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Fluorine in PDB 1pq6: Human Lxr Beta Hormone Receptor / GW3965 Complex

Protein crystallography data

The structure of Human Lxr Beta Hormone Receptor / GW3965 Complex, PDB code: 1pq6 was solved by M.Farnegardh, T.Bonn, S.Sun, J.Ljunggren, H.Ahola, A.Wilhelmsson, J.-A.Gustafsson, M.Carlquist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.71 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.717, 98.929, 175.815, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 26.2

Other elements in 1pq6:

The structure of Human Lxr Beta Hormone Receptor / GW3965 Complex also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Lxr Beta Hormone Receptor / GW3965 Complex (pdb code 1pq6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Human Lxr Beta Hormone Receptor / GW3965 Complex, PDB code: 1pq6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 1pq6

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Fluorine binding site 1 out of 9 in the Human Lxr Beta Hormone Receptor / GW3965 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Lxr Beta Hormone Receptor / GW3965 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1500

b:40.0
occ:1.00
 F41 A:9651500 0.0 40.0 1.0
C39 A:9651500 1.3 41.0 1.0
F42 A:9651500 2.2 42.7 1.0
F40 A:9651500 2.2 42.1 1.0
C20 A:9651500 2.3 39.4 1.0
C19 A:9651500 2.9 37.2 1.0
CL4 A:9651500 3.0 48.9 1.0
C21 A:9651500 3.4 37.1 1.0
CG A:GLN438 3.8 22.1 1.0
CD2 A:LEU345 3.9 23.5 1.0
CD1 A:LEU442 3.9 25.4 1.0
CE2 A:PHE349 4.2 22.3 1.0
C18 A:9651500 4.3 32.7 1.0
CZ A:PHE349 4.5 21.9 1.0
C22 A:9651500 4.5 34.9 1.0
CE1 A:PHE268 4.6 15.7 1.0
CD A:GLN438 4.6 22.7 1.0
CD2 A:HIS435 4.9 17.5 1.0
C23 A:9651500 4.9 33.2 1.0
CG A:LEU442 4.9 26.2 1.0

Fluorine binding site 2 out of 9 in 1pq6

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Fluorine binding site 2 out of 9 in the Human Lxr Beta Hormone Receptor / GW3965 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Lxr Beta Hormone Receptor / GW3965 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1500

b:42.1
occ:1.00
 F40 A:9651500 0.0 42.1 1.0
C39 A:9651500 1.3 41.0 1.0
F42 A:9651500 2.1 42.7 1.0
F41 A:9651500 2.2 40.0 1.0
C20 A:9651500 2.3 39.4 1.0
C21 A:9651500 2.8 37.1 1.0
NE2 A:HIS435 3.3 16.7 1.0
CD2 A:HIS435 3.6 17.5 1.0
C19 A:9651500 3.7 37.2 1.0
CG2 A:VAL439 3.8 23.1 1.0
CZ3 A:TRP457 4.0 26.7 1.0
CE3 A:TRP457 4.0 25.8 1.0
C22 A:9651500 4.2 34.9 1.0
CD2 A:LEU449 4.2 16.6 1.0
CD1 A:LEU442 4.3 25.4 1.0
CL4 A:9651500 4.4 48.9 1.0
CE1 A:HIS435 4.5 17.3 1.0
CG A:GLN438 4.8 22.1 1.0
C18 A:9651500 4.9 32.7 1.0
CG A:HIS435 4.9 18.5 1.0
CH2 A:TRP457 5.0 24.9 1.0

Fluorine binding site 3 out of 9 in 1pq6

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Fluorine binding site 3 out of 9 in the Human Lxr Beta Hormone Receptor / GW3965 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Lxr Beta Hormone Receptor / GW3965 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1500

b:42.7
occ:1.00
 F42 A:9651500 0.0 42.7 1.0
C39 A:9651500 1.3 41.0 1.0
F40 A:9651500 2.1 42.1 1.0
F41 A:9651500 2.2 40.0 1.0
C20 A:9651500 2.3 39.4 1.0
C19 A:9651500 2.9 37.2 1.0
CL4 A:9651500 3.0 48.9 1.0
CD2 A:LEU449 3.4 16.6 1.0
C21 A:9651500 3.5 37.1 1.0
CD1 A:LEU442 3.8 25.4 1.0
CE1 A:PHE268 4.1 15.7 1.0
CZ A:PHE268 4.2 15.5 1.0
C18 A:9651500 4.3 32.7 1.0
CZ3 A:TRP457 4.6 26.7 1.0
C22 A:9651500 4.6 34.9 1.0
OG1 A:THR272 4.8 18.8 1.0
CG A:LEU449 4.8 15.6 1.0
CE3 A:TRP457 4.9 25.8 1.0
CD1 A:LEU453 5.0 15.5 1.0

