Magnesium in PDB 1dno: A-Dna/Rna Dodecamer R(Gcg)D(Tatacgc) Mg Binding Sites

The structure of A-Dna/Rna Dodecamer R(Gcg)D(Tatacgc) Mg Binding Sites, PDB code: 1dno 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 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.200, 42.656, 49.315, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.2

The binding sites of Magnesium atom in the A-Dna/Rna Dodecamer R(Gcg)D(Tatacgc) Mg Binding Sites (pdb code 1dno). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the A-Dna/Rna Dodecamer R(Gcg)D(Tatacgc) Mg Binding Sites, PDB code: 1dno:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the A-Dna/Rna Dodecamer R(Gcg)D(Tatacgc) Mg 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/Rna Dodecamer R(Gcg)D(Tatacgc) Mg Binding Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg24 b:24.3 occ:1.00 O A:HOH215 2.0 22.3 1.0 O A:HOH216 2.1 16.5 1.0 O A:HOH217 2.1 23.4 1.0 O B:HOH219 2.1 27.1 1.0 O A:HOH218 2.1 17.6 1.0 O B:HOH220 2.1 19.9 1.0 O B:HOH148 3.6 28.7 1.0 O4 A:DT4 4.2 14.7 1.0 O B:HOH142 4.2 20.9 1.0 O6 A:G3 4.3 12.3 1.0 O B:HOH118 4.3 26.8 1.0 O A:HOH117 4.3 32.0 1.0 O A:HOH156 4.4 28.9 1.0 O A:HOH105 4.4 19.1 1.0 O A:HOH154 4.5 26.3 1.0 N7 A:G3 4.5 12.9 1.0 O A:HOH173 4.5 30.2 1.0 O4 B:DT16 4.5 12.7 1.0 N4 A:C2 4.6 14.2 1.0 N6 B:DA17 4.8 14.7 1.0 O B:HOH153 4.8 31.2 1.0 C6 A:G3 4.9 11.9 1.0 C4 A:C2 5.0 12.9 1.0 C5 A:C2 5.0 15.2 1.0

Magnesium binding site 2 out of 4 in the A-Dna/Rna Dodecamer R(Gcg)D(Tatacgc) Mg 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/Rna Dodecamer R(Gcg)D(Tatacgc) Mg Binding Sites within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg21 b:20.3 occ:1.00 O B:HOH202 2.1 29.4 1.0 O B:HOH200 2.1 26.9 1.0 O B:HOH198 2.1 20.9 1.0 O B:HOH201 2.1 24.7 1.0 O B:HOH197 2.1 29.7 1.0 O B:HOH199 2.1 18.6 1.0 O B:HOH119 4.1 19.7 1.0 O B:HOH138 4.1 21.5 1.0 O B:HOH108 4.1 16.4 1.0 N4 B:DC18 4.1 12.2 1.0 O B:HOH118 4.2 26.8 1.0 O B:HOH174 4.3 26.9 1.0 O6 B:DG19 4.3 10.8 1.0 O A:HOH139 4.5 30.7 1.0 O B:HOH103 4.5 18.1 1.0 C5 B:DC18 4.6 13.2 1.0 N7 B:DG19 4.7 16.3 1.0 C4 B:DC18 4.8 12.0 1.0

Magnesium binding site 3 out of 4 in the A-Dna/Rna Dodecamer R(Gcg)D(Tatacgc) Mg Binding Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A-Dna/Rna Dodecamer R(Gcg)D(Tatacgc) Mg Binding Sites within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg22 b:24.7 occ:1.00 O B:HOH208 2.1 19.9 1.0 O B:HOH203 2.1 27.7 1.0 O B:HOH206 2.1 32.6 1.0 O A:HOH205 2.1 27.0 1.0 O B:HOH204 2.1 21.4 1.0 O B:HOH207 2.1 24.2 1.0 O B:HOH181 3.9 46.3 1.0 O A:HOH105 4.0 19.1 1.0 O4 B:DT14 4.1 16.4 1.0 O B:HOH144 4.2 29.4 1.0 O B:HOH169 4.2 27.1 1.0 O6 B:G13 4.4 16.7 1.0 O B:HOH153 4.4 31.2 1.0 O A:HOH179 4.4 42.5 1.0 O A:HOH156 4.6 28.9 1.0 O4 A:DT6 4.6 13.9 1.0 N6 A:DA7 4.6 14.8 1.0 N7 B:G13 4.7 14.8 1.0 O A:HOH111 4.8 17.8 1.0 N4 B:C12 4.8 22.0 1.0 C5 B:C12 5.0 20.2 1.0

Magnesium binding site 4 out of 4 in the A-Dna/Rna Dodecamer R(Gcg)D(Tatacgc) Mg Binding Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A-Dna/Rna Dodecamer R(Gcg)D(Tatacgc) Mg Binding Sites within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg23 b:25.4 occ:1.00 O B:HOH213 2.0 19.7 1.0 O B:HOH214 2.0 46.6 1.0 O B:HOH210 2.1 39.8 1.0 O B:HOH212 2.1 23.8 1.0 O B:HOH209 2.1 24.8 1.0 O B:HOH211 2.1 44.7 1.0 OP1 B:DC20 3.7 16.2 1.0 O B:HOH151 3.9 27.6 1.0 O B:HOH135 4.0 30.5 1.0 O B:HOH152 4.3 28.2 1.0 O B:HOH160 4.3 34.2 1.0 O B:HOH162 4.6 25.2 1.0 C5' B:DC20 4.6 14.9 1.0 O3' B:DC20 4.6 15.4 1.0 O B:HOH191 4.9 40.7 1.0 O5' B:DC20 5.0 12.9 1.0 P B:DC20 5.0 14.8 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