Atomistry » Fluorine » PDB 1udb-1w5y » 1upv
Atomistry »
  Fluorine »
    PDB 1udb-1w5y »
      1upv »

Fluorine in PDB 1upv: Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist

Protein crystallography data

The structure of Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist, PDB code: 1upv was solved by S.Hoerer, A.Schmid, A.Heckel, R.M.Budzinski, H.Nar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 141.800, 43.200, 51.800, 90.00, 105.80, 90.00
R / Rfree (%) 21.5 / 27.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist (pdb code 1upv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist, PDB code: 1upv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 1upv

Go back to Fluorine Binding Sites List in 1upv
Fluorine binding site 1 out of 9 in the Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F462

b:52.0
occ:1.00
F22 A:444462 0.0 52.0 1.0
C19 A:444462 1.3 51.8 1.0
F20 A:444462 2.1 50.3 1.0
F21 A:444462 2.2 53.0 1.0
C16 A:444462 2.3 51.6 1.0
N15 A:444462 2.9 51.0 1.0
CD2 A:LEU313 3.1 9.0 1.0
C23 A:444462 3.4 43.9 1.0
CG A:LEU313 3.5 9.5 1.0
CG1 A:ILE353 3.7 10.9 1.0
C28 A:444462 3.7 39.6 1.0
CZ A:PHE349 3.8 11.3 1.0
S12 A:444462 4.0 57.4 1.0
CD1 A:LEU313 4.2 10.6 1.0
CD1 A:ILE353 4.2 12.4 1.0
O13 A:444462 4.2 57.9 1.0
C24 A:444462 4.2 39.8 1.0
CD1 A:ILE309 4.3 8.3 1.0
O14 A:444462 4.3 57.4 1.0
CG2 A:ILE353 4.3 11.5 1.0
CE1 A:PHE349 4.4 12.5 1.0
CB A:ILE353 4.7 10.2 1.0
CE2 A:PHE349 4.8 12.3 1.0
C27 A:444462 4.8 35.3 1.0
CB A:LEU313 4.8 8.2 1.0
CG1 A:ILE309 4.8 7.3 1.0
CA A:LEU313 5.0 8.4 1.0

Fluorine binding site 2 out of 9 in 1upv

Go back to Fluorine Binding Sites List in 1upv
Fluorine binding site 2 out of 9 in the Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F462

b:53.0
occ:1.00
F21 A:444462 0.0 53.0 1.0
C19 A:444462 1.3 51.8 1.0
F20 A:444462 2.1 50.3 1.0
F22 A:444462 2.2 52.0 1.0
C16 A:444462 2.3 51.6 1.0
CG2 A:ILE353 2.8 11.5 1.0
CD2 A:LEU313 3.0 9.0 1.0
CG1 A:ILE353 3.4 10.9 1.0
N15 A:444462 3.5 51.0 1.0
O13 A:444462 3.6 57.9 1.0
CB A:ILE353 3.7 10.2 1.0
CG2 A:THR316 3.7 11.4 1.0
OG1 A:THR316 3.8 12.4 1.0
CG A:LEU313 3.9 9.5 1.0
CB A:THR316 4.0 12.8 1.0
S12 A:444462 4.1 57.4 1.0
CD1 A:ILE353 4.2 12.4 1.0
CA A:LEU313 4.5 8.4 1.0
C23 A:444462 4.5 43.9 1.0
CA A:ILE353 4.7 9.6 1.0
CB A:LEU313 4.7 8.2 1.0
O14 A:444462 4.8 57.4 1.0

