Magnesium in PDB 3skz: Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to Guanosine

The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to Guanosine, PDB code: 3skz was solved by O.Pikovskaya, A.Polonskaia, D.J.Patel, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.806, 47.208, 227.279, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 27.5

The binding sites of Magnesium atom in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to Guanosine (pdb code 3skz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to Guanosine, PDB code: 3skz:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to Guanosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg228 b:51.0 occ:1.00 OP2 A:G59 2.6 54.0 1.0 OP2 A:C58 3.2 57.5 1.0 O5' A:C58 3.5 49.3 1.0 C8 A:G59 3.7 27.8 1.0 P A:C58 3.8 55.2 1.0 P A:G59 4.0 54.8 1.0 C5' A:G59 4.2 51.5 1.0 C3' A:C58 4.2 45.3 1.0 OP1 A:C58 4.2 56.0 1.0 N7 A:G59 4.3 29.7 1.0 O4' A:G59 4.4 40.3 1.0 O5' A:G59 4.5 55.9 1.0 O3' A:C58 4.5 34.5 1.0 C6 A:C58 4.6 49.6 1.0 C5' A:C58 4.7 49.5 1.0 C5 A:C58 4.7 49.9 1.0 N9 A:G59 4.8 30.1 1.0 C4' A:G59 4.9 48.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to Guanosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg172 b:73.5 occ:1.00 O6 B:G78 2.6 72.4 1.0 OP2 B:A32 2.7 54.8 1.0 N6 B:A77 3.3 81.4 1.0 N4 B:C61 3.5 37.8 1.0 C6 B:G78 3.7 75.1 1.0 C5' B:A32 3.8 62.2 1.0 P B:A32 3.9 54.9 1.0 O4 B:U62 4.0 52.3 1.0 OP2 B:G33 4.0 57.9 1.0 O5' B:A32 4.1 67.2 1.0 N1 B:G78 4.5 74.5 1.0 C6 B:A77 4.5 81.6 1.0 OP1 B:G33 4.6 49.9 1.0 C5 B:G78 4.6 78.6 1.0 C4' B:A32 4.8 63.0 1.0 C4 B:C61 4.8 71.1 1.0 P B:G33 4.8 53.7 1.0 OP1 B:A32 4.8 44.3 1.0 N7 B:G78 5.0 81.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to Guanosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to Guanosine within 5.0Å range:

O.Pikovskaya, A.Polonskaia, D.J.Patel, A.Serganov. Structural Principles of Nucleoside Selectivity in A 2'-Deoxyguanosine Riboswitch. Nat.Chem.Biol. V. 7 748 2011.
ISSN: ISSN 1552-4450
PubMed: 21841796
DOI: 10.1038/NCHEMBIO.631