Atomistry » Fluorine » PDB 5avz-5btd » 5b1s
Atomistry »
  Fluorine »
    PDB 5avz-5btd »
      5b1s »

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: Tue Jul 15 02:28:13 2025

Last articles

Mg in 7DDQ
Mg in 7DIY
Mg in 7DID
Mg in 7DHW
Mg in 7DIC
Mg in 7DFU
Mg in 7DFJ
Mg in 7DFK
Mg in 7DFH
Mg in 7DFG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy