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Fluorine in PDB 2p4y: Crystal Structure of Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator

Protein crystallography data

The structure of Crystal Structure of Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator, PDB code: 2p4y was solved by B.M.Mckeever, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.34 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.148, 59.859, 118.287, 90.00, 103.76, 90.00
R / Rfree (%) n/a / n/a

Other elements in 2p4y:

The structure of Crystal Structure of Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator (pdb code 2p4y). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator, PDB code: 2p4y:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2p4y

Go back to Fluorine Binding Sites List in 2p4y
Fluorine binding site 1 out of 6 in the Crystal Structure of Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator


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 Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F478

b:41.4
occ:1.00
F21 A:C03478 0.0 41.4 1.0
C20 A:C03478 1.3 40.8 1.0
F23 A:C03478 2.2 41.3 1.0
F22 A:C03478 2.2 39.8 1.0
O19 A:C03478 2.2 37.1 1.0
O3 A:TRS479 3.2 63.7 1.0
C3 A:TRS479 3.3 63.8 1.0
CE1 A:PHE363 3.4 56.5 1.0
CZ A:PHE363 3.4 56.9 1.0
CE1 A:HIS449 3.4 40.4 1.0
C6 A:C03478 3.5 33.2 1.0
NE2 A:HIS449 4.0 38.9 1.0
ND1 A:HIS449 4.1 40.9 1.0
CE A:LYS367 4.2 34.6 1.0
C5 A:C03478 4.4 32.4 1.0
OG A:SER289 4.4 31.9 1.0
C A:TRS479 4.4 63.7 1.0
C1 A:C03478 4.4 34.4 1.0
N A:TRS479 4.4 65.4 1.0
CE2 A:TYR327 4.5 40.5 1.0
CB A:CYS285 4.6 43.7 1.0
CD1 A:PHE363 4.6 54.9 1.0
CE2 A:PHE363 4.6 56.4 1.0
OH A:TYR327 4.7 42.8 1.0
SD A:MET364 4.7 46.0 1.0
NZ A:LYS367 4.7 32.4 1.0
O1 A:TRS479 4.8 61.5 1.0
C1 A:TRS479 4.9 62.7 1.0
CD2 A:HIS449 5.0 38.9 1.0

Fluorine binding site 2 out of 6 in 2p4y

Go back to Fluorine Binding Sites List in 2p4y
Fluorine binding site 2 out of 6 in the Crystal Structure of Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator


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 Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F478

b:39.8
occ:1.00
F22 A:C03478 0.0 39.8 1.0
C20 A:C03478 1.3 40.8 1.0
F21 A:C03478 2.2 41.4 1.0
F23 A:C03478 2.2 41.3 1.0
O19 A:C03478 2.3 37.1 1.0
C6 A:C03478 2.9 33.2 1.0
C5 A:C03478 3.3 32.4 1.0
SD A:MET364 3.5 46.0 1.0
CD2 A:LEU330 3.7 29.5 1.0
CE A:LYS367 3.8 34.6 1.0
C1 A:C03478 3.9 34.4 1.0
CE2 A:TYR327 4.1 40.5 1.0
CE A:MET364 4.2 48.0 1.0
CG A:LYS367 4.3 34.9 1.0
CZ A:PHE363 4.4 56.9 1.0
C4 A:C03478 4.5 34.0 1.0
CD2 A:TYR327 4.6 39.5 1.0
CD A:LYS367 4.6 35.3 1.0
CE1 A:PHE363 4.7 56.5 1.0
NZ A:LYS367 4.9 32.4 1.0
C2 A:C03478 4.9 34.8 1.0

Fluorine binding site 3 out of 6 in 2p4y

Go back to Fluorine Binding Sites List in 2p4y
Fluorine binding site 3 out of 6 in the Crystal Structure of Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator


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 Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F478

b:41.3
occ:1.00
F23 A:C03478 0.0 41.3 1.0
C20 A:C03478 1.3 40.8 1.0
F21 A:C03478 2.2 41.4 1.0
F22 A:C03478 2.2 39.8 1.0
O19 A:C03478 2.2 37.1 1.0
C6 A:C03478 2.9 33.2 1.0
C1 A:C03478 3.2 34.4 1.0
CE2 A:TYR327 3.3 40.5 1.0
OG A:SER289 3.6 31.9 1.0
CG2 A:ILE326 3.9 32.8 1.0
OH A:TYR327 4.1 42.8 1.0
C5 A:C03478 4.1 32.4 1.0
CD2 A:TYR327 4.1 39.5 1.0
CZ A:TYR327 4.2 41.5 1.0
C3 A:TRS479 4.3 63.8 1.0
C2 A:C03478 4.4 34.8 1.0
O1 A:TRS479 4.6 61.5 1.0
O3 A:TRS479 4.7 63.7 1.0
CE A:LYS367 4.8 34.6 1.0
CD2 A:LEU330 4.8 29.5 1.0
CE1 A:HIS449 4.9 40.4 1.0
CB A:SER289 4.9 33.4 1.0

