Potassium in PDB 2fd0: Hiv-1 Dis Kissing-Loop in Complex with Lividomycin

The structure of Hiv-1 Dis Kissing-Loop in Complex with Lividomycin, PDB code: 2fd0 was solved by E.Ennifar, J.C.Paillart, R.Marquet, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.94 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	27.137, 115.335, 95.254, 90.00, 90.00, 90.00
R / Rfree (%)	24.5 / 24.5

The structure of Hiv-1 Dis Kissing-Loop in Complex with Lividomycin also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Potassium atom in the Hiv-1 Dis Kissing-Loop in Complex with Lividomycin (pdb code 2fd0). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Hiv-1 Dis Kissing-Loop in Complex with Lividomycin, PDB code: 2fd0:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Hiv-1 Dis Kissing-Loop in Complex with Lividomycin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Hiv-1 Dis Kissing-Loop in Complex with Lividomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:K1002 b:55.0 occ:0.96 O A:HOH1024 2.6 39.6 1.0 O6 A:G4 2.6 36.0 1.0 O A:HOH1042 2.7 68.9 1.0 O4 A:5BU3 3.0 35.5 1.0 C6 A:G4 3.6 36.7 1.0 C4 A:5BU3 3.8 35.9 1.0 O A:HOH1037 3.9 53.8 1.0 BR A:5BU3 3.9 42.0 0.5 O A:HOH1041 4.0 58.3 1.0 N7 A:G4 4.0 38.9 1.0 N4 A:C20 4.1 33.1 1.0 C5 A:G4 4.2 37.7 1.0 O6 A:G19 4.2 34.5 1.0 C5 A:5BU3 4.3 35.8 1.0 N4 A:C5 4.3 35.5 1.0 N6 A:A21 4.7 34.8 1.0 N3 A:5BU3 4.7 37.1 1.0 N1 A:G4 4.8 36.9 1.0 O A:HOH1039 4.9 74.1 1.0

Potassium binding site 2 out of 4 in the Hiv-1 Dis Kissing-Loop in Complex with Lividomycin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Hiv-1 Dis Kissing-Loop in Complex with Lividomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:K44 b:46.0 occ:0.80 O6 A:G23 2.8 36.7 1.0 C6 A:G23 3.9 35.8 1.0 N6 A:A22 3.9 35.5 1.0 N7 A:G23 4.2 33.1 1.0 N4 A:C1 4.3 34.9 1.0 N7 A:A22 4.4 34.2 1.0 C5 A:G23 4.5 34.7 1.0 C6 A:A22 4.7 36.3 1.0 C5 A:A22 4.9 35.9 1.0

Potassium binding site 3 out of 4 in the Hiv-1 Dis Kissing-Loop in Complex with Lividomycin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Hiv-1 Dis Kissing-Loop in Complex with Lividomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:K2002 b:55.7 occ:0.95 O6 B:G4 2.5 51.5 1.0 O B:HOH2033 2.5 48.8 1.0 O B:HOH2028 2.6 45.6 1.0 O4 B:5BU3 2.8 35.2 1.0 C4 B:5BU3 3.5 35.1 1.0 C6 B:G4 3.6 49.5 1.0 BR B:5BU3 3.8 42.6 0.5 N7 B:G4 3.9 48.4 1.0 O B:HOH2034 4.0 48.8 1.0 C5 B:5BU3 4.1 35.6 1.0 C5 B:G4 4.1 49.8 1.0 N4 B:C20 4.1 52.3 1.0 O B:HOH2031 4.2 48.8 1.0 N6 B:A21 4.2 51.6 1.0 O6 B:G19 4.5 43.4 1.0 N3 B:5BU3 4.5 38.3 1.0 N4 B:C5 4.7 54.4 1.0 N1 B:G4 4.8 51.3 1.0

Potassium binding site 4 out of 4 in the Hiv-1 Dis Kissing-Loop in Complex with Lividomycin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Hiv-1 Dis Kissing-Loop in Complex with Lividomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:K90 b:76.5 occ:0.46 O B:HOH2021 2.6 45.1 1.0 OP1 B:5BU3 2.8 34.7 1.0 O B:HOH2008 3.5 40.9 1.0 O B:HOH2032 3.7 76.1 0.5 P B:5BU3 4.1 36.5 1.0 OP2 B:5BU3 4.5 34.4 1.0 OP1 B:C15 4.7 36.7 1.0 O3' B:U2 4.7 33.2 1.0

E.Ennifar, J.C.Paillart, A.Bodlenner, P.Walter, J.-M.Weibel, A.-M.Aubertin, P.Pale, P.Dumas, R.Marquet. Targeting the Dimerization Initiation Site of Hiv-1 Rna with Aminoglycosides: From Crystal to Cell. Nucleic Acids Res. V. 34 2328 2006.
ISSN: ISSN 0305-1048
PubMed: 16679451
DOI: 10.1093/NAR/GKL317