Magnesium in PDB 6p2h: Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches

The structure of Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches, PDB code: 6p2h was solved by M.M.Matyjasik, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.95 / 2.80
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.805, 91.805, 77.756, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 27.6

The structure of Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches also contains other interesting chemical elements:

Cobalt

(Co)

5 atoms

The binding sites of Magnesium atom in the Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches (pdb code 6p2h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches, PDB code: 6p2h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:39.3 occ:1.00 OP1 A:A24 2.2 37.6 1.0 O A:HOH205 2.4 41.0 1.0 O A:HOH209 2.7 47.8 1.0 P A:A24 3.6 44.6 1.0 O3' A:A23 4.2 41.3 1.0 O2' A:U75 4.4 63.7 1.0 OP2 A:A24 4.4 50.5 1.0 O5' A:A24 4.7 43.2 1.0 C5' A:A24 4.8 41.7 1.0 C5 A:U73 5.0 38.1 1.0

Magnesium binding site 2 out of 5 in the Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:57.6 occ:1.00 OP2 A:A24 2.3 50.5 1.0 OP2 A:A23 2.5 45.1 1.0 P A:A24 3.4 44.6 1.0 O5' A:A24 3.4 43.2 1.0 MG A:MG110 3.4 35.7 1.0 P A:A23 3.6 49.9 1.0 O5' A:A23 3.8 42.0 1.0 O3' A:U22 3.9 34.7 1.0 OP1 A:A24 4.3 37.6 1.0 C5' A:A23 4.3 41.3 1.0 OP1 A:A77 4.4 50.8 1.0 OP2 A:A77 4.4 55.8 1.0 N3 A:NCO104 4.5 67.5 1.0 O3' A:A23 4.6 41.3 1.0 C5' A:A24 4.7 41.7 1.0 O4' A:A24 4.7 39.5 1.0 C3' A:A23 4.8 42.8 1.0 OP1 A:A23 4.9 32.1 1.0 P A:A77 4.9 42.0 1.0

Magnesium binding site 3 out of 5 in the Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:67.9 occ:1.00 O4 A:U57 3.7 59.2 1.0 N4 A:NCO106 4.5 51.4 0.5 C4 A:U57 4.9 52.6 1.0

Magnesium binding site 4 out of 5 in the Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg110 b:35.7 occ:1.00 O2' A:U22 2.5 29.9 1.0 O6 A:GNG101 2.6 35.7 1.0 O3' A:U22 2.7 34.7 1.0 N1 A:NCO104 3.1 40.8 1.0 C2' A:U22 3.4 37.1 1.0 OP2 A:A23 3.4 45.1 1.0 MG A:MG108 3.4 57.6 1.0 C3' A:U22 3.6 29.8 1.0 P A:A23 3.7 49.9 1.0 C6 A:GNG101 3.8 28.4 1.0 C1' A:U22 3.8 30.6 1.0 N4 A:C78 3.9 36.2 1.0 O2 A:U22 4.2 34.5 1.0 N3 A:NCO104 4.5 67.5 1.0 N6 A:NCO104 4.6 60.6 1.0 C5 A:GNG101 4.6 26.0 1.0 O5' A:A23 4.6 42.0 1.0 N7 A:GNG101 4.6 25.9 1.0 OP1 A:A77 4.7 50.8 1.0 C4' A:U22 4.8 27.4 1.0 N1 A:GNG101 4.8 31.3 1.0 CO A:NCO104 4.8 97.5 1.0 O4' A:U22 4.8 26.9 1.0 OP1 A:A23 4.8 32.1 1.0 N1 A:U22 4.8 23.5 1.0 C2 A:U22 4.9 28.3 1.0 O6 A:G21 5.0 38.1 1.0

Magnesium binding site 5 out of 5 in the Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg111 b:36.8 occ:1.00 O6 A:G38 4.0 47.3 1.0 N7 A:G38 4.1 36.0 1.0 C6 A:G38 4.7 48.5 1.0 C5 A:G38 4.8 44.2 1.0 OP2 A:G37 4.9 37.1 1.0

M.M.Matyjasik, R.T.Batey. Structural Basis For 2'-Deoxyguanosine Recognition By the 2'-Dg-II Class of Riboswitches. Nucleic Acids Res. V. 47 10931 2019.
ISSN: ESSN 1362-4962
PubMed: 31598729
DOI: 10.1093/NAR/GKZ839