Magnesium in PDB 1dnt: Rna/Dna Dodecamer R(Gc)D(Gtatacgc) with Magnesium Binding Sites

The structure of Rna/Dna Dodecamer R(Gc)D(Gtatacgc) with Magnesium Binding Sites, PDB code: 1dnt was solved by H.Robinson, Y.-G.Gao, R.Sanishvili, A.Joachimiak, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.538, 43.725, 45.466, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 26.9

The binding sites of Magnesium atom in the Rna/Dna Dodecamer R(Gc)D(Gtatacgc) with Magnesium Binding Sites (pdb code 1dnt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Rna/Dna Dodecamer R(Gc)D(Gtatacgc) with Magnesium Binding Sites, PDB code: 1dnt:

Magnesium binding site 1 out of 1 in the Rna/Dna Dodecamer R(Gc)D(Gtatacgc) with Magnesium Binding Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rna/Dna Dodecamer R(Gc)D(Gtatacgc) with Magnesium Binding Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg21 b:46.4 occ:1.00 O A:HOH147 2.1 27.2 1.0 O A:HOH146 2.1 39.4 1.0 O A:HOH150 2.1 0.9 1.0 O B:HOH151 2.1 42.2 1.0 O A:HOH149 2.1 33.3 1.0 O A:HOH148 2.1 57.7 1.0 O6 A:DG3 3.9 22.2 1.0 O B:HOH103 4.0 31.9 1.0 O B:HOH107 4.0 34.6 1.0 N7 A:DG3 4.2 24.8 1.0 O A:HOH130 4.3 52.9 1.0 O4 B:DT16 4.6 20.9 1.0 O4 A:DT4 4.6 22.3 1.0 O A:HOH124 4.6 38.8 1.0 C6 A:DG3 4.7 23.9 1.0 N6 A:DA5 4.7 29.9 1.0 C5 A:DG3 4.8 22.4 1.0 N4 A:C2 4.9 34.2 1.0

H.Robinson, Y.G.Gao, R.Sanishvili, A.Joachimiak, A.H.Wang. Hexahydrated Magnesium Ions Bind in the Deep Major Groove and at the Outer Mouth of A-Form Nucleic Acid Duplexes. Nucleic Acids Res. V. 28 1760 2000.
ISSN: ISSN 0305-1048
PubMed: 10734195
DOI: 10.1093/NAR/28.8.1760