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Fluorine in PDB 3vjh: Human Ppar Gamma Ligand Binding Domain in Complex with JKPL35

Protein crystallography data

The structure of Human Ppar Gamma Ligand Binding Domain in Complex with JKPL35, PDB code: 3vjh was solved by D.Tomioka, N.Kuwabara, H.Hashimoto, M.Sato, T.Shimizu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.22
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.973, 60.489, 117.956, 90.00, 103.35, 90.00
R / Rfree (%) 20.6 / 24.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Ppar Gamma Ligand Binding Domain in Complex with JKPL35 (pdb code 3vjh). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human Ppar Gamma Ligand Binding Domain in Complex with JKPL35, PDB code: 3vjh:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3vjh

Go back to Fluorine Binding Sites List in 3vjh
Fluorine binding site 1 out of 3 in the Human Ppar Gamma Ligand Binding Domain in Complex with JKPL35


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Ppar Gamma Ligand Binding Domain in Complex with JKPL35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:0.2
occ:1.00
F1 A:J35501 0.0 0.2 1.0
C16 A:J35501 1.3 98.2 1.0
F2 A:J35501 2.1 0.0 1.0
F3 A:J35501 2.2 97.2 1.0
C6 A:J35501 2.3 92.4 1.0
C5 A:J35501 2.8 92.1 1.0
C7 A:J35501 3.5 90.5 1.0
C3 A:J35501 4.1 93.8 1.0
N A:SER342 4.2 57.3 1.0
CD1 A:ILE341 4.3 58.6 1.0
CB A:ILE341 4.3 56.8 1.0
CB A:SER342 4.5 62.4 1.0
C2 A:J35501 4.6 90.6 1.0
CA A:SER342 4.6 58.5 1.0
CG1 A:ILE341 4.8 59.0 1.0
C1 A:J35501 4.9 93.7 1.0
CG2 A:ILE341 4.9 55.2 1.0

Fluorine binding site 2 out of 3 in 3vjh

Go back to Fluorine Binding Sites List in 3vjh
Fluorine binding site 2 out of 3 in the Human Ppar Gamma Ligand Binding Domain in Complex with JKPL35


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Ppar Gamma Ligand Binding Domain in Complex with JKPL35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:97.2
occ:1.00
F3 A:J35501 0.0 97.2 1.0
C16 A:J35501 1.3 98.2 1.0
F2 A:J35501 2.2 0.0 1.0
F1 A:J35501 2.2 0.2 1.0
C6 A:J35501 2.3 92.4 1.0
C7 A:J35501 2.7 90.5 1.0
C5 A:J35501 3.6 92.1 1.0
C2 A:J35501 4.1 90.6 1.0
O A:HOH634 4.2 79.2 1.0
CD1 A:ILE341 4.3 58.6 1.0
C3 A:J35501 4.7 93.8 1.0
CE A:MET348 4.8 64.2 1.0
CA A:GLY284 4.8 67.8 1.0
C1 A:J35501 5.0 93.7 1.0
CB A:ILE341 5.0 56.8 1.0
O A:ILE281 5.0 63.6 1.0

Fluorine binding site 3 out of 3 in 3vjh

Go back to Fluorine Binding Sites List in 3vjh
Fluorine binding site 3 out of 3 in the Human Ppar Gamma Ligand Binding Domain in Complex with JKPL35


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Ppar Gamma Ligand Binding Domain in Complex with JKPL35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:0.0
occ:1.00
F2 A:J35501 0.0 0.0 1.0
C16 A:J35501 1.3 98.2 1.0
F1 A:J35501 2.1 0.2 1.0
F3 A:J35501 2.2 97.2 1.0
C6 A:J35501 2.3 92.4 1.0
C5 A:J35501 3.0 92.1 1.0
CA A:GLY284 3.2 67.8 1.0
C7 A:J35501 3.3 90.5 1.0
C A:GLY284 3.5 67.2 1.0
O A:GLY284 3.7 62.6 1.0
O A:HOH634 4.2 79.2 1.0
C3 A:J35501 4.3 93.8 1.0
N A:CYS285 4.3 68.2 1.0
N A:GLY284 4.4 69.6 1.0
C2 A:J35501 4.5 90.6 1.0
O A:ILE281 4.7 63.6 1.0
C1 A:J35501 4.9 93.7 1.0

Reference:

N.Kuwabara, T.Oyama, D.Tomioka, M.Ohashi, J.Yanagisawa, T.Shimizu, H.Miyachi. Peroxisome Proliferator-Activated Receptors (Ppars) Have Multiple Binding Points That Accommodate Ligands in Various Conformations: Phenylpropanoic Acid-Type Ppar Ligands Bind to Ppar in Different Conformations, Depending on the Subtype. J.Med.Chem. V. 55 893 2012.
ISSN: ISSN 0022-2623
PubMed: 22185225
DOI: 10.1021/JM2014293
Page generated: Sun Dec 13 11:57:03 2020

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