Potassium in PDB 2fcy: Hiv-1 Dis Kissing-Loop in Complex with Neomycin

The structure of Hiv-1 Dis Kissing-Loop in Complex with Neomycin, PDB code: 2fcy 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)	18.22 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	27.105, 113.702, 96.165, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 25.3

The structure of Hiv-1 Dis Kissing-Loop in Complex with Neomycin 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 Neomycin (pdb code 2fcy). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Hiv-1 Dis Kissing-Loop in Complex with Neomycin, PDB code: 2fcy:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in the Hiv-1 Dis Kissing-Loop in Complex with Neomycin


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 Neomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:K1002 b:62.9 occ:1.00 N1 A:A8 2.7 16.2 1.0 C2 A:A8 3.4 14.0 1.0 C6 A:A8 3.8 10.9 1.0 N6 A:A8 3.9 16.0 1.0 C2 A:A9 4.1 12.8 1.0 N3 A:A9 4.5 13.4 1.0 N3 A:A8 4.7 12.1 1.0 N1 A:A9 4.7 8.9 1.0

Potassium binding site 2 out of 6 in the Hiv-1 Dis Kissing-Loop in Complex with Neomycin


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 Neomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:K1003 b:53.5 occ:1.00 OP1 A:A8 2.6 32.0 1.0 O A:HOH1033 3.0 38.4 1.0 OP2 A:A9 3.0 30.2 1.0 O4 A:NMY1001 3.0 23.2 1.0 O A:HOH1031 3.2 39.1 1.0 O A:HOH1008 3.3 37.5 1.0 O A:HOH1036 3.3 46.6 1.0 P A:A8 3.9 31.5 1.0 C3 A:NMY1001 4.0 21.6 1.0 O3 A:NMY1001 4.1 24.5 1.0 C4 A:NMY1001 4.1 21.1 1.0 OP2 A:A8 4.3 32.1 1.0 P A:A9 4.4 31.6 1.0 O5' A:A8 4.5 32.0 1.0 O B:HOH2023 4.6 36.8 1.0 C5 A:NMY1001 4.8 18.9 1.0 O A:HOH1025 4.8 31.2 1.0 O3' A:A8 4.8 28.8 1.0 N7 A:A9 4.9 14.1 1.0 C8 A:A9 4.9 17.3 1.0

Potassium binding site 3 out of 6 in the Hiv-1 Dis Kissing-Loop in Complex with Neomycin


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 Neomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:K1004 b:55.0 occ:1.00 O A:HOH1016 2.7 42.8 1.0 O6 A:G4 2.8 22.1 1.0 O4 A:5BU3 2.8 35.0 1.0 C4 A:5BU3 3.7 35.2 1.0 C6 A:G4 3.8 24.8 1.0 BR A:5BU3 3.8 41.0 0.4 O A:HOH1042 3.8 39.0 1.0 N7 A:G4 4.1 28.9 1.0 O A:HOH1018 4.2 50.4 1.0 N4 A:C20 4.2 26.8 1.0 C5 A:5BU3 4.3 36.8 1.0 C5 A:G4 4.3 28.5 1.0 O A:HOH1039 4.4 40.9 1.0 N6 A:A21 4.6 21.2 1.0 O6 A:G19 4.6 28.2 1.0 N3 A:5BU3 4.8 33.8 1.0 O A:HOH1038 4.9 40.9 1.0 N4 A:C5 5.0 25.0 1.0

Potassium binding site 4 out of 6 in the Hiv-1 Dis Kissing-Loop in Complex with Neomycin


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 Neomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:K1005 b:58.2 occ:0.67 O4' A:A8 3.2 25.4 1.0 C1' A:A8 4.1 23.5 1.0 C4' A:A8 4.3 27.2 1.0 C5' A:A8 4.4 29.3 1.0 OP1 A:G7 4.5 36.2 1.0 N9 A:A8 4.5 16.7 1.0 C8 A:A8 4.7 15.9 1.0

Potassium binding site 5 out of 6 in the Hiv-1 Dis Kissing-Loop in Complex with Neomycin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Hiv-1 Dis Kissing-Loop in Complex with Neomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:K2002 b:46.4 occ:1.00 OP2 B:A9 2.8 27.4 1.0 O4 B:NMY2001 2.9 25.5 1.0 O B:HOH2019 2.9 32.0 1.0 OP1 B:A8 2.9 44.6 1.0 C4 B:NMY2001 4.0 24.6 1.0 P B:A8 4.0 45.6 1.0 C3 B:NMY2001 4.1 23.5 1.0 OP2 B:A8 4.1 45.3 1.0 P B:A9 4.1 29.3 1.0 O3 B:NMY2001 4.2 27.6 1.0 O A:HOH1035 4.3 35.0 1.0 C5 B:NMY2001 4.5 22.8 1.0 OP1 B:A9 4.5 34.4 1.0 O5' B:A8 4.8 41.0 1.0 O A:HOH1040 4.9 47.9 1.0 O3' B:A8 5.0 31.3 1.0

Potassium binding site 6 out of 6 in the Hiv-1 Dis Kissing-Loop in Complex with Neomycin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Hiv-1 Dis Kissing-Loop in Complex with Neomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:K2003 b:49.7 occ:1.00 O B:HOH2022 2.5 33.4 1.0 O6 B:G4 2.8 35.2 1.0 O4 B:5BU3 2.8 24.5 1.0 O B:HOH2032 3.2 45.9 1.0 C4 B:5BU3 3.4 25.5 1.0 BR B:5BU3 3.7 29.6 0.4 C6 B:G4 3.8 38.4 1.0 O B:HOH2040 3.8 50.1 1.0 C5 B:5BU3 3.9 25.1 1.0 O B:HOH2027 4.0 51.7 1.0 N7 B:G4 4.2 39.9 1.0 N4 B:C20 4.3 50.3 1.0 N3 B:5BU3 4.3 24.3 1.0 C5 B:G4 4.4 39.5 1.0 N6 B:A21 4.5 49.4 1.0 O6 B:G19 4.6 39.3 1.0 N4 B:C5 4.8 50.5 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