Magnesium in PDB 1dnz: A-Dna Decamer Accggccggt with Magnesium Binding Sites

The structure of A-Dna Decamer Accggccggt with Magnesium Binding Sites, PDB code: 1dnz 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)	20.00 / 1.60
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	38.502, 38.502, 77.631, 90.00, 90.00, 120.00
R / Rfree (%)	22.7 / 27.9

The binding sites of Magnesium atom in the A-Dna Decamer Accggccggt with Magnesium Binding Sites (pdb code 1dnz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the A-Dna Decamer Accggccggt with Magnesium Binding Sites, PDB code: 1dnz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the A-Dna Decamer Accggccggt 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 A-Dna Decamer Accggccggt with Magnesium Binding Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg21 b:36.1 occ:1.00 O A:HOH130 2.1 33.2 1.0 O A:HOH129 2.1 44.0 1.0 O A:HOH128 2.1 35.8 1.0 O A:HOH125 2.1 31.6 1.0 O A:HOH127 2.1 26.2 1.0 O A:HOH126 2.1 39.8 1.0 O A:HOH107 3.7 27.2 1.0 O6 A:DG8 4.1 16.5 1.0 O A:HOH117 4.3 36.2 1.0 O6 A:DG9 4.4 19.9 1.0 N7 A:DG8 4.4 21.1 1.0 O A:HOH113 4.5 39.3 1.0 N4 A:DC7 4.7 18.1 1.0 C6 A:DG8 4.8 19.6 1.0 C5 A:DG8 5.0 19.8 1.0

Magnesium binding site 2 out of 2 in the A-Dna Decamer Accggccggt with Magnesium Binding Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A-Dna Decamer Accggccggt with Magnesium Binding Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg22 b:17.8 occ:0.50 O A:HOH134 2.1 21.4 0.5 O A:HOH131 2.1 34.6 0.5 O A:HOH132 2.1 23.5 0.5 O A:HOH135 2.1 12.9 0.5 O A:HOH133 2.1 15.7 0.5 O A:HOH136 2.1 16.1 0.5 O A:HOH101 2.4 13.1 0.5 O6 A:DG5 3.9 22.2 1.0 O A:HOH102 3.9 18.6 0.5 N7 A:DG4 4.0 23.3 1.0 O6 A:DG4 4.1 18.0 1.0 O A:HOH118 4.1 31.3 1.0 O A:HOH103 4.3 28.9 1.0 O A:HOH116 4.4 30.4 1.0 C6 A:DG4 4.6 22.0 1.0 O A:HOH104 4.6 23.7 1.0 C5 A:DG4 4.6 14.4 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