Magnesium in PDB 3skl: Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak

The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak, PDB code: 3skl 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 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.002, 34.955, 111.057, 90.00, 92.45, 90.00
R / Rfree (%)	21.9 / 26.4

The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak also contains other interesting chemical elements:

Iridium

(Ir)

10 atoms

The binding sites of Magnesium atom in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak (pdb code 3skl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak, PDB code: 3skl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak


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, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:45.8 occ:1.00 O3G A:GTP22 2.0 69.7 1.0 O2A A:GTP22 2.8 59.8 1.0 O1B A:GTP22 3.3 66.2 1.0 PG A:GTP22 3.4 70.3 1.0 O2G A:GTP22 3.7 70.0 1.0 OP2 A:U82 4.1 44.2 1.0 PA A:GTP22 4.2 59.3 1.0 PB A:GTP22 4.2 66.7 1.0 O3B A:GTP22 4.3 68.5 1.0 O1G A:GTP22 4.4 70.6 1.0 O3A A:GTP22 4.6 62.6 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak


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, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:15.0 occ:1.00 O6 B:GNG120 2.5 37.3 1.0 O3' B:C30 2.9 33.6 1.0 O2' B:C30 3.0 28.3 1.0 OP2 B:A31 3.3 34.7 1.0 C6 B:GNG120 3.7 37.4 1.0 P B:A31 3.7 33.4 1.0 C2' B:C30 3.8 30.5 1.0 N6 B:IRI408 3.8 0.1 0.3 N6 B:A78 3.9 52.5 1.0 C3' B:C30 3.9 32.0 1.0 C1' B:C30 4.0 31.9 1.0 O2 B:C30 4.3 33.4 1.0 C5 B:GNG120 4.4 37.5 1.0 N7 B:GNG120 4.5 37.2 1.0 N4 B:C79 4.6 37.1 1.0 N1 B:GNG120 4.7 37.2 1.0 C5' B:A31 4.7 36.0 1.0 N4 B:IRI408 4.7 0.1 0.3 OP1 B:A31 4.8 33.0 1.0 O5' B:A31 4.8 33.4 1.0 N1 B:C30 4.9 33.0 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak


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, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:23.8 occ:1.00 O6 B:G85 2.5 55.3 1.0 O6 B:G23 2.8 43.3 1.0 O6 B:GTP22 3.2 50.5 1.0 N4 B:C24 3.4 55.0 1.0 O4 B:U86 3.6 54.0 1.0 C6 B:G85 3.6 55.3 1.0 C6 B:G23 3.8 43.1 1.0 C6 B:GTP22 3.9 50.6 1.0 N7 B:G23 4.0 42.9 1.0 N3 B:U86 4.2 53.7 1.0 C4 B:U86 4.3 53.6 1.0 C5 B:G23 4.3 43.0 1.0 N1 B:G85 4.4 55.0 1.0 N4 B:CCC87 4.4 55.1 1.0 C4 B:C24 4.5 55.0 1.0 C5 B:GTP22 4.5 50.3 1.0 N1 B:GTP22 4.6 50.4 1.0 N7 B:GTP22 4.7 50.0 1.0 C5 B:G85 4.7 55.1 1.0 N3 B:C24 4.9 55.1 1.0 N6 B:A84 5.0 52.9 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak


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, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:30.3 occ:1.00 OP1 B:U72 4.4 51.8 1.0 O5' B:U72 5.0 49.9 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg205 b:12.4 occ:1.00 N3 B:G32 2.8 35.8 1.0 O6 B:G34 2.9 30.8 1.0 N7 B:G33 3.0 35.5 1.0 O6 B:G33 3.2 35.6 1.0 O2' B:G32 3.4 36.6 1.0 C2 B:G32 3.4 36.0 1.0 C5 B:G33 3.5 35.8 1.0 N2 B:G32 3.6 36.1 1.0 C4 B:G32 3.6 36.3 1.0 C6 B:G33 3.6 35.3 1.0 N7 B:G34 3.8 30.9 1.0 C6 B:G34 3.8 31.2 1.0 C1' B:G32 3.8 35.9 1.0 N9 B:G32 4.0 35.9 1.0 C8 B:G33 4.1 35.5 1.0 C5 B:G34 4.1 31.6 1.0 C2' B:G32 4.2 36.6 1.0 N1 B:G32 4.6 35.8 1.0 O3' B:G32 4.6 35.6 1.0 N4 B:C50 4.7 45.0 1.0 C5 B:G32 4.7 36.1 1.0 C4 B:G33 4.7 35.8 1.0 O4 B:U35 4.7 36.0 1.0 N1 B:G33 4.8 35.5 1.0 N6 B:A49 4.8 40.0 1.0 N9 B:G33 5.0 35.5 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg206 b:28.9 occ:0.50 O2' B:C68 2.5 45.8 1.0 OP2 B:U69 3.3 45.5 1.0 C2' B:C68 3.3 45.5 1.0 O3' B:C68 3.4 46.3 1.0 C3' B:C68 3.5 45.7 1.0 C5' B:U69 3.6 42.6 1.0 P B:U69 3.9 46.7 1.0 O5' B:U69 4.2 44.9 1.0 N6 B:A42 4.5 41.4 1.0 C4' B:U69 4.7 40.6 1.0 C1' B:C68 4.7 44.8 1.0 C4' B:C68 5.0 45.8 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