Fluorine binding site 3 out of 9 in 1upv

Go back to Fluorine Binding Sites List in 1upv
Fluorine binding site 3 out of 9 in the Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F462

b:50.3
occ:1.00
F20 A:444462 0.0 50.3 1.0
C19 A:444462 1.3 51.8 1.0
F21 A:444462 2.1 53.0 1.0
F22 A:444462 2.1 52.0 1.0
C16 A:444462 2.4 51.6 1.0
O13 A:444462 2.6 57.9 1.0
N15 A:444462 2.7 51.0 1.0
S12 A:444462 2.8 57.4 1.0
O14 A:444462 3.0 57.4 1.0
OG1 A:THR316 3.1 12.4 1.0
CD2 A:LEU313 3.5 9.0 1.0
CG A:LEU313 3.5 9.5 1.0
C23 A:444462 3.7 43.9 1.0
CA A:LEU313 3.8 8.4 1.0
N A:LEU313 3.9 7.4 1.0
O A:MET312 3.9 7.8 1.0
CB A:THR316 3.9 12.8 1.0
C A:MET312 3.9 7.6 1.0
C28 A:444462 4.1 39.6 1.0
CB A:MET312 4.3 7.8 1.0
CG2 A:THR316 4.3 11.4 1.0
CB A:LEU313 4.3 8.2 1.0
C01 A:444462 4.4 58.6 1.0
CD1 A:LEU313 4.7 10.6 1.0
CA A:MET312 4.8 8.1 1.0
O A:HOH2031 4.9 50.0 1.0
C24 A:444462 4.9 39.8 1.0
CD1 A:ILE309 4.9 8.3 1.0
CG2 A:ILE353 4.9 11.5 1.0
O A:ILE309 4.9 7.5 1.0

Fluorine binding site 4 out of 9 in 1upv

Go back to Fluorine Binding Sites List in 1upv
Fluorine binding site 4 out of 9 in the Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F462

b:26.3
occ:1.00
F36 A:444462 0.0 26.3 1.0
C34 A:444462 1.3 26.1 1.0
F37 A:444462 2.1 26.6 1.0
F35 A:444462 2.1 26.4 1.0
C33 A:444462 2.4 27.3 1.0
F40 A:444462 2.6 24.9 1.0
C26 A:444462 2.8 31.6 1.0
C38 A:444462 3.0 25.7 1.0
C25 A:444462 3.0 35.7 1.0
CB A:PHE271 3.4 5.5 1.0
O42 A:444462 3.6 23.7 1.0
F41 A:444462 3.6 27.1 1.0
N A:THR272 3.9 6.4 1.0
C27 A:444462 4.0 35.3 1.0
C A:PHE271 4.0 6.0 1.0
F39 A:444462 4.1 25.3 1.0
C24 A:444462 4.1 39.8 1.0
CA A:PHE271 4.4 6.0 1.0
CA A:THR272 4.4 7.4 1.0
CE1 A:PHE268 4.4 7.5 1.0
O A:PHE271 4.4 6.1 1.0
CG A:PHE271 4.5 6.8 1.0
CD1 A:PHE268 4.5 7.9 1.0
O A:PHE268 4.6 4.5 1.0
OG1 A:THR272 4.6 10.9 1.0
C28 A:444462 4.9 39.6 1.0
C23 A:444462 5.0 43.9 1.0
CB A:THR272 5.0 7.8 1.0
CD1 A:PHE271 5.0 7.0 1.0

Fluorine binding site 5 out of 9 in 1upv

Go back to Fluorine Binding Sites List in 1upv
Fluorine binding site 5 out of 9 in the Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F462

