.4 20.0 1.0 C2 R:C68 4.7 25.9 1.0 N9 R:G51 4.7 23.7 1.0 C4' R:G52 4.8 34.6 1.0 C1' R:C68 4.9 25.4 1.0 C1' R:G52 5.0 31.5 1.0

Magnesium binding site 3 out of 5 in the 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg103 b:48.5 occ:1.00 OP2 R:A82 2.2 63.8 1.0 C5' R:A82 3.1 39.0 1.0 P R:A82 3.5 58.4 1.0 O5' R:U81 3.7 49.7 1.0 C3' R:U81 3.7 46.7 1.0 O5' R:A82 3.8 44.7 1.0 O3' R:U81 4.1 51.3 1.0 C8 R:A82 4.1 30.9 1.0 C4' R:A82 4.3 31.3 1.0 OP2 R:U81 4.3 65.2 1.0 P R:U81 4.3 61.4 1.0 C5' R:U81 4.4 45.7 1.0 O4' R:A82 4.4 37.8 1.0 OP1 R:U81 4.5 59.3 1.0 C2' R:U81 4.6 45.4 1.0 C4' R:U81 4.6 51.8 1.0 C6 R:U81 4.7 30.0 1.0 OP1 R:A82 4.8 39.7 1.0 N7 R:A82 4.8 31.0 1.0 C3' R:A82 4.9 32.2 1.0

Magnesium binding site 4 out of 5 in the 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg104 b:53.5 occ:1.00 O R:HOH293 2.1 49.1 1.0 O R:HOH276 2.1 53.0 1.0 N3 R:C58 3.7 38.5 1.0 N4 R:C58 4.0 30.6 1.0 C4 R:C58 4.4 33.8 1.0 C2 R:C58 4.7 29.4 1.0 O2 R:C58 4.8 29.2 1.0

Magnesium binding site 5 out of 5 in the 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:35.8 occ:1.00 OP1 A:G44 2.3 38.5 1.0 OP2 A:C45 2.4 21.8 1.0 O2' A:U16 3.2 28.3 1.0 P A:C45 3.4 18.5 1.0 O3' A:U16 3.6 19.0 1.0 P A:G44 3.8 35.4 1.0 OP1 A:C45 3.8 35.1 1.0 O3' A:G44 4.1 21.6 1.0 C5' A:G44 4.1 32.5 1.0 C3' A:U16 4.3 31.4 1.0 C4' A:U16 4.3 36.2 1.0 C2' A:U16 4.3 28.6 1.0 O5' A:G44 4.4 32.3 1.0 O A:HOH219 4.5 26.1 1.0 C3' A:G44 4.6 19.0 1.0 C5' A:A17 4.6 32.9 1.0 OP1 A:A17 4.6 32.7 1.0 O3' A:A43 4.7 44.3 1.0 OP2 A:G44 4.7 36.4 1.0 O5' A:C45 4.8 23.3 1.0 P A:A17 4.8 38.2 1.0 OP1 A:G66 4.8 27.5 1.0 C4' A:G44 4.9 19.0 1.0

A.Ren, X.C.Wang, C.A.Kellenberger, K.R.Rajashankar, R.A.Jones, M.C.Hammond, D.J.Patel. Structural Basis For Molecular Discrimination By A 3',3'-Cgamp Sensing Riboswitch. Cell Rep V. 11 1 2015.
ISSN: ESSN 2211-1247
PubMed: 25818298
DOI: 10.1016/J.CELREP.2015.03.004