Magnesium in PDB 3slm: Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine-5'-Monophosphate

The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine-5'-Monophosphate, PDB code: 3slm was solved by O.Pikovskaya, A.Polonskaia, D.J.Patel, A.A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.54 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.954, 66.058, 72.503, 90.00, 117.95, 90.00
R / Rfree (%)	20 / 24.9

The binding sites of Magnesium atom in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine-5'-Monophosphate (pdb code 3slm). 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 2'- Deoxyguanosine-5'-Monophosphate, PDB code: 3slm:
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 2'- Deoxyguanosine-5'-Monophosphate


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-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1 b:55.3 occ:1.00 O1A A:GTP22 2.7 68.7 1.0 O3B A:GTP22 3.0 73.2 1.0 O2B A:GTP22 3.6 73.0 1.0 O5' A:GTP22 3.7 48.6 1.0 PA A:GTP22 3.7 63.4 1.0 PB A:GTP22 3.8 86.3 1.0 PG A:GTP22 4.1 85.0 1.0 O1G A:GTP22 4.2 60.3 1.0 O3A A:GTP22 4.3 69.5 1.0 O4' A:GTP22 4.6 48.6 1.0 O3G A:GTP22 4.7 73.6 1.0 C5' A:GTP22 4.9 52.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine-5'-Monophosphate


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-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg7 b:27.9 occ:0.50 O2 A:U70 3.9 52.3 1.0 C1' A:U70 4.3 40.7 1.0 O4' A:U70 4.7 43.7 1.0 C2 A:U70 4.7 50.4 1.0 N1 A:U70 5.0 49.9 1.0 O2' A:U70 5.0 41.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine-5'-Monophosphate


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-5'-Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg12 b:34.7 occ:1.00 C6 B:U72 3.5 38.6 1.0 O2' B:U72 3.7 43.2 1.0 C5 B:U72 3.8 36.2 1.0 C2' B:U72 4.1 39.8 1.0 C5 B:U73 4.3 36.4 1.0 N1 B:U72 4.3 40.8 1.0 OP1 B:G47 4.7 33.4 1.0 C1' B:U72 4.8 37.6 1.0 C4 B:U72 4.8 35.5 1.0 O4 B:U73 4.9 27.9 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