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Fluorine in PDB 3k8s: Crystal Structure of Pparg in Complex with T2384

Protein crystallography data

The structure of Crystal Structure of Pparg in Complex with T2384, PDB code: 3k8s was solved by Z.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 91.553, 62.396, 118.943, 90.00, 102.63, 90.00
R / Rfree (%) 22.6 / 27.3

Other elements in 3k8s:

The structure of Crystal Structure of Pparg in Complex with T2384 also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Pparg in Complex with T2384 (pdb code 3k8s). 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 Pparg in Complex with T2384, PDB code: 3k8s:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 3k8s

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Fluorine binding site 1 out of 9 in the Crystal Structure of Pparg in Complex with T2384


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 Pparg in Complex with T2384 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:70.7
occ:1.00
 F29 A:Z271 0.0 70.7 1.0
C28 A:Z271 1.4 68.9 1.0
F31 A:Z271 2.2 71.8 1.0
F30 A:Z271 2.2 68.0 1.0
C27 A:Z271 2.4 68.3 1.0
O A:PHE360 2.9 77.8 1.0
C26 A:Z271 3.2 67.3 1.0
C32 A:Z271 3.3 68.5 1.0
CB A:PHE360 3.5 78.8 1.0
C A:PHE360 3.6 78.6 1.0
CA A:PHE360 3.7 79.8 1.0
CB A:PHE363 3.7 65.9 1.0
CD2 A:PHE360 3.8 77.7 1.0
CD2 A:PHE363 3.9 65.4 1.0
CG A:PHE363 4.1 65.2 1.0
CG A:PHE360 4.2 77.5 1.0
CD1 A:LEU356 4.2 77.4 1.0
C25 A:Z271 4.5 67.6 1.0
C33 A:Z271 4.6 69.7 1.0
N A:GLY361 4.8 77.4 1.0
CE2 A:PHE363 4.9 64.7 1.0
CD1 A:PHE282 4.9 67.0 1.0
CB A:PHE282 5.0 63.5 1.0
CE2 A:PHE360 5.0 77.6 1.0

Fluorine binding site 2 out of 9 in 3k8s

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Fluorine binding site 2 out of 9 in the Crystal Structure of Pparg in Complex with T2384


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 Pparg in Complex with T2384 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:68.0
occ:1.00
 F30 A:Z271 0.0 68.0 1.0
C28 A:Z271 1.4 68.9 1.0
F31 A:Z271 2.2 71.8 1.0
F29 A:Z271 2.2 70.7 1.0
C27 A:Z271 2.4 68.3 1.0
C26 A:Z271 2.8 67.3 1.0
CD1 A:LEU356 3.5 77.4 1.0
C32 A:Z271 3.7 68.5 1.0
CG2 A:ILE281 3.8 56.9 1.0
CD2 A:LEU353 3.8 45.1 1.0
CB A:ILE281 4.1 60.0 1.0
C25 A:Z271 4.2 67.6 1.0
O A:PHE360 4.5 77.8 1.0
N A:PHE282 4.5 61.5 1.0
C A:ILE281 4.7 61.3 1.0
SG A:CYS285 4.7 54.1 1.0
CA A:PHE282 4.8 62.5 1.0
C33 A:Z271 4.8 69.7 1.0
O A:ILE281 5.0 61.1 1.0

Fluorine binding site 3 out of 9 in 3k8s

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Fluorine binding site 3 out of 9 in the Crystal Structure of Pparg in Complex with T2384


