Magnesium in PDB 5u3g: Structure of the Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium

The structure of Structure of the Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium, PDB code: 5u3g was solved by R.A.Battaglia, I.R.Price, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.71 / 2.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	67.441, 78.371, 98.844, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 21.3

The structure of Structure of the Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium also contains other interesting chemical elements:

Potassium

(K)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium (pdb code 5u3g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the Structure of the Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium, PDB code: 5u3g:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in the Structure of the Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium


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 Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:42.9 occ:1.00 OP1 B:G33 1.9 45.8 1.0 O B:HOH207 1.9 44.6 1.0 O B:HOH210 1.9 43.9 1.0 OP2 B:C77 2.0 44.6 1.0 O B:HOH214 2.0 48.0 1.0 OP1 B:C76 2.2 39.1 1.0 P B:G33 3.2 52.7 1.0 P B:C77 3.5 44.4 1.0 P B:C76 3.5 47.6 1.0 H8 B:G33 3.6 51.0 1.0 O3' B:A32 3.8 57.4 1.0 H5'' B:C76 3.9 54.3 1.0 OP2 B:G33 3.9 70.5 1.0 N7 B:G33 4.0 46.9 1.0 OP2 B:C76 4.1 50.7 1.0 O5' B:C77 4.1 38.2 1.0 C8 B:G33 4.2 42.5 1.0 H3' B:C76 4.2 46.1 1.0 OP1 B:C77 4.2 39.3 1.0 O5' B:C76 4.2 52.4 1.0 MG B:MG105 4.3 56.8 1.0 O5' B:G33 4.4 52.0 1.0 OP2 B:G80 4.4 52.8 1.0 OP2 B:C78 4.5 49.5 1.0 O2' B:G79 4.5 53.4 1.0 C5' B:C76 4.6 45.2 1.0 O3' B:C76 4.6 41.9 1.0 O3' B:G75 4.6 44.4 1.0 HO2' B:G79 4.7 64.1 1.0 O B:HOH201 4.7 63.2 1.0 HO2' B:A32 4.8 72.5 1.0 C3' B:C76 4.8 38.4 1.0 O3' B:G79 4.8 44.9 1.0 H62 B:A34 4.9 44.6 1.0

Magnesium binding site 2 out of 24 in the Structure of the Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium


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 Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:65.9 occ:1.00 MG B:MG113 3.2 83.4 1.0 OP2 B:G31 3.3 42.1 1.0 MG B:MG110 3.8 54.6 1.0 O B:HOH206 4.0 42.6 1.0 OP2 B:A5 4.4 44.5 1.0 H8 B:G31 4.7 49.1 1.0 N7 B:G31 4.7 40.0 1.0 P B:G31 4.7 38.1 1.0 OP2 B:C30 4.7 38.2 1.0 O B:HOH221 4.9 52.7 0.5 O B:HOH208 4.9 59.2 1.0 OP1 B:A5 4.9 50.8 1.0 C8 B:G31 5.0 40.9 1.0

Magnesium binding site 3 out of 24 in the Structure of the Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium


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 Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:79.4 occ:1.00 N7 B:G52 3.5 49.1 1.0 H1 B:G48 3.6 68.7 1.0 O6 B:G52 3.9 57.7 1.0 OP2 B:A51 4.1 57.3 1.0 C5 B:G52 4.3 48.4 1.0 N1 B:G48 4.4 57.3 1.0 H22 B:G48 4.4 70.6 1.0 C6 B:G52 4.4 50.1 1.0 C8 B:G52 4.6 57.9 1.0 O6 B:G48 4.6 57.4 1.0 H8 B:G52 4.7 69.5 1.0 C6 B:G48 5.0 52.7 1.0

Magnesium binding site 4 out of 24 in the Structure of the Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium


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 Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:83.4 occ:1.00 O6 B:G48 3.2 57.4 1.0 OP1 B:A50 3.6 57.8 1.0 C6 B:G48 3.8 52.7 1.0 N7 B:G48 4.0 55.5 1.0 C5 B:G48 4.1 45.4 1.0 OP2 B:A50 4.4 55.5 1.0 P B:A50 4.4 52.0 1.0 N1 B:G48 4.8 57.3 1.0 H1 B:G48 5.0 68.7 1.0

Magnesium binding site 5 out of 24 in the Structure of the Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium


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 Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:56.8 occ:1.00 OP2 B:G33 1.7 70.5 1.0 O B:HOH203 2.0 61.0 1.0 OP1 B:C77 2.2 39.3 1.0 P B:G33 3.0 52.7 1.0 P B:C77 3.3 44.4 1.0 H5' B:G33 3.5 54.7 1.0 OP1 B:G33 3.5 45.8 1.0 OP2 B:C77 3.6 44.6 1.0 MG B:MG112 3.7 55.2 1.0 O B:HOH214 3.7 48.0 1.0 O3' B:A32 3.9 57.4 1.0 O5' B:G33 4.0 52.0 1.0 H3' B:A32 4.1 56.4 1.0 C5' B:G33 4.2 45.6 1.0 H5'' B:C77 4.3 54.9 1.0 O5' B:C77 4.3 38.2 1.0 MG B:MG101 4.3 42.9 1.0 H4' B:A32 4.4 55.3 1.0 C3' B:A32 4.4 47.0 1.0 O3' B:C76 4.5 41.9 1.0 H5'' B:G33 4.7 54.7 1.0 C5' B:C77 4.8 45.7 1.0 H8 B:G33 4.9 51.0 1.0 C4' B:A32 4.9 46.1 1.0 H5' B:A32 4.9 58.1 1.0

Magnesium binding site 6 out of 24 in the Structure of the Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium


