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Fluorine in PDB 5b1s: Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine

Enzymatic activity of Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine

All present enzymatic activity of Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine:
2.5.1.16;

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine, PDB code: 5b1s was solved by Y.Amano, Y.Tateishi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.02 / 1.58
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.484, 68.163, 94.458, 87.91, 87.18, 80.27
R / Rfree (%) 18.5 / 23.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine (pdb code 5b1s). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine, PDB code: 5b1s:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5b1s

Go back to Fluorine Binding Sites List in 5b1s
Fluorine binding site 1 out of 4 in the Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine


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 Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:16.0
occ:1.00
 F10 A:BSX502 0.0 16.0 1.0
C3 A:BSX502 1.4 14.0 1.0
C6 A:BSX502 2.4 14.4 1.0
C1 A:BSX502 2.4 12.9 1.0
O A:HOH626 2.9 12.9 1.0
C2 A:BSX502 2.9 13.9 1.0
CA A:THR170 3.2 12.2 1.0
C5 A:BSX502 3.4 15.4 1.0
NE2 A:GLN64 3.4 12.0 1.0
N A:ASP171 3.4 11.6 1.0
O A:THR169 3.5 12.4 1.0
C4 A:BSX502 3.6 12.6 1.0
C A:THR170 3.6 11.5 1.0
C9 A:BSX502 3.6 12.7 1.0
OE1 A:GLN64 3.7 14.0 1.0
OD2 A:ASP171 3.8 12.6 1.0
CD A:GLN64 3.9 12.5 1.0
OE1 A:GLN201 3.9 15.4 1.0
C7 A:BSX502 4.1 11.0 1.0
CG A:ASP171 4.1 12.9 1.0
N A:THR170 4.2 10.5 1.0
CB A:THR170 4.2 10.7 1.0
C A:THR169 4.2 11.4 1.0
N8 A:BSX502 4.3 12.7 1.0
CG2 A:THR170 4.4 12.2 1.0
CA A:ASP171 4.5 11.7 1.0
OD1 A:ASP171 4.5 12.4 1.0
O A:THR170 4.5 13.0 1.0
CD A:GLN201 4.6 10.4 1.0
CB A:ASP171 4.8 11.7 1.0
CG A:GLN201 4.8 10.8 1.0

Fluorine binding site 2 out of 4 in 5b1s

Go back to Fluorine Binding Sites List in 5b1s
Fluorine binding site 2 out of 4 in the Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine


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 Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:17.9
occ:1.00
 F10 B:BSX502 0.0 17.9 1.0
C3 B:BSX502 1.3 15.5 1.0
C6 B:BSX502 2.2 14.5 1.0
C1 B:BSX502 2.4 14.4 1.0
O B:HOH660 2.9 14.1 1.0
C2 B:BSX502 3.0 14.4 1.0
CA B:THR170 3.3 12.9 1.0
C5 B:BSX502 3.3 15.8 1.0
NE2 B:GLN64 3.5 12.5 1.0
O B:THR169 3.5 13.7 1.0
N B:ASP171 3.5 12.0 1.0
C9 B:BSX502 3.5 13.9 1.0
C4 B:BSX502 3.6 14.6 1.0
C B:THR170 3.6 12.4 1.0
OE1 B:GLN64 3.7 13.5 1.0
OD2 B:ASP171 3.9 12.7 1.0
C7 B:BSX502 3.9 12.7 1.0
CD B:GLN64 3.9 13.5 1.0
NE2 B:GLN201 4.0 11.0 1.0
N B:THR170 4.2 11.3 1.0
C B:THR169 4.2 12.3 1.0
CG B:ASP171 4.2 12.3 1.0
CB B:THR170 4.2 12.9 1.0
N8 B:BSX502 4.3 12.9 1.0
CG2 B:THR170 4.5 12.0 1.0
O B:THR170 4.5 13.0 1.0
CA B:ASP171 4.5 13.3 1.0
CD B:GLN201 4.6 9.8 1.0
OD1 B:ASP171 4.6 14.8 1.0
CG B:GLN201 4.8 10.2 1.0
CB B:ASP171 4.9 11.7 1.0
CG B:S4M501 5.0 18.9 1.0

Fluorine binding site 3 out of 4 in 5b1s

Go back to Fluorine Binding Sites List in 5b1s
Fluorine binding site 3 out of 4 in the Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine


