Magnesium in PDB 2oiy: Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site

The structure of Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site, PDB code: 2oiy was solved by E.Ennifar, P.Walter, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	43.963, 47.550, 57.633, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 25

The structure of Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site also contains other interesting chemical elements:

Potassium

(K)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site (pdb code 2oiy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site, PDB code: 2oiy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site


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 Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg74 b:39.5 occ:0.86 O B:HOH80 1.9 48.8 0.8 O B:HOH61 1.9 40.4 1.0 O B:HOH34 2.0 30.9 1.0 O A:HOH158 2.4 26.8 0.5 O A:HOH141 3.0 46.8 1.0 O B:HOH85 3.3 33.4 0.5 O6 A:G19 3.7 20.6 1.0 O B:HOH41 3.9 39.0 1.0 O4 B:U3 4.2 34.0 1.0 O B:HOH108 4.3 48.9 1.0 N4 B:C5 4.3 22.5 1.0 O6 B:G4 4.3 25.9 1.0 O6 A:G18 4.5 24.9 1.0 N7 A:G18 4.7 28.5 1.0 C6 A:G19 4.8 20.1 1.0 O B:HOH87 4.9 48.7 0.9 C4 B:U3 4.9 31.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site


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 Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg98 b:40.8 occ:0.76 O A:HOH129 1.9 34.0 1.0 O A:HOH136 2.1 33.0 0.9 O A:HOH146 2.2 35.1 0.9 O A:HOH163 2.3 32.9 1.0 O A:HOH125 2.6 48.9 0.9 O4 A:U6 3.7 23.5 1.0 O A:HOH102 3.8 26.8 1.0 O A:HOH114 4.0 40.2 1.0 O B:HOH63 4.2 41.5 1.0 C5 A:U6 4.2 22.9 1.0 O B:HOH84 4.3 49.5 1.0 C4 A:U6 4.3 24.5 1.0 O A:HOH150 4.4 35.3 1.0 O B:HOH35 4.4 42.5 1.0 N7 A:G7 4.6 26.4 1.0 O6 A:G7 5.0 27.6 1.0

E.Ennifar, P.Walter, P.Dumas. Cation-Dependent Cleavage of the Duplex Form of the Subtype-B Hiv-1 Rna Dimerization Initiation Site. Nucleic Acids Res. V. 38 5807 2010.
ISSN: ISSN 0305-1048
PubMed: 20460458
DOI: 10.1093/NAR/GKQ344