Magnesium in PDB 412d: Duplex [5'-D(Gcgta+Tacgc)]2 with Incorporated 2'-O-Methyl- [Tri(Oxyethyl)] Ribonucleoside

The structure of Duplex [5'-D(Gcgta+Tacgc)]2 with Incorporated 2'-O-Methyl- [Tri(Oxyethyl)] Ribonucleoside, PDB code: 412d was solved by V.Tereshko, S.Portmann, E.C.Tay, P.Martin, F.Natt, K.H.Altmann, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.640, 43.620, 45.470, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22

The binding sites of Magnesium atom in the Duplex [5'-D(Gcgta+Tacgc)]2 with Incorporated 2'-O-Methyl- [Tri(Oxyethyl)] Ribonucleoside (pdb code 412d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Duplex [5'-D(Gcgta+Tacgc)]2 with Incorporated 2'-O-Methyl- [Tri(Oxyethyl)] Ribonucleoside, PDB code: 412d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Duplex [5'-D(Gcgta+Tacgc)]2 with Incorporated 2'-O-Methyl- [Tri(Oxyethyl)] Ribonucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Duplex [5'-D(Gcgta+Tacgc)]2 with Incorporated 2'-O-Methyl- [Tri(Oxyethyl)] Ribonucleoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:24.6 occ:1.00 O B:HOH140 2.1 28.8 1.0 O A:HOH125 2.1 25.4 1.0 O A:HOH105 2.1 13.9 1.0 O A:HOH129 2.2 22.8 1.0 O A:HOH121 2.2 19.9 1.0 O B:HOH122 2.2 22.0 1.0 O A:HOH131 3.9 19.5 1.0 O A:HOH130 3.9 20.6 1.0 O A:HOH170 4.1 46.8 1.0 O B:HOH127 4.1 22.3 1.0 O B:HOH169 4.1 30.5 1.0 O A:HOH147 4.1 32.2 1.0 O B:HOH173 4.2 47.7 1.0 O6 A:DG3 4.3 15.8 1.0 N7 A:DG3 4.3 15.6 1.0 O A:HOH187 4.4 50.0 1.0 O B:HOH145 4.4 27.0 1.0 O4 A:DT4 4.5 13.1 1.0 N6 A:DA5 4.5 11.8 1.0 O4 B:12616 4.6 12.0 1.0 N4 A:DC2 4.9 14.7 1.0 C6 A:DG3 4.9 13.4 1.0 O A:HOH112 5.0 19.9 1.0 C5 A:DG3 5.0 14.8 1.0

Magnesium binding site 2 out of 2 in the Duplex [5'-D(Gcgta+Tacgc)]2 with Incorporated 2'-O-Methyl- [Tri(Oxyethyl)] Ribonucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Duplex [5'-D(Gcgta+Tacgc)]2 with Incorporated 2'-O-Methyl- [Tri(Oxyethyl)] Ribonucleoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg158 b:50.0 occ:1.00 O B:HOH126 2.1 21.9 1.0 O B:HOH166 2.3 28.6 1.0 O B:HOH150 2.4 31.8 1.0 O B:HOH149 3.7 38.8 1.0 O B:HOH162 3.7 27.1 1.0 N4 B:DC18 4.3 15.1 1.0 O A:HOH185 4.3 36.8 1.0 O B:HOH148 4.3 25.5 1.0 O A:HOH193 4.4 50.0 1.0 C5 B:DC18 4.5 16.2 1.0 N7 B:DG19 4.7 15.6 1.0 O6 B:DG19 4.7 14.5 1.0 O B:HOH186 4.8 38.0 1.0 C4 B:DC18 4.8 16.4 1.0

V.Tereshko, S.Portmann, E.C.Tay, P.Martin, F.Natt, K.H.Altmann, M.Egli. Correlating Structure and Stability of Dna Duplexes with Incorporated 2'-O-Modified Rna Analogues. Biochemistry V. 37 10626 1998.
ISSN: ISSN 0006-2960
PubMed: 9692952
DOI: 10.1021/BI980392A