Potassium in PDB 2qek: Hiv-1 Subtype F Dis Rna Extended Duplex Form

The structure of Hiv-1 Subtype F Dis Rna Extended Duplex Form, PDB code: 2qek was solved by S.Freisz, E.Ennifar, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.69 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.773, 37.355, 44.965, 90.00, 111.24, 90.00
R / Rfree (%)	25.1 / 26.5

The structure of Hiv-1 Subtype F Dis Rna Extended Duplex Form also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Potassium atom in the Hiv-1 Subtype F Dis Rna Extended Duplex Form (pdb code 2qek). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Hiv-1 Subtype F Dis Rna Extended Duplex Form, PDB code: 2qek:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Hiv-1 Subtype F Dis Rna Extended Duplex Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Hiv-1 Subtype F Dis Rna Extended Duplex Form within 5.0Å range: probe atom residue distance (Å) B Occ A:K9002 b:40.4 occ:1.00 O6 A:G4 2.7 37.5 1.0 O4 A:U3 2.8 39.3 1.0 O A:HOH9020 2.9 38.9 1.0 C4 A:U3 3.7 40.4 1.0 C6 A:G4 3.8 39.0 1.0 O A:HOH9017 4.1 50.6 1.0 N7 A:G4 4.2 38.3 1.0 N6 B:A21 4.2 37.1 1.0 N4 B:C20 4.2 40.4 1.0 C5 A:U3 4.3 40.0 1.0 C5 A:G4 4.4 38.0 1.0 N4 A:C5 4.4 27.7 1.0 N3 A:U3 4.6 39.9 1.0 O6 B:G19 4.7 33.3 1.0

Potassium binding site 2 out of 3 in the Hiv-1 Subtype F Dis Rna Extended Duplex Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Hiv-1 Subtype F Dis Rna Extended Duplex Form within 5.0Å range: probe atom residue distance (Å) B Occ A:K9003 b:39.9 occ:1.00 O6 A:G7 2.6 32.4 1.0 O4 A:U6 2.7 30.2 1.0 O A:HOH9005 2.7 45.0 1.0 O A:HOH9010 2.8 37.6 1.0 O A:HOH9021 3.1 36.6 1.0 C4 A:U6 3.6 32.1 1.0 C6 A:G7 3.6 31.1 1.0 N6 A:A8 3.9 31.1 1.0 N7 A:G7 4.0 31.2 1.0 C5 A:G7 4.2 30.4 1.0 C5 A:U6 4.2 29.9 1.0 N4 B:C17 4.3 31.8 1.0 N6 B:A18 4.3 29.5 1.0 O A:HOH9017 4.4 50.6 1.0 N3 A:U6 4.6 30.0 1.0 C6 A:A8 4.7 32.0 1.0 N1 A:G7 4.9 28.8 1.0 N1 A:A8 5.0 32.6 1.0

Potassium binding site 3 out of 3 in the Hiv-1 Subtype F Dis Rna Extended Duplex Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Hiv-1 Subtype F Dis Rna Extended Duplex Form within 5.0Å range: probe atom residue distance (Å) B Occ B:K9001 b:38.8 occ:1.00 O6 B:G4 2.7 37.6 1.0 O B:HOH9012 2.7 34.1 1.0 O4 B:U3 2.7 40.0 1.0 O A:HOH9025 2.8 42.2 1.0 O A:HOH9006 3.6 41.4 1.0 C4 B:U3 3.6 40.9 1.0 C6 B:G4 3.8 39.1 1.0 O A:HOH9012 3.9 37.1 1.0 N4 A:C20 4.1 39.3 1.0 C5 B:U3 4.1 39.9 1.0 N7 B:G4 4.2 37.3 1.0 N6 A:A21 4.3 39.4 1.0 C5 B:G4 4.4 37.5 1.0 N3 B:U3 4.6 40.3 1.0 O6 A:G19 4.6 34.3 1.0 O A:HOH9048 4.8 37.4 1.0 N4 B:C5 4.8 39.6 1.0 N1 B:G4 5.0 38.9 1.0

S.Freisz, K.Lang, R.Micura, P.Dumas, E.Ennifar. Binding of Aminoglycoside Antibiotics to the Duplex Form of the Hiv-1 Genomic Rna Dimerization Initiation Site. Angew.Chem.Int.Ed.Engl. V. 47 4110 2008.
ISSN: ISSN 1433-7851
PubMed: 18435520
DOI: 10.1002/ANIE.200800726