Magnesium in PDB 4yb0: 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp

The structure of 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp, PDB code: 4yb0 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)	85.10 / 2.12
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	174.829, 44.901, 68.210, 90.00, 103.33, 90.00
R / Rfree (%)	22.8 / 26.2

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

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp (pdb code 4yb0). 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 C-Di-Gmp, PDB code: 4yb0:
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 C-Di-Gmp


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 C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg103 b:73.2 occ:1.00 O R:HOH226 1.8 49.6 1.0 O R:HOH205 2.0 47.2 1.0 O R:HOH208 2.1 58.3 1.0 O R:HOH214 2.3 55.4 1.0 OP1 R:G28 3.1 46.7 1.0 N7 R:G26 3.2 45.6 1.0 O6 R:G26 3.6 44.5 1.0 C5 R:G26 3.7 38.7 1.0 OP2 R:G28 3.7 62.7 1.0 P R:G28 3.8 54.5 1.0 C6 R:G26 3.9 43.4 1.0 C8 R:G26 4.1 47.0 1.0 O R:HOH202 4.3 55.5 1.0 O3' R:C27 4.6 45.3 1.0 C4 R:G26 4.8 45.3 1.0 O R:HOH215 4.9 47.1 1.0 N9 R:G26 5.0 47.6 1.0

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


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 C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg104 b:81.1 occ:1.00 OP2 R:A12 2.1 80.1 1.0 OP2 R:A11 2.5 94.8 1.0 OP1 R:A11 2.6 90.7 1.0 P R:A11 2.8 0.3 1.0 O5' R:A11 3.5 84.4 1.0 P R:A12 3.5 95.0 1.0 OP1 R:A12 4.2 92.5 1.0 O3' R:C10 4.3 88.7 1.0 O3' R:A11 4.4 75.3 1.0 C3' R:A11 4.4 76.4 1.0 O5' R:A12 4.5 77.1 1.0 O1P R:C2E102 4.6 71.8 1.0 C5' R:A11 4.6 79.5 1.0 N7 R:A12 5.0 71.6 1.0

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


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 C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg105 b:52.4 occ:1.00 O R:HOH213 1.9 63.7 1.0 O2' R:A41 2.6 62.2 1.0 O3' R:A41 2.9 55.0 1.0 OP2 R:A42 3.1 61.4 1.0 O61 R:C2E102 3.1 49.7 1.0 N7 R:G8 3.3 67.0 1.0 C2' R:A41 3.6 53.4 1.0 P R:A42 3.6 55.4 1.0 O6 R:G8 3.7 54.1 1.0 C3' R:A41 3.8 49.1 1.0 C5 R:G8 3.8 53.6 1.0 O5' R:A42 3.9 74.0 1.0 C1' R:A41 3.9 49.1 1.0 C6 R:G8 4.0 57.4 1.0 N71 R:C2E102 4.1 49.5 1.0 C61 R:C2E102 4.1 47.1 1.0 C8 R:G8 4.2 63.6 1.0 C51 R:C2E102 4.4 45.7 1.0 N4 R:C75 4.6 49.3 1.0 C4 R:G8 4.9 49.5 1.0 O4' R:A41 4.9 44.5 1.0 N9 R:A41 4.9 55.0 1.0 OP1 R:A42 4.9 59.4 1.0 C4' R:A41 4.9 40.7 1.0

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


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 C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:0.8 occ:1.00 O A:HOH203 2.0 0.7 1.0 O A:HOH208 2.2 0.8 1.0 OP1 A:G28 2.5 0.7 1.0 O A:HOH202 2.7 0.8 1.0 O6 A:G26 3.1 0.3 1.0 P A:G28 3.4 0.7 1.0 OP2 A:G28 3.6 0.8 1.0 N7 A:G26 3.6 0.2 1.0 C6 A:G26 3.6 0.1 1.0 C5 A:G26 3.8 0.7 1.0 O3' A:C27 4.2 0.7 1.0 C8 A:G26 4.7 0.4 1.0 N1 A:G26 4.7 0.3 1.0 O5' A:G28 4.7 0.0 1.0

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


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 C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:59.4 occ:1.00 O A:HOH215 2.4 57.5 1.0 O2' A:A41 2.9 57.8 1.0 O3' A:A41 3.1 57.3 1.0 O61 A:C2E102 3.2 55.9 1.0 OP2 A:A42 3.3 71.3 1.0 P A:A42 3.7 65.6 1.0 O5' A:A42 3.7 78.6 1.0 N7 A:G8 3.8 53.6 1.0 C2' A:A41 3.8 52.6 1.0 O6 A:G8 3.9 60.6 1.0 C1' A:A41 4.0 55.9 1.0 C3' A:A41 4.1 52.5 1.0 C61 A:C2E102 4.2 57.3 1.0 C5 A:G8 4.3 49.0 1.0 C6 A:G8 4.3 56.9 1.0 N4 A:C75 4.3 52.1 1.0 N71 A:C2E102 4.4 62.9 1.0 O6 A:G74 4.4 62.4 1.0 OP2 A:A6 4.6 92.6 1.0 C51 A:C2E102 4.7 59.6 1.0 C8 A:G8 4.7 55.5 1.0 N9 A:A41 4.9 55.6 1.0 O4' A:A41 4.9 54.2 1.0 C5' A:A42 5.0 59.5 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