Fluorine binding site 4 out of 6 in 2p4y

Go back to Fluorine Binding Sites List in 2p4y
Fluorine binding site 4 out of 6 in the Crystal Structure of Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator


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 Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F478

b:42.1
occ:1.00
F21 B:C03478 0.0 42.1 1.0
C20 B:C03478 1.3 41.1 1.0
F22 B:C03478 2.1 42.6 1.0
F23 B:C03478 2.1 45.5 1.0
O19 B:C03478 2.2 41.2 1.0
C6 B:C03478 3.5 38.5 1.0
CE1 B:HIS449 3.5 53.9 1.0
CZ B:PHE363 3.8 60.8 1.0
O B:HOH509 3.9 47.2 1.0
NE2 B:HIS449 4.1 53.4 1.0
OG B:SER289 4.1 45.2 1.0
CE1 B:PHE363 4.2 60.7 1.0
ND1 B:HIS449 4.2 53.6 1.0
C1 B:C03478 4.4 38.3 1.0
C5 B:C03478 4.4 38.6 1.0
CE B:MET364 4.5 54.4 1.0
CE2 B:TYR327 4.6 43.2 1.0
CE2 B:PHE363 4.7 59.5 1.0
CB B:CYS285 4.7 46.5 1.0
OH B:TYR327 4.7 48.0 1.0
CE B:LYS367 4.9 39.0 1.0

Fluorine binding site 5 out of 6 in 2p4y

Go back to Fluorine Binding Sites List in 2p4y
Fluorine binding site 5 out of 6 in the Crystal Structure of Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator


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 Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F478

b:42.6
occ:1.00
F22 B:C03478 0.0 42.6 1.0
C20 B:C03478 1.3 41.1 1.0
F21 B:C03478 2.1 42.1 1.0
F23 B:C03478 2.2 45.5 1.0
O19 B:C03478 2.2 41.2 1.0
CE B:MET364 2.9 54.4 1.0
C6 B:C03478 3.0 38.5 1.0
C5 B:C03478 3.3 38.6 1.0
SD B:MET364 3.9 51.6 1.0
CE B:LYS367 4.1 39.0 1.0
C1 B:C03478 4.1 38.3 1.0
CZ B:PHE363 4.2 60.8 1.0
CD2 B:LEU330 4.2 30.5 1.0
CE2 B:TYR327 4.4 43.2 1.0
CE2 B:PHE363 4.5 59.5 1.0
C4 B:C03478 4.5 38.9 1.0
CE1 B:PHE363 4.8 60.7 1.0
CG B:LYS367 4.9 42.6 1.0
CB B:CYS285 4.9 46.5 1.0
CD B:LYS367 4.9 40.7 1.0
CE1 B:HIS449 4.9 53.9 1.0
CD2 B:TYR327 4.9 40.2 1.0
NZ B:LYS367 5.0 39.4 1.0

Fluorine binding site 6 out of 6 in 2p4y

Go back to Fluorine Binding Sites List in 2p4y
Fluorine binding site 6 out of 6 in the Crystal Structure of Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator


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 Human Ppar-Gamma-Ligand Binding Domain Complexed with An Indole-Based Modulator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F478

b:45.5
occ:1.00
F23 B:C03478 0.0 45.5 1.0
C20 B:C03478 1.3 41.1 1.0
F21 B:C03478 2.1 42.1 1.0
F22 B:C03478 2.2 42.6 1.0
O19 B:C03478 2.2 41.2 1.0
C6 B:C03478 2.8 38.5 1.0
C1 B:C03478 3.2 38.3 1.0
CE2 B:TYR327 3.3 43.2 1.0
CG2 B:ILE326 3.8 33.5 1.0
OG B:SER289 3.8 45.2 1.0
C5 B:C03478 3.9 38.6 1.0
CD2 B:TYR327 4.0 40.2 1.0
CZ B:TYR327 4.3 44.6 1.0
OH B:TYR327 4.3 48.0 1.0
C2 B:C03478 4.4 37.1 1.0
CD2 B:LEU330 4.7 30.5 1.0
C4 B:C03478 4.9 38.9 1.0
CE B:MET364 5.0 54.4 1.0

Reference:

M.Einstein, T.E.Akiyama, G.A.Castriota, C.F.Wang, B.Mckeever, R.T.Mosley, J.W.Becker, D.E.Moller, P.T.Meinke, H.B.Wood, J.P.Berger. The Differential Interactions of Peroxisome Proliferator-Activated Receptor Gamma Ligands with TYR473 Is A Physical Basis For Their Unique Biological Activities. Mol.Pharmacol. V. 73 62 2008.
ISSN: ISSN 0026-895X
PubMed: 17940191
DOI: 10.1124/MOL.107.041202
Page generated: Wed Oct 28 14:47:01 2020

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