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

The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak, PDB code: 3skr 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 / 3.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.530, 35.018, 110.761, 90.00, 92.18, 90.00
R / Rfree (%)	23.6 / 29.9

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

Cobalt

(Co)

9 atoms

The binding sites of Magnesium atom in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt Hexammine Soak (pdb code 3skr). 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, Cobalt Hexammine Soak, PDB code: 3skr:
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, Cobalt 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, Cobalt Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:2.0 occ:1.00 O6 A:GNG120 2.6 18.6 1.0 O3' A:C31 2.7 31.6 1.0 OP2 A:A32 3.1 32.5 1.0 P A:A32 3.3 33.1 1.0 O2' A:C31 3.3 25.5 1.0 O5' A:A32 3.4 32.8 1.0 C6 A:GNG120 3.5 19.0 1.0 N1 A:NCO401 3.8 89.5 1.0 C1' A:C31 3.8 27.9 1.0 C3' A:C31 3.8 28.5 1.0 N6 A:A79 3.9 42.9 1.0 C2' A:C31 3.9 27.6 1.0 O2 A:C31 3.9 29.0 1.0 C5 A:GNG120 4.2 19.2 1.0 N7 A:GNG120 4.3 18.6 1.0 C5' A:A32 4.4 33.8 1.0 N1 A:GNG120 4.5 18.6 1.0 OP1 A:A32 4.7 32.8 1.0 O4' A:C31 4.7 27.9 1.0 C2 A:C31 4.8 28.8 1.0 N1 A:C31 4.8 28.3 1.0 N4 A:C80 4.8 34.3 1.0 C4' A:C31 4.9 27.9 1.0 N2 A:NCO401 5.0 89.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt 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, Cobalt Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:13.3 occ:1.00 OP2 A:C61 4.2 40.8 1.0 OP2 A:U62 4.3 46.7 1.0 OP1 A:G47 4.7 25.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt 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, Cobalt Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:25.1 occ:1.00 OP1 A:C60 2.7 36.2 1.0 O3' A:G59 3.7 34.2 1.0 P A:C60 3.7 35.2 1.0 O5' A:C60 4.2 34.2 1.0 O4' A:C61 4.4 45.2 1.0 O2' A:G59 4.6 29.6 1.0 C1' A:C61 4.9 44.8 1.0 C5' A:C60 4.9 35.1 1.0 C3' A:G59 5.0 32.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cobalt 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, Cobalt Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:51.3 occ:1.00 OP2 B:A40 2.6 69.7 1.0 P B:A40 3.7 69.5 1.0 OP1 B:C39 4.0 76.2 1.0 OP1 B:A40 4.0 69.2 1.0 OP2 B:C39 4.4 75.4 1.0 O3' B:C39 4.6 70.1 1.0 P B:C39 4.7 75.7 1.0 O5' B:A40 4.9 69.6 1.0 C3' B:C39 4.9 71.0 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