Fluorine in PDB 5tbp: Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003

Protein crystallography data

The structure of Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003, PDB code: 5tbp was solved by A.E.Aleshin, R.C.Liddington, Y.Su, X.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.15 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.640, 99.380, 109.860, 90.00, 99.15, 90.00
R / Rfree (%) 19.6 / 24.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003 (pdb code 5tbp). 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 Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003, PDB code: 5tbp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5tbp

Go back to Fluorine Binding Sites List in 5tbp
Fluorine binding site 1 out of 6 in the Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003


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 Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:64.0
occ:0.94
F21 A:7A4501 0.0 64.0 0.9
C19 A:7A4501 1.3 63.6 0.9
C20 A:7A4501 2.4 64.0 0.9
C18 A:7A4501 2.4 65.3 0.9
H11 A:7A4501 2.6 76.7 0.9
H20 A:7A4501 2.6 78.3 0.9
HD11 C:LEU451 2.7 80.9 1.0
HB3 A:LEU301 2.9 49.1 1.0
HA A:ARG302 2.9 64.2 1.0
HB2 A:LEU301 3.3 49.1 1.0
C A:LEU301 3.3 48.8 1.0
N A:ARG302 3.4 53.5 1.0
O A:LEU301 3.4 46.5 1.0
HG3 A:ARG302 3.4 83.6 1.0
CB A:LEU301 3.5 40.9 1.0
HD13 C:LEU451 3.5 80.9 1.0
CD1 C:LEU451 3.5 67.4 1.0
CA A:ARG302 3.6 53.5 1.0
C04 A:7A4501 3.6 68.3 0.9
C17 A:7A4501 3.7 61.3 0.9
HD21 C:LEU451 3.7 78.4 1.0
H A:ARG302 3.7 64.2 1.0
HD1 A:TRP305 3.7 62.6 1.0
CA A:LEU301 4.0 45.6 1.0
CG A:ARG302 4.1 69.7 1.0
HG2 A:ARG302 4.1 83.6 1.0
HD12 C:LEU451 4.1 80.9 1.0
C05 A:7A4501 4.2 65.9 0.9
HB3 A:TRP305 4.2 49.3 1.0
HG21 C:ILE447 4.2 0.1 1.0
CB A:ARG302 4.2 60.7 1.0
CD2 C:LEU451 4.4 65.3 1.0
HD22 C:LEU451 4.4 78.4 1.0
HB2 A:ARG302 4.4 72.9 1.0
CD1 A:TRP305 4.4 52.1 1.0
HD11 A:LEU276 4.4 69.4 1.0
H19 A:7A4501 4.4 73.5 0.9
HG22 C:ILE447 4.5 0.1 1.0
O A:VAL298 4.5 55.1 1.0
CG C:LEU451 4.5 68.5 1.0
HD13 A:LEU301 4.6 64.0 1.0
HG23 C:ILE447 4.6 0.1 1.0
HA A:LEU301 4.6 54.7 1.0
CG2 C:ILE447 4.6 90.1 1.0
HG13 A:VAL298 4.7 68.2 1.0
CG A:LEU301 4.8 46.6 1.0
HG C:LEU451 4.8 82.3 1.0
C A:ARG302 4.8 49.8 1.0
HD12 A:LEU301 4.9 64.0 1.0
CG A:TRP305 5.0 48.8 1.0

Fluorine binding site 2 out of 6 in 5tbp

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Fluorine binding site 2 out of 6 in the Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003


