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

Protein crystallography data

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

Other elements in 2fd0:

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

Potassium Binding Sites:

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 2fd0

Go back to Potassium Binding Sites List in 2fd0
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 2fd0

Go back to Potassium Binding Sites List in 2fd0
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 2fd0

Go back to Potassium Binding Sites List in 2fd0
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 2fd0

Go back to Potassium Binding Sites List in 2fd0
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

Reference:

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
Page generated: Sun Dec 13 23:09:36 2020

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