b:26.6
occ:1.00
F37 A:444462 0.0 26.6 1.0
C34 A:444462 1.3 26.1 1.0
F36 A:444462 2.1 26.3 1.0
F35 A:444462 2.2 26.4 1.0
C33 A:444462 2.4 27.3 1.0
C26 A:444462 2.8 31.6 1.0
O42 A:444462 2.8 23.7 1.0
C27 A:444462 3.2 35.3 1.0
CB A:ALA275 3.5 6.8 1.0
C25 A:444462 3.7 35.7 1.0
C38 A:444462 3.7 25.7 1.0
CA A:THR272 3.9 7.4 1.0
CD1 A:LEU453 4.0 7.1 1.0
N A:THR272 4.1 6.4 1.0
F40 A:444462 4.1 24.9 1.0
CZ3 A:TRP457 4.1 14.1 1.0
O A:PHE271 4.1 6.1 1.0
F41 A:444462 4.2 27.1 1.0
C A:PHE271 4.2 6.0 1.0
C28 A:444462 4.3 39.6 1.0
OG1 A:THR272 4.3 10.9 1.0
CD2 A:LEU449 4.5 7.2 1.0
C24 A:444462 4.6 39.8 1.0
CB A:PHE271 4.7 5.5 1.0
F39 A:444462 4.7 25.3 1.0
CB A:THR272 4.8 7.8 1.0
CH2 A:TRP457 4.8 14.5 1.0
C A:THR272 4.9 7.3 1.0
O A:THR272 4.9 6.8 1.0
C23 A:444462 4.9 43.9 1.0
CA A:ALA275 4.9 7.1 1.0
CE3 A:TRP457 4.9 14.4 1.0

Fluorine binding site 6 out of 9 in 1upv

Go back to Fluorine Binding Sites List in 1upv
Fluorine binding site 6 out of 9 in the Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F462

b:26.4
occ:1.00
F35 A:444462 0.0 26.4 1.0
C34 A:444462 1.3 26.1 1.0
F36 A:444462 2.1 26.3 1.0
F37 A:444462 2.2 26.6 1.0
C33 A:444462 2.3 27.3 1.0
F41 A:444462 2.6 27.1 1.0
O42 A:444462 2.7 23.7 1.0
C38 A:444462 2.8 25.7 1.0
F40 A:444462 3.1 24.9 1.0
CD2 A:LEU449 3.1 7.2 1.0
C26 A:444462 3.6 31.6 1.0
CE1 A:PHE268 3.6 7.5 1.0
OG1 A:THR272 3.9 10.9 1.0
F39 A:444462 4.0 25.3 1.0
C25 A:444462 4.3 35.7 1.0
CD1 A:PHE268 4.4 7.9 1.0
CZ A:PHE268 4.4 6.6 1.0
C27 A:444462 4.5 35.3 1.0
CG A:LEU449 4.5 8.4 1.0
CA A:THR272 4.6 7.4 1.0
CD1 A:LEU453 4.7 7.1 1.0
N A:THR272 4.8 6.4 1.0
CB A:THR272 4.8 7.8 1.0
CZ3 A:TRP457 5.0 14.1 1.0

Fluorine binding site 7 out of 9 in 1upv

Go back to Fluorine Binding Sites List in 1upv
Fluorine binding site 7 out of 9 in the Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F462

b:25.3
occ:1.00
F39 A:444462 0.0 25.3 1.0
C38 A:444462 1.3 25.7 1.0
F41 A:444462 2.1 27.1 1.0
F40 A:444462 2.2 24.9 1.0
C33 A:444462 2.4 27.3 1.0
C26 A:444462 2.8 31.6 1.0
O42 A:444462 2.9 23.7 1.0
C25 A:444462 3.2 35.7 1.0
CD2 A:HIS435 3.2 2.7 1.0
NE2 A:HIS435 3.5 2.0 1.0
C34 A:444462 3.7 26.1 1.0
CG A:GLN438 3.8 4.2 1.0
C27 A:444462 3.8 35.3 1.0
CE2 A:PHE349 3.9 12.3 1.0
CZ A:PHE349 3.9 11.3 1.0
F35 A:444462 4.0 26.4 1.0
F36 A:444462 4.1 26.3 1.0
CD1 A:LEU345 4.2 12.5 1.0
C24 A:444462 4.3 39.8 1.0
CB A:GLN438 4.4 4.3 1.0
CG A:HIS435 4.5 3.0 1.0
CG2 A:VAL439 4.5 2.5 1.0
CD2 A:LEU442 4.5 10.7 1.0
CD2 A:PHE349 4.6 11.3 1.0
CD2 A:LEU345 4.7 10.3 1.0
CE1 A:PHE349 4.7 12.5 1.0
CE1 A:HIS435 4.7 2.8 1.0
F37 A:444462 4.7 26.6 1.0
C28 A:444462 4.8 39.6 1.0
O A:HIS435 4.8 4.8 1.0
C23 A:444462 5.0 43.9 1.0