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 Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:73.3
occ:0.87
F21 A:7A4502 0.0 73.3 0.9
C19 A:7A4502 1.3 74.6 0.9
C20 A:7A4502 2.4 77.7 0.9
C18 A:7A4502 2.4 77.6 0.9
HB1 A:ALA271 2.5 88.1 1.0
H11 A:7A4502 2.6 93.2 0.9
H20 A:7A4502 2.6 93.1 0.9
HG23 A:THR328 2.9 98.5 1.0
HB2 A:GLN275 3.0 77.7 1.0
O A:ALA271 3.2 73.3 1.0
HB3 A:ALA327 3.3 92.3 1.0
CB A:ALA271 3.3 73.4 1.0
HB3 A:ALA271 3.4 88.1 1.0
C A:ALA271 3.4 68.2 1.0
HG22 A:THR328 3.4 98.5 1.0
CG2 A:THR328 3.5 82.1 1.0
HA A:ALA272 3.6 79.5 1.0
C04 A:7A4502 3.6 77.8 0.9
C17 A:7A4502 3.7 78.3 0.9
HG21 A:THR328 3.7 98.5 1.0
N A:ALA272 3.9 67.2 1.0
CA A:ALA271 3.9 71.2 1.0
OE1 A:GLN275 3.9 65.7 1.0
CB A:GLN275 3.9 64.7 1.0
HB2 A:ALA271 4.1 88.1 1.0
HG2 A:GLN275 4.1 87.6 1.0
C05 A:7A4502 4.2 80.6 0.9
HA A:ALA271 4.2 85.5 1.0
CB A:ALA327 4.2 76.9 1.0
HB3 A:GLN275 4.2 77.7 1.0
CD A:GLN275 4.2 74.3 1.0
CA A:ALA272 4.3 66.2 1.0
CG A:GLN275 4.3 73.0 1.0
H A:ALA272 4.3 80.7 1.0
H A:GLN275 4.4 72.3 1.0
HB1 A:ALA327 4.4 92.3 1.0
H19 A:7A4502 4.5 94.0 0.9
H3 A:7A4501 4.5 93.4 0.9
H A:THR328 4.5 98.5 1.0
HB2 A:ALA327 4.7 92.3 1.0
N A:THR328 4.7 82.0 1.0
CB A:THR328 4.9 86.7 1.0
H A:ALA327 4.9 91.1 1.0
HB2 A:ALA272 5.0 81.5 1.0
N A:GLN275 5.0 60.3 1.0

Fluorine binding site 3 out of 6 in 5tbp

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Fluorine binding site 3 out of 6 in the Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003


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 Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:97.4
occ:0.89
F21 A:7A4503 0.0 97.4 0.9
C19 A:7A4503 1.3 94.4 0.9
C20 A:7A4503 2.4 91.8 0.9
C18 A:7A4503 2.4 92.2 0.9
HD22 A:LEU436 2.5 94.3 1.0
H20 A:7A4503 2.6 0.7 0.9
H11 A:7A4503 2.6 0.2 0.9
HD13 A:LEU436 3.3 0.6 1.0
CD2 A:LEU436 3.4 78.6 1.0
C04 A:7A4503 3.6 90.1 0.9
C17 A:7A4503 3.7 90.2 0.9
HD21 A:LEU436 3.7 94.3 1.0
HB3 A:LEU436 3.7 94.5 1.0
HB2 A:PHE439 3.7 0.7 1.0
H32 C:GOL501 3.8 0.7 1.0
HB3 A:PHE439 3.8 0.7 1.0
HO3 C:GOL501 3.8 0.5 1.0
HD23 A:LEU436 4.0 94.3 1.0
CD1 A:LEU436 4.0 88.0 1.0
O3 C:GOL501 4.1 92.9 1.0
HD22 C:LEU433 4.1 0.4 1.0
CB A:PHE439 4.1 89.7 1.0
CG A:LEU436 4.1 82.0 1.0
CG A:PHE439 4.2 93.1 1.0
C05 A:7A4503 4.2 90.1 0.9
HD11 A:LEU436 4.3 0.6 1.0
C3 C:GOL501 4.4 93.9 1.0
CB A:LEU436 4.4 78.7 1.0
H19 A:7A4503 4.4 0.2 0.9
CD2 A:PHE439 4.5 93.1 1.0
HD2 A:PHE439 4.5 0.7 1.0
CD1 A:PHE439 4.6 93.7 1.0
HD1 A:PHE439 4.8 0.4 1.0
HD12 A:LEU436 4.9 0.6 1.0
H31 C:GOL501 4.9 0.7 1.0
HD23 C:LEU433 4.9 0.4 1.0
CD2 C:LEU433 4.9 85.3 1.0
HZ2 C:TRP305 5.0 96.1 1.0
HB2 A:LEU436 5.0 94.5 1.0

Fluorine binding site 4 out of 6 in 5tbp

Go back to Fluorine Binding Sites List in 5tbp
Fluorine binding site 4 out of 6 in the Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003


