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Bromine 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:

Potassium (K) 4 atoms
Chlorine (Cl) 1 atom

Bromine Binding Sites:

The binding sites of Bromine 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 Bromine atom.
In total 2 binding sites of Bromine where determined in the Hiv-1 Dis Kissing-Loop in Complex with Lividomycin, PDB code: 2fd0:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 2fd0

Go back to Bromine Binding Sites List in 2fd0
Bromine binding site 1 out of 2 in the Hiv-1 Dis Kissing-Loop in Complex with Lividomycin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br3

b:42.0
occ:0.46
BR A:5BU3 0.0 42.0 0.5
C5 A:5BU3 1.9 35.8 1.0
C6 A:5BU3 2.9 37.3 1.0
C4 A:5BU3 2.9 35.9 1.0
O4 A:5BU3 3.1 35.5 1.0
O A:HOH1042 3.5 68.9 1.0
OP2 A:5BU3 3.5 42.0 1.0
C6 A:U2 3.7 37.6 1.0
C5 A:U2 3.8 37.1 1.0
K A:K1002 3.9 55.0 1.0
C3' A:U2 4.0 40.8 1.0
N1 A:U2 4.0 39.4 1.0
N3 A:5BU3 4.1 37.1 1.0
O5' A:U2 4.1 42.5 1.0
C4 A:U2 4.2 38.1 1.0
N1 A:5BU3 4.2 37.6 1.0
OP2 A:U2 4.3 43.0 1.0
N3 A:U2 4.4 39.2 1.0
C2 A:U2 4.4 38.4 1.0
C2' A:U2 4.4 40.4 1.0
O5' A:5BU3 4.4 41.7 1.0
P A:5BU3 4.5 41.5 1.0
C2 A:5BU3 4.7 37.2 1.0
C1' A:U2 4.7 39.2 1.0
O3' A:U2 4.8 41.7 1.0
O4 A:U2 4.8 37.3 1.0
P A:U2 4.9 43.2 1.0
N7 A:G4 4.9 38.9 1.0

Bromine binding site 2 out of 2 in 2fd0

Go back to Bromine Binding Sites List in 2fd0
Bromine binding site 2 out of 2 in the Hiv-1 Dis Kissing-Loop in Complex with Lividomycin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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
B:Br3

b:42.6
occ:0.50
BR B:5BU3 0.0 42.6 0.5
C5 B:5BU3 1.9 35.6 1.0
C6 B:5BU3 2.8 37.9 1.0
C4 B:5BU3 2.9 35.1 1.0
O4 B:5BU3 3.2 35.2 1.0
O B:HOH2028 3.6 45.6 1.0
OP2 B:5BU3 3.6 34.4 1.0
C5 B:U2 3.7 33.0 1.0
C4 B:U2 3.7 34.8 1.0
O B:HOH2014 3.7 36.3 1.0
N3 B:U2 3.7 32.9 1.0
K B:K2002 3.8 55.7 0.9
C6 B:U2 3.8 31.3 1.0
N1 B:U2 3.9 33.0 1.0
C2 B:U2 3.9 33.3 1.0
N1 B:5BU3 4.1 38.9 1.0
N3 B:5BU3 4.1 38.3 1.0
C3' B:U2 4.1 34.6 1.0
O4 B:U2 4.2 36.1 1.0
O5' B:5BU3 4.3 35.8 1.0
C2' B:U2 4.4 35.0 1.0
P B:5BU3 4.5 36.5 1.0
O2 B:U2 4.6 34.0 1.0
C1' B:U2 4.7 34.2 1.0
C2 B:5BU3 4.7 39.7 1.0
O5' B:U2 4.8 32.7 1.0
O3' B:U2 4.9 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: Sat Dec 12 02:05:43 2020

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