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 Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:20.0
occ:1.00
 F10 C:BSX502 0.0 20.0 1.0
C3 C:BSX502 1.4 16.0 1.0
C6 C:BSX502 2.3 15.9 1.0
C1 C:BSX502 2.4 16.1 1.0
O C:HOH625 2.9 15.8 1.0
C2 C:BSX502 3.0 16.3 1.0
CA C:THR170 3.3 12.8 1.0
C5 C:BSX502 3.3 16.4 1.0
NE2 C:GLN64 3.5 14.1 1.0
N C:ASP171 3.5 11.6 1.0
O C:THR169 3.5 13.3 1.0
C C:THR170 3.6 12.8 1.0
C4 C:BSX502 3.6 16.4 1.0
OE1 C:GLN64 3.6 14.3 1.0
C9 C:BSX502 3.6 16.4 1.0
OD2 C:ASP171 3.8 12.4 1.0
CD C:GLN64 3.9 15.3 1.0
OE1 C:GLN201 3.9 14.4 1.0
C7 C:BSX502 4.1 14.3 1.0
N C:THR170 4.1 13.2 1.0
C C:THR169 4.2 13.8 1.0
CG C:ASP171 4.2 12.7 1.0
CB C:THR170 4.2 12.9 1.0
N8 C:BSX502 4.3 11.2 1.0
CG2 C:THR170 4.3 14.6 1.0
O C:THR170 4.5 14.5 1.0
CD C:GLN201 4.5 11.1 1.0
CA C:ASP171 4.6 12.2 1.0
OD1 C:ASP171 4.6 14.9 1.0
CG C:GLN201 4.7 10.5 1.0
CB C:ASP171 4.9 13.8 1.0

Fluorine binding site 4 out of 4 in 5b1s

Go back to Fluorine Binding Sites List in 5b1s
Fluorine binding site 4 out of 4 in the Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine


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 Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F502

b:17.4
occ:1.00
 F10 D:BSX502 0.0 17.4 1.0
C3 D:BSX502 1.4 15.9 1.0
C6 D:BSX502 2.3 15.1 1.0
C1 D:BSX502 2.4 14.8 1.0
C2 D:BSX502 2.8 12.7 1.0
O D:HOH637 3.0 12.2 1.0
CA D:THR170 3.2 10.9 1.0
C5 D:BSX502 3.3 12.9 1.0
NE2 D:GLN64 3.4 12.1 1.0
N D:ASP171 3.5 11.3 1.0
O D:THR169 3.5 13.0 1.0
C4 D:BSX502 3.6 13.7 1.0
C9 D:BSX502 3.6 16.6 1.0
C D:THR170 3.6 11.3 1.0
OE1 D:GLN64 3.6 12.0 1.0
OD2 D:ASP171 3.8 13.0 1.0
NE2 D:GLN201 3.9 10.7 1.0
CD D:GLN64 3.9 12.2 1.0
C7 D:BSX502 4.1 14.0 1.0
CG D:ASP171 4.1 11.8 1.0
N D:THR170 4.1 11.2 1.0
CB D:THR170 4.2 10.5 1.0
C D:THR169 4.2 10.9 1.0
N8 D:BSX502 4.3 11.9 1.0
CA D:ASP171 4.5 12.5 1.0
O D:THR170 4.5 12.1 1.0
CG2 D:THR170 4.5 11.8 1.0
CD D:GLN201 4.6 10.5 1.0
OD1 D:ASP171 4.6 13.5 1.0
CB D:ASP171 4.8 11.6 1.0
CG D:GLN201 4.8 9.5 1.0
O D:ILE63 5.0 12.0 1.0
CG D:S4M501 5.0 17.6 1.0

Reference:

R.Yoshino, N.Yasuo, Y.Hagiwara, T.Ishida, D.K.Inaoka, Y.Amano, Y.Tateishi, K.Ohno, I.Namatame, T.Niimi, M.Orita, K.Kita, Y.Akiyama, M.Sekijima. In Silico, in Vitro, X-Ray Crystallography, and Integrated Strategies For Discovering Spermidine Synthase Inhibitors For Chagas Disease Sci Rep V. 7 6666 2017.
ISSN: ESSN 2045-2322
PubMed: 28751689
DOI: 10.1038/S41598-017-06411-9
Page generated: Thu Aug 1 08:01:28 2024

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