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 Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:97.4
occ:0.87
F21 B:7A4501 0.0 97.4 0.9
C19 B:7A4501 1.3 93.6 0.9
C20 B:7A4501 2.4 90.8 0.9
C18 B:7A4501 2.4 91.8 0.9
H11 B:7A4501 2.6 0.9 0.9
H20 B:7A4501 2.6 0.1 0.9
HD13 D:LEU436 2.7 94.4 1.0
HD22 D:LEU436 2.8 94.5 1.0
CD1 D:LEU436 3.5 78.7 1.0
C04 B:7A4501 3.6 96.8 0.9
CD2 D:LEU436 3.6 78.7 1.0
C17 B:7A4501 3.7 89.1 0.9
HD11 D:LEU436 3.7 94.4 1.0
HB3 D:LEU436 3.8 92.1 1.0
HD22 B:LEU433 3.8 99.2 1.0
HD21 D:LEU436 3.8 94.5 1.0
HB2 D:PHE439 3.9 99.2 1.0
HB3 D:PHE439 4.0 99.2 1.0
CG D:LEU436 4.0 78.4 1.0
C05 B:7A4501 4.2 89.3 0.9
HD12 D:LEU436 4.2 94.4 1.0
CG D:PHE439 4.3 87.4 1.0
CB D:PHE439 4.3 82.7 1.0
HO3 B:GOL502 4.3 0.8 1.0
CB D:LEU436 4.4 76.8 1.0
HD23 D:LEU436 4.4 94.5 1.0
H19 B:7A4501 4.5 0.9 0.9
CD2 D:PHE439 4.5 85.4 1.0
HZ2 B:TRP305 4.6 85.4 1.0
HD2 D:PHE439 4.6 0.4 1.0
O3 B:GOL502 4.6 99.0 0.9
CD1 D:PHE439 4.6 85.5 1.0
CD2 B:LEU433 4.7 82.7 1.0
H32 B:GOL502 4.7 0.6 1.0
HD23 B:LEU433 4.7 99.2 1.0
HB2 D:LEU436 4.7 92.1 1.0
HD1 D:PHE439 4.8 0.6 1.0
HG D:LEU436 4.9 94.1 1.0
HB3 B:LEU433 4.9 85.6 1.0

Fluorine binding site 5 out of 6 in 5tbp

Go back to Fluorine Binding Sites List in 5tbp
Fluorine binding site 5 out of 6 in the Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003


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 Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:79.2
occ:0.87
F21 D:7A4501 0.0 79.2 0.9
C19 D:7A4501 1.3 73.1 0.9
C20 D:7A4501 2.4 73.0 0.9
C18 D:7A4501 2.4 70.8 0.9
HD11 B:LEU451 2.6 97.3 1.0
H11 D:7A4501 2.6 87.7 0.9
H20 D:7A4501 2.6 84.9 0.9
HB3 D:LEU301 2.6 75.6 1.0
HB2 D:LEU301 3.0 75.6 1.0
HD13 B:LEU451 3.2 97.3 1.0
CB D:LEU301 3.2 63.0 1.0
C D:LEU301 3.2 65.0 1.0
HA D:ARG302 3.2 80.8 1.0
CD1 B:LEU451 3.3 81.1 1.0
O D:LEU301 3.3 61.4 1.0
N D:ARG302 3.4 63.5 1.0
HD21 B:LEU451 3.4 98.2 1.0
C04 D:7A4501 3.6 73.8 0.9
C17 D:7A4501 3.7 71.3 0.9
H D:ARG302 3.7 76.2 1.0
HG3 D:ARG302 3.7 97.0 1.0
CA D:ARG302 3.8 67.3 1.0
CA D:LEU301 3.8 63.3 1.0
HD22 B:LEU451 3.9 98.2 1.0
HD12 B:LEU451 3.9 97.3 1.0
HD1 D:TRP305 4.0 78.8 1.0
CD2 B:LEU451 4.0 81.8 1.0
C05 D:7A4501 4.2 74.5 0.9
O D:VAL298 4.2 68.7 1.0
CG B:LEU451 4.2 83.2 1.0
HD13 D:LEU301 4.3 83.4 1.0
HG2 D:ARG302 4.3 97.0 1.0
HG13 D:VAL298 4.3 95.1 1.0
CG D:ARG302 4.3 80.8 1.0
HG21 B:ILE447 4.4 0.1 1.0
HA D:LEU301 4.4 76.0 1.0
HB3 D:TRP305 4.4 64.2 1.0
H19 D:7A4501 4.4 85.6 0.9
CG D:LEU301 4.5 65.8 1.0
HD11 D:LEU276 4.5 75.2 1.0
CB D:ARG302 4.6 71.2 1.0
HG22 B:ILE447 4.6 0.1 1.0
CD1 D:TRP305 4.6 65.7 1.0
HD12 D:LEU301 4.6 83.4 1.0
HG B:LEU451 4.7 99.9 1.0
HA D:VAL298 4.7 82.4 1.0
CD1 D:LEU301 4.7 69.5 1.0
HB2 D:ARG302 4.8 85.5 1.0
HG23 B:ILE447 4.8 0.1 1.0
HD22 D:LEU301 4.8 78.4 1.0
CG2 B:ILE447 4.8 89.3 1.0
N D:LEU301 4.9 62.7 1.0
H D:LEU301 4.9 75.3 1.0
HD23 B:LEU451 4.9 98.2 1.0