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 Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg106 b:64.7 occ:1.00 O3' B:A34 3.4 49.8 1.0 OP2 B:G35 3.8 60.6 1.0 HO2' B:A34 4.0 58.2 1.0 H4' B:A34 4.0 54.1 1.0 P B:G35 4.1 49.9 1.0 O5' B:G35 4.2 58.9 1.0 OP2 B:A61 4.3 58.0 1.0 N7 B:A61 4.3 52.4 1.0 O2' B:A34 4.5 48.5 1.0 H8 B:A61 4.5 60.4 1.0 C3' B:A34 4.5 43.0 1.0 C8 B:A61 4.6 50.3 1.0 C4' B:A34 4.7 45.1 1.0 H5'' B:A34 4.7 60.9 1.0

Magnesium binding site 7 out of 24 in the Structure of the Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium


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 Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg107 b:82.5 occ:1.00 H61 B:A32 2.4 64.0 1.0 N1 B:A32 3.1 53.1 1.0 N6 B:A32 3.2 53.4 1.0 H1' B:A8 3.2 66.2 1.0 H1' B:G35 3.3 59.1 1.0 C6 B:A32 3.6 49.8 1.0 O4' B:G35 3.8 49.4 1.0 H62 B:A32 3.9 64.0 1.0 C1' B:G35 4.0 49.2 1.0 C1' B:A8 4.2 55.1 1.0 O2' B:A8 4.2 51.6 1.0 C2 B:A32 4.2 48.1 1.0 H2 B:A32 4.3 57.7 1.0 H22 B:G75 4.3 62.9 1.0 N3 B:A8 4.5 50.0 1.0 N2 B:G75 4.6 52.4 1.0 H4' B:G35 4.6 57.0 1.0 H1 B:G75 4.7 72.0 1.0 O4' B:A8 4.7 49.8 1.0 N9 B:G35 4.8 48.3 1.0 O2' B:G35 4.8 55.0 1.0 HO2' B:A8 4.8 62.0 1.0 C4' B:G35 4.9 47.5 1.0 C2' B:A8 4.9 51.4 1.0 H21 B:G75 4.9 62.9 1.0 C2 B:G75 5.0 57.5 1.0 N1 B:G75 5.0 60.0 1.0

Magnesium binding site 8 out of 24 in the Structure of the Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium


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 Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg108 b:72.2 occ:1.00 H5 B:C18 2.8 60.5 1.0 H41 B:C18 3.2 56.0 1.0 N7 B:G17 3.7 48.3 1.0 C5 B:C18 3.7 50.4 1.0 OP2 B:G17 3.8 52.4 1.0 H8 B:G17 3.9 51.8 1.0 C8 B:G17 3.9 43.2 1.0 N4 B:C18 4.0 46.7 1.0 H3' B:G17 4.2 62.2 1.0 C4 B:C18 4.4 46.7 1.0 C5 B:G17 4.5 45.1 1.0 O5' B:G17 4.6 47.1 1.0 H42 B:C18 4.7 56.0 1.0 C6 B:C18 4.8 46.9 1.0 N9 B:G17 4.8 46.5 1.0 OP2 B:C18 4.8 55.7 1.0 H6 B:C18 4.8 56.3 1.0 P B:G17 4.9 60.4 1.0

Magnesium binding site 9 out of 24 in the Structure of the Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium


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 Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg109 b:82.6 occ:1.00 N7 B:G9 3.8 48.5 1.0 O6 B:G10 4.2 45.3 1.0 N7 B:G10 4.3 41.3 1.0 O6 B:G9 4.3 40.5 1.0 C5 B:G9 4.6 43.4 1.0 OP2 B:A8 4.6 60.1 1.0 C8 B:G9 4.7 46.2 1.0 C6 B:G9 4.7 37.2 1.0 H8 B:G9 4.9 55.5 1.0 C6 B:G10 5.0 41.4 1.0 C5 B:G10 5.0 44.0 1.0

Magnesium binding site 10 out of 24 in the Structure of the Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium


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 Dickeya Dadantii Ykkc Riboswitch Bound to Guanidinium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg110 b:54.6 occ:1.00 MG B:MG111 2.5 63.3 1.0 N7 B:G31 2.8 40.0 1.0 MG B:MG113 2.8 83.4 1.0 OP2 B:C30 2.9 38.2 1.0 O6 B:G31 3.1 39.7 1.0 H5 B:C30 3.5 47.2 1.0 C5 B:G31 3.5 36.9 1.0 C6 B:G31 3.7 38.2 1.0 O B:HOH208 3.7 59.2 1.0 MG B:MG102 3.8 65.9 1.0 C5 B:C30 3.8 39.4 1.0 C8 B:G31 3.9 40.9 1.0 H6 B:C30 4.1 52.7 1.0 P B:C30 4.1 38.3 1.0 H8 B:G31 4.1 49.1 1.0 C6 B:C30 4.2 43.9 1.0 O5' B:C30 4.2 38.4 1.0 H3' B:C30 4.3 45.0 1.0 O B:HOH220 4.4 43.4 1.0 H3' B:C29 4.4 45.4 1.0 C4 B:C30 4.5 43.2 1.0 H41 B:C30 4.6 47.7 1.0 OP2 B:G31 4.8 42.1 1.0 C4 B:G31 4.8 39.0 1.0 N4 B:C30 4.9 39.7 1.0 OP1 B:C30 5.0 38.3 1.0 N9 B:G31 5.0 39.1 1.0

R.A.Battaglia, I.R.Price, A.Ke. Structural Basis For Guanidine Sensing By the Ykkc Family of Riboswitches. Rna V. 23 578 2017.
ISSN: ESSN 1469-9001
PubMed: 28096518
DOI: 10.1261/RNA.060186.116