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Bromine in PDB 1yxp: Hiv-1 Dis Rna Subtype F- Zn Soaked

Protein crystallography data

The structure of Hiv-1 Dis Rna Subtype F- Zn Soaked, PDB code: 1yxp was solved by E.Ennifar, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.98 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 27.275, 118.629, 93.334, 90.00, 90.00, 90.00
R / Rfree (%) 27 / 30.3

Other elements in 1yxp:

The structure of Hiv-1 Dis Rna Subtype F- Zn Soaked also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Hiv-1 Dis Rna Subtype F- Zn Soaked (pdb code 1yxp). 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 Rna Subtype F- Zn Soaked, PDB code: 1yxp:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 1yxp

Go back to Bromine Binding Sites List in 1yxp
Bromine binding site 1 out of 2 in the Hiv-1 Dis Rna Subtype F- Zn Soaked


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 Rna Subtype F- Zn Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br3

b:50.0
occ:0.19
BR A:5BU3 0.0 50.0 0.2
C5 A:5BU3 1.9 49.3 1.0
C6 A:5BU3 2.8 49.6 1.0
C4 A:5BU3 2.9 50.7 1.0
O4 A:5BU3 3.2 51.2 1.0
C5 A:U2 3.6 44.8 1.0
C6 A:U2 3.7 44.4 1.0
C4 A:U2 3.9 44.6 1.0
N1 A:U2 4.1 46.7 1.0
N1 A:5BU3 4.1 50.7 1.0
N3 A:5BU3 4.1 49.8 1.0
OP2 A:5BU3 4.2 54.5 1.0
N3 A:U2 4.2 45.1 1.0
C2 A:U2 4.3 46.9 1.0
C3' A:U2 4.4 50.9 1.0
O4 A:U2 4.5 43.6 1.0
O5' A:5BU3 4.6 54.4 1.0
C2' A:U2 4.6 50.2 1.0
O5' A:U2 4.7 49.0 1.0
C2 A:5BU3 4.7 50.5 1.0
OP2 A:U2 4.9 46.3 1.0
C1' A:U2 4.9 49.0 1.0
P A:5BU3 4.9 57.0 1.0

Bromine binding site 2 out of 2 in 1yxp

Go back to Bromine Binding Sites List in 1yxp
Bromine binding site 2 out of 2 in the Hiv-1 Dis Rna Subtype F- Zn Soaked


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 Rna Subtype F- Zn Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br3

b:50.0
occ:0.22
BR B:5BU3 0.0 50.0 0.2
C5 B:5BU3 1.9 45.7 1.0
C6 B:5BU3 2.8 45.9 1.0
C4 B:5BU3 2.9 46.0 1.0
O4 B:5BU3 3.1 45.8 1.0
C5 B:U2 3.3 42.9 1.0
C6 B:U2 3.4 44.1 1.0
C4 B:U2 3.7 44.2 1.0
N1 B:U2 3.8 47.0 1.0
OP2 B:5BU3 3.9 53.1 1.0
N3 B:U2 4.0 43.4 1.0
N1 B:5BU3 4.1 47.1 1.0
C2 B:U2 4.1 46.0 1.0
N3 B:5BU3 4.1 43.8 1.0
C3' B:U2 4.2 51.8 1.0
O4 B:U2 4.3 42.9 1.0
C2' B:U2 4.4 50.9 1.0
O5' B:5BU3 4.5 53.0 1.0
O5' B:U2 4.6 54.3 1.0
C1' B:U2 4.6 49.7 1.0
C2 B:5BU3 4.7 45.5 1.0
P B:5BU3 4.8 55.1 1.0
N7 B:G4 4.8 42.0 1.0
OP2 B:U2 4.9 53.7 1.0
O2 B:U2 4.9 47.0 1.0
O6 B:G4 5.0 36.4 1.0

Reference:

E.Ennifar, P.Dumas. Polymorphism of Bulged-Out Residues in Hiv-1 Rna Dis Kissing Complex and Structure Comparison with Solution Studies. J.Mol.Biol. V. 356 771 2006.
ISSN: ISSN 0022-2836
PubMed: 16403527
DOI: 10.1016/J.JMB.2005.12.022
Page generated: Sat Dec 12 02:04:50 2020

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