Fluorine binding site 4 out of 9 in 1pq6

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Fluorine binding site 4 out of 9 in the Human Lxr Beta Hormone Receptor / GW3965 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Lxr Beta Hormone Receptor / GW3965 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2500

b:43.6
occ:1.00
 F41 B:9652500 0.0 43.6 1.0
C39 B:9652500 1.3 43.1 1.0
F40 B:9652500 2.2 42.9 1.0
F42 B:9652500 2.2 43.1 1.0
C20 B:9652500 2.3 41.5 1.0
C19 B:9652500 3.1 40.2 1.0
C21 B:9652500 3.3 39.0 1.0
CL4 B:9652500 3.3 52.4 1.0
CG B:GLN438 3.8 26.9 1.0
CD1 B:LEU442 4.0 34.9 1.0
CD2 B:LEU345 4.2 22.4 1.0
CE2 B:PHE349 4.2 28.1 1.0
CZ B:PHE349 4.4 29.8 1.0
C18 B:9652500 4.4 34.2 1.0
C22 B:9652500 4.5 37.8 1.0
CE1 B:PHE268 4.6 19.9 1.0
CD B:GLN438 4.7 27.3 1.0
CD2 B:HIS435 4.8 24.3 1.0
C23 B:9652500 4.9 37.1 1.0
NE2 B:HIS435 4.9 23.7 1.0
CD2 B:PHE349 5.0 29.4 1.0
CB B:GLN438 5.0 27.1 1.0

Fluorine binding site 5 out of 9 in 1pq6

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Fluorine binding site 5 out of 9 in the Human Lxr Beta Hormone Receptor / GW3965 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Lxr Beta Hormone Receptor / GW3965 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2500

b:42.9
occ:1.00
 F40 B:9652500 0.0 42.9 1.0
C39 B:9652500 1.3 43.1 1.0
F42 B:9652500 2.2 43.1 1.0
F41 B:9652500 2.2 43.6 1.0
C20 B:9652500 2.3 41.5 1.0
C21 B:9652500 2.7 39.0 1.0
C19 B:9652500 3.7 40.2 1.0
NE2 B:HIS435 3.7 23.7 1.0
CD2 B:LEU449 3.8 28.1 1.0
CZ3 B:TRP457 4.0 35.3 1.0
CG1 B:VAL439 4.1 27.6 1.0
CE3 B:TRP457 4.1 35.2 1.0
C22 B:9652500 4.1 37.8 1.0
CD1 B:LEU449 4.1 29.3 1.0
CD1 B:LEU442 4.2 34.9 1.0
CD2 B:HIS435 4.2 24.3 1.0
CL4 B:9652500 4.4 52.4 1.0
CG B:LEU449 4.6 30.1 1.0
CB B:VAL439 4.6 28.4 1.0
CE1 B:HIS435 4.8 26.7 1.0
C18 B:9652500 4.9 34.2 1.0
C23 B:9652500 5.0 37.1 1.0

Fluorine binding site 6 out of 9 in 1pq6

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Fluorine binding site 6 out of 9 in the Human Lxr Beta Hormone Receptor / GW3965 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Lxr Beta Hormone Receptor / GW3965 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2500

b:43.1
occ:1.00
 F42 B:9652500 0.0 43.1 1.0
C39 B:9652500 1.3 43.1 1.0
F40 B:9652500 2.2 42.9 1.0
F41 B:9652500 2.2 43.6 1.0
C20 B:9652500 2.3 41.5 1.0
CL4 B:9652500 2.7 52.4 1.0
C19 B:9652500 2.8 40.2 1.0
CD2 B:LEU449 3.3 28.1 1.0
C21 B:9652500 3.5 39.0 1.0
CE1 B:PHE268 3.8 19.9 1.0
CZ B:PHE268 3.8 20.8 1.0
CD1 B:LEU442 4.1 34.9 1.0
C18 B:9652500 4.2 34.2 1.0
CG2 B:THR272 4.5 14.8 1.0
C22 B:9652500 4.6 37.8 1.0
CG B:LEU449 4.7 30.1 1.0
CD1 B:LEU449 4.9 29.3 1.0
CD1 B:PHE268 4.9 20.0 1.0
C23 B:9652500 4.9 37.1 1.0
CE2 B:PHE268 5.0 20.8 1.0