Fluorine binding site 6 out of 6 in 5tbp

Go back to Fluorine Binding Sites List in 5tbp
Fluorine binding site 6 out of 6 in the Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003


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 Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F502

b:80.0
occ:0.94
F21 D:7A4502 0.0 80.0 0.9
C19 D:7A4502 1.3 82.5 0.9
C20 D:7A4502 2.4 85.9 0.9
C18 D:7A4502 2.4 83.5 0.9
HB1 D:ALA271 2.4 78.2 1.0
H11 D:7A4502 2.6 0.0 0.9
H20 D:7A4502 2.6 0.2 0.9
O D:ALA271 2.7 69.3 1.0
HB2 D:GLN275 2.8 82.3 1.0
C D:ALA271 2.9 66.5 1.0
CB D:ALA271 3.1 65.1 1.0
HB3 D:ALA271 3.1 78.2 1.0
HA D:ALA272 3.1 74.8 1.0
HG23 D:THR328 3.4 0.4 1.0
N D:ALA272 3.4 65.1 1.0
HB3 D:ALA327 3.5 98.6 1.0
CA D:ALA271 3.5 65.7 1.0
C04 D:7A4502 3.6 83.6 0.9
CB D:GLN275 3.6 68.6 1.0
C17 D:7A4502 3.7 87.8 0.9
CA D:ALA272 3.7 62.3 1.0
HB3 D:GLN275 3.8 82.3 1.0
HG22 D:THR328 3.9 0.4 1.0
H D:ALA272 3.9 78.2 1.0
HA D:ALA271 3.9 78.8 1.0
HB2 D:ALA271 3.9 78.2 1.0
CG2 D:THR328 4.0 85.4 1.0
H D:GLN275 4.0 75.5 1.0
HG2 D:GLN275 4.0 94.5 1.0
H4 D:7A4501 4.1 89.3 0.9
HG21 D:THR328 4.1 0.4 1.0
C05 D:7A4502 4.2 87.6 0.9
CG D:GLN275 4.2 78.7 1.0
OE1 D:GLN275 4.3 80.7 1.0
CB D:ALA327 4.4 82.2 1.0
HB2 D:ALA272 4.4 78.4 1.0
H19 D:7A4502 4.5 0.3 0.9
CD D:GLN275 4.5 83.4 1.0
HB1 D:ALA327 4.5 98.6 1.0
N D:GLN275 4.7 62.9 1.0
CB D:ALA272 4.7 65.3 1.0
O D:ILE268 4.8 67.0 1.0
CA D:GLN275 4.8 65.4 1.0
HB2 D:ALA327 4.8 98.6 1.0
N D:ALA271 4.8 68.4 1.0
C D:ALA272 4.8 63.4 1.0
H3 D:7A4501 4.9 89.3 0.9
C16 D:7A4501 4.9 74.5 0.9
H D:THR328 5.0 0.8 1.0

Reference:

L.Chen, A.E.Aleshin, G.Alitongbieke, Y.Zhou, X.Zhang, X.Ye, M.Hu, G.Ren, Z.Chen, Y.Ma, D.Zhang, S.Liu, W.Gao, L.Cai, L.Wu, Z.Zeng, F.Jiang, J.Liu, H.Zhou, G.Cadwell, R.C.Liddington, Y.Su, X.K.Zhang. Modulation of Nongenomic Activation of PI3K Signalling By Tetramerization of N-Terminally-Cleaved Rxr Alpha. Nat Commun V. 8 16066 2017.
ISSN: ESSN 2041-1723
PubMed: 28714476
DOI: 10.1038/NCOMMS16066
Page generated: Sun Dec 13 12:37:53 2020

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