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

The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, PDB code: 3ski 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 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.930, 47.795, 228.281, 90.00, 90.00, 90.00
R / Rfree (%)	25.3 / 28.1

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

Magnesium binding site 1 out of 4 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine


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 2'- Deoxyguanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:47.9 occ:1.00 OP1 A:G23 4.6 34.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine


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 2'- Deoxyguanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:38.5 occ:1.00 OP1 A:C31 2.6 12.3 1.0 O2' A:G53 2.6 15.3 1.0 O A:HOH15 2.7 22.6 1.0 O3' A:A30 3.2 19.6 1.0 P A:C31 3.3 11.4 1.0 N6 A:A32 3.4 21.4 1.0 O5' A:C31 3.5 11.8 1.0 C2' A:G53 3.5 15.9 1.0 C6 A:C31 3.6 13.6 1.0 C5 A:C31 3.6 14.1 1.0 OP1 A:A54 4.0 17.8 1.0 O A:HOH143 4.0 39.9 1.0 O3' A:G53 4.1 18.6 1.0 O2' A:A30 4.1 19.8 1.0 C6 A:A32 4.2 21.3 1.0 C3' A:G53 4.4 18.1 1.0 P A:A54 4.5 18.8 1.0 C3' A:A30 4.5 19.1 1.0 C5' A:C31 4.7 13.9 1.0 OP2 A:C31 4.7 14.1 1.0 C5 A:A32 4.8 20.5 1.0 C1' A:G53 4.8 15.7 1.0 OP2 A:A54 4.8 18.9 1.0 N1 A:A32 4.8 20.6 1.0 C2' A:A30 4.9 19.5 1.0 N1 A:C31 4.9 13.8 1.0 N7 A:A32 5.0 20.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine


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 2'- Deoxyguanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg228 b:37.6 occ:1.00 OP2 A:G59 2.3 24.9 1.0 O5' A:C58 3.3 26.4 1.0 OP2 A:C58 3.4 25.6 1.0 P A:G59 3.5 27.0 1.0 C3' A:C58 3.5 24.9 1.0 C8 A:G59 3.5 23.4 1.0 C5' A:G59 3.7 25.1 1.0 P A:C58 3.8 27.4 1.0 O4' A:G59 3.9 23.6 1.0 O5' A:G59 3.9 26.2 1.0 O3' A:C58 3.9 26.5 1.0 C6 A:C58 4.0 22.6 1.0 N7 A:G59 4.2 22.1 1.0 C5' A:C58 4.3 27.2 1.0 C5 A:C58 4.4 21.8 1.0 C4' A:C58 4.4 26.1 1.0 C4' A:G59 4.4 24.4 1.0 C2' A:C58 4.4 23.6 1.0 OP1 A:C58 4.4 29.2 1.0 N9 A:G59 4.6 22.3 1.0 N1 A:C58 4.6 22.4 1.0 OP1 A:G59 4.8 27.9 1.0 C1' A:G59 4.8 22.2 1.0 C1' A:C58 4.9 23.5 1.0 O4' A:C58 4.9 25.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg206 b:46.7 occ:1.00 O B:HOH99 2.3 34.4 1.0 N7 B:A67 2.4 31.5 1.0 N6 B:A67 3.3 29.1 1.0 C5 B:A67 3.4 30.9 1.0 C8 B:A67 3.5 32.9 1.0 C6 B:A67 3.8 29.8 1.0 N7 B:A66 3.9 38.3 1.0 C8 B:A66 4.3 39.5 1.0 OP2 B:A67 4.3 38.7 1.0 C5 B:A66 4.4 37.5 1.0 C4 B:A67 4.6 31.6 1.0 N9 B:A67 4.6 33.1 1.0 C5 B:C68 4.7 33.2 1.0 OP2 B:A66 4.9 42.8 1.0 C6 B:A66 4.9 36.1 1.0 N4 B:C68 4.9 32.3 1.0 N9 B:A66 4.9 39.5 1.0 O B:HOH164 5.0 28.6 1.0 N6 B:A66 5.0 35.5 1.0

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