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 Pparg in Complex with T2384 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:71.8
occ:1.00
 F31 A:Z271 0.0 71.8 1.0
C28 A:Z271 1.4 68.9 1.0
F29 A:Z271 2.2 70.7 1.0
F30 A:Z271 2.2 68.0 1.0
C27 A:Z271 2.4 68.3 1.0
C32 A:Z271 2.9 68.5 1.0
CA A:PHE282 2.9 62.5 1.0
N A:PHE282 3.1 61.5 1.0
CB A:PHE282 3.1 63.5 1.0
C26 A:Z271 3.7 67.3 1.0
CD1 A:PHE282 3.7 67.0 1.0
C A:ILE281 3.8 61.3 1.0
CD2 A:PHE360 3.9 77.7 1.0
CG A:PHE282 3.9 65.6 1.0
O A:ALA278 3.9 68.4 1.0
O A:ILE281 4.2 61.1 1.0
C33 A:Z271 4.3 69.7 1.0
CB A:ILE281 4.4 60.0 1.0
C A:PHE282 4.4 62.3 1.0
SG A:CYS285 4.5 54.1 1.0
CG2 A:ILE281 4.5 56.9 1.0
CE2 A:PHE360 4.6 77.6 1.0
CA A:ILE281 4.7 60.9 1.0
CB A:PHE360 4.8 78.8 1.0
CG A:PHE360 4.8 77.5 1.0
O A:PHE282 4.8 60.3 1.0
C25 A:Z271 4.9 67.6 1.0
CE1 A:PHE282 5.0 67.8 1.0

Fluorine binding site 4 out of 9 in 3k8s

Go back to Fluorine Binding Sites List in 3k8s
Fluorine binding site 4 out of 9 in the Crystal Structure of Pparg in Complex with T2384


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 Pparg in Complex with T2384 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:0.8
occ:1.00
 F29 B:Z272 0.0 0.8 1.0
C28 B:Z272 1.4 0.5 1.0
F31 B:Z272 2.2 0.5 1.0
F30 B:Z272 2.2 0.7 1.0
C27 B:Z272 2.4 0.6 1.0
C26 B:Z272 2.9 0.7 1.0
CG2 B:ILE281 3.0 73.9 1.0
CD2 B:LEU353 3.2 73.4 1.0
C32 B:Z272 3.6 0.3 1.0
SD B:MET348 3.6 57.3 1.0
F30 B:Z271 3.8 84.9 1.0
CD1 B:LEU353 4.2 72.8 1.0
C26 B:Z271 4.2 79.0 1.0
C25 B:Z272 4.2 1.0 1.0
CG B:LEU353 4.2 73.3 1.0
SG B:CYS285 4.3 71.9 1.0
CB B:ILE281 4.5 75.1 1.0
C27 B:Z271 4.7 79.9 1.0
CE B:MET348 4.7 56.3 1.0
C25 B:Z271 4.7 78.4 1.0
O B:ILE281 4.8 76.2 1.0
C28 B:Z271 4.8 81.6 1.0
C33 B:Z272 4.8 0.7 1.0
SD B:MET364 4.8 72.2 1.0
CD1 B:ILE281 5.0 73.0 1.0
CG B:MET348 5.0 55.8 1.0

Fluorine binding site 5 out of 9 in 3k8s

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Fluorine binding site 5 out of 9 in the Crystal Structure of Pparg in Complex with T2384


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 Pparg in Complex with T2384 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:0.7
occ:1.00
 F30 B:Z272 0.0 0.7 1.0
C28 B:Z272 1.4 0.5 1.0
F31 B:Z272 2.2 0.5 1.0
F29 B:Z272 2.2 0.8 1.0
C27 B:Z272 2.4 0.6 1.0
SG B:CYS285 2.8 71.9 1.0
C32 B:Z272 2.8 0.3 1.0
CL16 B:Z271 3.2 76.6 1.0
C15 B:Z271 3.6 74.9 1.0
C14 B:Z271 3.6 74.3 1.0
C26 B:Z272 3.7 0.7 1.0
C25 B:Z271 3.7 78.4 1.0
C26 B:Z271 3.8 79.0 1.0
SD B:MET364 4.1 72.2 1.0
C24 B:Z271 4.2 78.0 1.0
C33 B:Z272 4.2 0.7 1.0
C27 B:Z271 4.3 79.9 1.0
CG2 B:ILE281 4.4 73.9 1.0
CB B:CYS285 4.5 69.6 1.0
C13 B:Z271 4.6 74.5 1.0
C17 B:Z271 4.7 77.0 1.0
F30 B:Z271 4.7 84.9 1.0
C33 B:Z271 4.7 78.2 1.0
C32 B:Z271 4.8 78.8 1.0
CE B:MET364 4.8 74.5 1.0
C25 B:Z272 4.9 1.0 1.0
O B:ILE281 4.9 76.2 1.0
CD2 B:LEU353 4.9 73.4 1.0