Fluorine binding site 8 out of 9 in 1upv

Go back to Fluorine Binding Sites List in 1upv
Fluorine binding site 8 out of 9 in the Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F462

b:24.9
occ:1.00
F40 A:444462 0.0 24.9 1.0
C38 A:444462 1.3 25.7 1.0
F41 A:444462 2.1 27.1 1.0
F39 A:444462 2.2 25.3 1.0
C33 A:444462 2.4 27.3 1.0
F36 A:444462 2.6 26.3 1.0
C34 A:444462 2.8 26.1 1.0
C25 A:444462 2.9 35.7 1.0
C26 A:444462 3.1 31.6 1.0
F35 A:444462 3.1 26.4 1.0
CD2 A:LEU345 3.5 10.3 1.0
O42 A:444462 3.5 23.7 1.0
CD1 A:LEU345 3.6 12.5 1.0
CD2 A:LEU442 4.0 10.7 1.0
F37 A:444462 4.1 26.6 1.0
CG A:LEU345 4.1 11.9 1.0
C24 A:444462 4.3 39.8 1.0
C27 A:444462 4.4 35.3 1.0
CE1 A:PHE268 4.6 7.5 1.0
CD1 A:PHE268 4.7 7.9 1.0
CG A:GLN438 4.7 4.2 1.0
CE2 A:PHE349 4.9 12.3 1.0

Fluorine binding site 9 out of 9 in 1upv

Go back to Fluorine Binding Sites List in 1upv
Fluorine binding site 9 out of 9 in the Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of the Human Liver X Receptor Beta Ligand Binding Domain in Complex with A Synthetic Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F462

b:27.1
occ:1.00
F41 A:444462 0.0 27.1 1.0
C38 A:444462 1.3 25.7 1.0
F39 A:444462 2.1 25.3 1.0
F40 A:444462 2.1 24.9 1.0
C33 A:444462 2.3 27.3 1.0
O42 A:444462 2.6 23.7 1.0
F35 A:444462 2.6 26.4 1.0
C34 A:444462 3.0 26.1 1.0
CD2 A:LEU442 3.4 10.7 1.0
F36 A:444462 3.6 26.3 1.0
C26 A:444462 3.6 31.6 1.0
CG2 A:VAL439 3.8 2.5 1.0
NE2 A:HIS435 4.1 2.0 1.0
F37 A:444462 4.2 26.6 1.0
C25 A:444462 4.3 35.7 1.0
CE1 A:PHE268 4.4 7.5 1.0
CD2 A:LEU449 4.5 7.2 1.0
CD2 A:HIS435 4.5 2.7 1.0
CA A:VAL439 4.5 2.8 1.0
CG A:GLN438 4.6 4.2 1.0
C27 A:444462 4.7 35.3 1.0
CG A:LEU442 4.7 8.9 1.0
N A:VAL439 4.7 2.8 1.0
CB A:VAL439 4.8 2.9 1.0
CD2 A:LEU345 4.8 10.3 1.0

Reference:

S.Hoerer, A.Schmid, A.Heckel, R.M.Budzinski, H.Nar. Crystal Structure of the Human Liver X Receptor Beta Ligand-Binding Domain in Complex with A Synthetic Agonist J.Mol.Biol. V. 334 853 2003.
ISSN: ISSN 0022-2836
PubMed: 14643652
DOI: 10.1016/J.JMB.2003.10.033
Page generated: Sun Dec 13 11:33:13 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy