Potassium 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:

Magnesium

(Mg)

2 atoms

The binding sites of Potassium 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 Potassium atom.
In total 3 binding sites of Potassium where determined in the Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site, PDB code: 2oiy:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 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 Potassium with other atoms in the K 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:K24 b:32.8 occ:0.78 O2 A:C20 2.8 24.5 1.0 O2 B:C5 2.9 26.6 1.0 O A:HOH138 2.9 35.0 0.9 O B:HOH51 3.0 27.8 1.0 O B:HOH33 3.2 29.9 1.0 N2 B:G4 3.4 24.7 1.0 N2 A:G19 3.5 24.9 1.0 C2 A:C20 3.9 22.7 1.0 C2 B:C5 4.0 25.8 1.0 C1' A:C20 4.3 23.4 1.0 C1' B:C5 4.4 25.1 1.0 C2 B:G4 4.5 24.6 1.0 C2 A:G19 4.5 23.9 1.0 N1 A:C20 4.6 24.4 1.0 O2' B:C5 4.6 23.6 1.0 O2' A:C20 4.7 24.7 1.0 N1 B:C5 4.7 25.4 1.0 N3 A:C20 4.8 23.5 1.0 N3 B:C5 4.9 24.6 1.0 C2' B:C5 4.9 23.6 1.0 C2' A:C20 4.9 24.9 1.0

Potassium binding site 2 out of 3 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 Potassium with other atoms in the K 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:K25 b:32.0 occ:0.68 O4 A:U6 2.8 23.5 1.0 O6 A:G7 2.9 27.6 1.0 O B:HOH60 2.9 39.4 0.9 O6 B:G18 3.0 26.1 1.0 O B:HOH63 3.1 41.5 1.0 O A:HOH135 3.1 39.9 0.9 O A:HOH165 3.2 32.5 0.8 N4 B:C17 3.3 28.2 1.0 N4 A:C5 3.5 24.3 1.0 O A:HOH111 3.7 19.8 0.5 C4 A:U6 3.8 24.5 1.0 C6 A:G7 3.8 28.1 1.0 O A:HOH163 3.9 32.9 1.0 N3 A:U6 4.0 21.7 1.0 O B:HOH101 4.1 44.5 0.9 C6 B:G18 4.1 25.6 1.0 O A:HOH129 4.2 34.0 1.0 O6 B:G19 4.2 21.4 1.0 C4 B:C17 4.4 29.7 1.0 N7 B:G18 4.5 29.8 1.0 N1 A:G7 4.6 28.7 1.0 O A:HOH134 4.6 20.1 0.5 C5 B:G18 4.7 27.4 1.0 C4 A:C5 4.7 23.1 1.0 C5 A:G7 4.8 27.6 1.0 N3 B:C17 4.8 29.3 1.0

Potassium binding site 3 out of 3 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 Potassium with other atoms in the K binding site number 3 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 B:K24 b:27.8 occ:0.95 O2 B:C20 2.7 24.5 1.0 O2' B:C20 2.8 26.2 1.0 O A:HOH101 3.0 28.6 1.0 O4' B:A21 3.0 29.8 1.0 C2' B:C20 3.4 28.0 1.0 C1' B:A21 3.7 28.6 1.0 C1' B:C20 3.8 27.0 1.0 N2 A:G4 3.8 23.3 1.0 C2 B:C20 3.9 26.6 1.0 C4' B:A21 4.1 31.7 1.0 N9 B:A21 4.2 26.9 1.0 N1 B:C20 4.4 26.8 1.0 C8 B:A21 4.5 27.4 1.0 C5' B:A21 4.6 30.8 1.0 O2 A:C5 4.8 20.1 1.0 C3' B:C20 4.9 28.0 1.0 O B:HOH36 4.9 31.8 1.0 N3 B:C20 5.0 25.1 1.0 C2' B:A21 5.0 30.2 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