Fluorine binding site 6 out of 9 in 3k8s

Go back to Fluorine Binding Sites List in 3k8s
Fluorine binding site 6 out of 9 in the Crystal Structure of Pparg in Complex with T2384


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 Pparg in Complex with T2384 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:0.5
occ:1.00
 F31 B:Z272 0.0 0.5 1.0
C28 B:Z272 1.4 0.5 1.0
F30 B:Z272 2.2 0.7 1.0
F29 B:Z272 2.2 0.8 1.0
C27 B:Z272 2.4 0.6 1.0
C26 B:Z272 3.2 0.7 1.0
CL16 B:Z271 3.4 76.6 1.0
C32 B:Z272 3.4 0.3 1.0
CG1 B:VAL339 3.5 34.5 1.0
SD B:MET364 3.7 72.2 1.0
CD1 B:LEU353 3.8 72.8 1.0
CE B:MET364 4.2 74.5 1.0
CD2 B:LEU353 4.3 73.4 1.0
CG2 B:ILE341 4.3 57.0 1.0
C25 B:Z272 4.5 1.0 1.0
SD B:MET348 4.5 57.3 1.0
CG B:LEU353 4.6 73.3 1.0
C33 B:Z272 4.7 0.7 1.0
C15 B:Z271 4.7 74.9 1.0
CB B:MET348 4.7 52.0 1.0
CB B:VAL339 4.8 40.7 1.0
CG2 B:VAL339 5.0 34.6 1.0
SG B:CYS285 5.0 71.9 1.0

Fluorine binding site 7 out of 9 in 3k8s

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Fluorine binding site 7 out of 9 in the Crystal Structure of Pparg in Complex with T2384


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 Pparg in Complex with T2384 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:83.0
occ:1.00
 F29 B:Z271 0.0 83.0 1.0
C28 B:Z271 1.4 81.6 1.0
F31 B:Z271 2.2 80.1 1.0
F30 B:Z271 2.2 84.9 1.0
C27 B:Z271 2.4 79.9 1.0
O B:PHE360 2.9 82.0 1.0
C26 B:Z271 3.2 79.0 1.0
C32 B:Z271 3.3 78.8 1.0
CB B:PHE360 3.3 80.8 1.0
CA B:PHE360 3.5 82.2 1.0
C B:PHE360 3.6 81.0 1.0
CD2 B:PHE360 3.6 81.4 1.0
CG B:PHE360 3.9 80.8 1.0
CD1 B:LEU356 4.0 75.8 1.0
CD2 B:PHE363 4.1 83.8 1.0
CB B:PHE363 4.3 80.2 1.0
C25 B:Z271 4.5 78.4 1.0
C33 B:Z271 4.6 78.2 1.0
O B:ALA278 4.6 83.0 1.0
CG B:PHE363 4.6 82.4 1.0
N B:GLY361 4.8 79.3 1.0
CE2 B:PHE360 4.8 81.8 1.0
CD1 B:PHE282 4.9 73.7 1.0
CB B:PHE282 4.9 76.2 1.0
N B:PHE360 5.0 83.8 1.0

Fluorine binding site 8 out of 9 in 3k8s

Go back to Fluorine Binding Sites List in 3k8s
Fluorine binding site 8 out of 9 in the Crystal Structure of Pparg in Complex with T2384