Fluorine binding site 7 out of 9 in 1pq6

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Fluorine binding site 7 out of 9 in the Human Lxr Beta Hormone Receptor / GW3965 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Human Lxr Beta Hormone Receptor / GW3965 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F3500

b:39.6
occ:1.00
 F41 D:9653500 0.0 39.6 1.0
C39 D:9653500 1.3 39.2 1.0
F42 D:9653500 2.2 39.4 1.0
F40 D:9653500 2.2 41.5 1.0
C20 D:9653500 2.3 36.4 1.0
C19 D:9653500 3.0 35.2 1.0
C21 D:9653500 3.2 33.1 1.0
CL4 D:9653500 3.3 47.9 1.0
CG D:GLN438 3.8 31.2 1.0
CD1 D:LEU442 4.0 30.9 1.0
CE2 D:PHE349 4.2 25.2 1.0
C18 D:9653500 4.4 30.4 1.0
C22 D:9653500 4.4 31.4 1.0
CZ D:PHE349 4.6 25.3 1.0
CD2 D:LEU345 4.7 19.6 1.0
NE2 D:HIS435 4.7 31.7 1.0
CD D:GLN438 4.7 31.8 1.0
CD2 D:HIS435 4.8 30.5 1.0
CG1 D:VAL439 4.9 30.3 1.0
C23 D:9653500 4.9 30.5 1.0
CE1 D:PHE268 5.0 11.8 1.0

Fluorine binding site 8 out of 9 in 1pq6

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Fluorine binding site 8 out of 9 in the Human Lxr Beta Hormone Receptor / GW3965 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Human Lxr Beta Hormone Receptor / GW3965 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F3500

b:41.5
occ:1.00
 F40 D:9653500 0.0 41.5 1.0
C39 D:9653500 1.3 39.2 1.0
F42 D:9653500 2.2 39.4 1.0
F41 D:9653500 2.2 39.6 1.0
C20 D:9653500 2.4 36.4 1.0
C21 D:9653500 2.8 33.1 1.0
NE2 D:HIS435 3.5 31.7 1.0
CD2 D:LEU449 3.6 35.9 1.0
C19 D:9653500 3.7 35.2 1.0
CG1 D:VAL439 3.8 30.3 1.0
CE3 D:TRP457 3.9 39.1 1.0
CZ3 D:TRP457 3.9 39.9 1.0
C22 D:9653500 4.2 31.4 1.0
CD2 D:HIS435 4.2 30.5 1.0
CL4 D:9653500 4.4 47.9 1.0
CD1 D:LEU442 4.4 30.9 1.0
CG D:LEU449 4.5 35.6 1.0
CE1 D:HIS435 4.6 32.0 1.0
C18 D:9653500 4.9 30.4 1.0
CD2 D:TRP457 4.9 38.9 1.0
CB D:VAL439 5.0 30.8 1.0
CH2 D:TRP457 5.0 39.9 1.0

Fluorine binding site 9 out of 9 in 1pq6

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Fluorine binding site 9 out of 9 in the Human Lxr Beta Hormone Receptor / GW3965 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Human Lxr Beta Hormone Receptor / GW3965 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F3500

b:39.4
occ:1.00
 F42 D:9653500 0.0 39.4 1.0
C39 D:9653500 1.3 39.2 1.0
F40 D:9653500 2.2 41.5 1.0
F41 D:9653500 2.2 39.6 1.0
C20 D:9653500 2.3 36.4 1.0
CL4 D:9653500 2.7 47.9 1.0
C19 D:9653500 2.8 35.2 1.0
C21 D:9653500 3.5 33.1 1.0
CD2 D:LEU449 4.1 35.9 1.0
CG2 D:THR272 4.1 15.8 1.0
C18 D:9653500 4.2 30.4 1.0
CD1 D:LEU442 4.2 30.9 1.0
CG D:LEU449 4.3 35.6 1.0
CZ D:PHE268 4.3 12.7 1.0
CE1 D:PHE268 4.5 11.8 1.0
C22 D:9653500 4.7 31.4 1.0
CZ3 D:TRP457 4.9 39.9 1.0
C23 D:9653500 4.9 30.5 1.0

Reference:

M.Farnegardh, T.Bonn, S.Sun, J.Ljunggren, H.Ahola, A.Wilhelmsson, J.-A.Gustafsson, M.Carlquist. The Three-Dimensional Structure of the Liver X Receptor Beta Reveals A Flexible Ligand-Binding Pocket That Can Accommodate Fundamentally Different Ligands. J.Biol.Chem. V. 278 38821 2003.
ISSN: ISSN 0021-9258
PubMed: 12819202
DOI: 10.1074/JBC.M304842200
Page generated: Wed Jul 31 12:21:10 2024

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