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 Pparg in Complex with T2384 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:84.9
occ:1.00
 F30 B:Z271 0.0 84.9 1.0
C28 B:Z271 1.4 81.6 1.0
F31 B:Z271 2.2 80.1 1.0
F29 B:Z271 2.2 83.0 1.0
C27 B:Z271 2.4 79.9 1.0
C26 B:Z271 2.8 79.0 1.0
CG2 B:ILE281 3.1 73.9 1.0
CD1 B:LEU356 3.3 75.8 1.0
C32 B:Z271 3.7 78.8 1.0
CB B:ILE281 3.7 75.1 1.0
F29 B:Z272 3.8 0.8 1.0
CD2 B:LEU353 3.9 73.4 1.0
C25 B:Z271 4.2 78.4 1.0
C B:ILE281 4.5 76.2 1.0
O B:PHE360 4.5 82.0 1.0
N B:PHE282 4.5 77.1 1.0
CD1 B:ILE281 4.5 73.0 1.0
O B:ALA278 4.7 83.0 1.0
F30 B:Z272 4.7 0.7 1.0
CG1 B:ILE281 4.7 74.6 1.0
O B:ILE281 4.7 76.2 1.0
CA B:ILE281 4.8 75.5 1.0
CG B:LEU356 4.8 76.1 1.0
C33 B:Z271 4.8 78.2 1.0
CA B:PHE282 4.9 76.6 1.0
C28 B:Z272 4.9 0.5 1.0

Fluorine binding site 9 out of 9 in 3k8s

Go back to Fluorine Binding Sites List in 3k8s
Fluorine binding site 9 out of 9 in the Crystal Structure of Pparg in Complex with T2384


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 Pparg in Complex with T2384 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:80.1
occ:1.00
 F31 B:Z271 0.0 80.1 1.0
C28 B:Z271 1.4 81.6 1.0
F29 B:Z271 2.2 83.0 1.0
F30 B:Z271 2.2 84.9 1.0
C27 B:Z271 2.4 79.9 1.0
C32 B:Z271 2.9 78.8 1.0
CA B:PHE282 3.0 76.6 1.0
N B:PHE282 3.0 77.1 1.0
CB B:PHE282 3.1 76.2 1.0
O B:ALA278 3.4 83.0 1.0
C B:ILE281 3.5 76.2 1.0
C26 B:Z271 3.7 79.0 1.0
CG2 B:ILE281 3.8 73.9 1.0
CD1 B:PHE282 3.8 73.7 1.0
CB B:ILE281 3.9 75.1 1.0
O B:ILE281 4.0 76.2 1.0
CG B:PHE282 4.0 75.1 1.0
CD2 B:PHE360 4.1 81.4 1.0
C33 B:Z271 4.3 78.2 1.0
CA B:ILE281 4.3 75.5 1.0
C B:PHE282 4.5 77.0 1.0
C B:ALA278 4.5 82.9 1.0
SG B:CYS285 4.8 71.9 1.0
CE2 B:PHE360 4.8 81.8 1.0
CB B:PHE360 4.8 80.8 1.0
CG B:PHE360 4.8 80.8 1.0
C25 B:Z271 4.9 78.4 1.0
CD1 B:LEU356 4.9 75.8 1.0
N B:ILE281 5.0 76.1 1.0

Reference:

Y.Li, Z.Wang, N.Furukawa, P.Escaron, J.Weiszmann, G.Lee, M.Lindstrom, J.Liu, X.Liu, H.Xu, O.Plotnikova, V.Prasad, N.Walker, R.M.Learned, J.-L.Chen. T2384, A Novel Antidiabetic Agent with Unique Peroxisome Proliferator-Activated Receptor Gamma Binding Properties J.Biol.Chem. V. 283 9168 2008.
ISSN: ISSN 0021-9258
PubMed: 18263587
DOI: 10.1074/JBC.M800104200
Page generated: Wed Jul 31 19:48:18 2024

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