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Fluorine in PDB 2ags: Trypanosoma Rangeli Sialidase in Complex with 2-Keto-3- Deoxy-D-Glycero-D-Galacto-2,3-Difluoro-Nononic Acid (2,3- Difluoro-Kdn)

Enzymatic activity of Trypanosoma Rangeli Sialidase in Complex with 2-Keto-3- Deoxy-D-Glycero-D-Galacto-2,3-Difluoro-Nononic Acid (2,3- Difluoro-Kdn)

All present enzymatic activity of Trypanosoma Rangeli Sialidase in Complex with 2-Keto-3- Deoxy-D-Glycero-D-Galacto-2,3-Difluoro-Nononic Acid (2,3- Difluoro-Kdn):
3.2.1.18;

Protein crystallography data

The structure of Trypanosoma Rangeli Sialidase in Complex with 2-Keto-3- Deoxy-D-Glycero-D-Galacto-2,3-Difluoro-Nononic Acid (2,3- Difluoro-Kdn), PDB code: 2ags was solved by M.F.Amaya, P.M.Alzari, A.Buschiazzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.672, 95.569, 105.816, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 18.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Trypanosoma Rangeli Sialidase in Complex with 2-Keto-3- Deoxy-D-Glycero-D-Galacto-2,3-Difluoro-Nononic Acid (2,3- Difluoro-Kdn) (pdb code 2ags). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Trypanosoma Rangeli Sialidase in Complex with 2-Keto-3- Deoxy-D-Glycero-D-Galacto-2,3-Difluoro-Nononic Acid (2,3- Difluoro-Kdn), PDB code: 2ags:

Fluorine binding site 1 out of 1 in 2ags

Go back to Fluorine Binding Sites List in 2ags
Fluorine binding site 1 out of 1 in the Trypanosoma Rangeli Sialidase in Complex with 2-Keto-3- Deoxy-D-Glycero-D-Galacto-2,3-Difluoro-Nononic Acid (2,3- Difluoro-Kdn)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Trypanosoma Rangeli Sialidase in Complex with 2-Keto-3- Deoxy-D-Glycero-D-Galacto-2,3-Difluoro-Nononic Acid (2,3- Difluoro-Kdn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F700

b:18.0
occ:1.00
 F1 A:FKD700 0.0 18.0 1.0
C3 A:FKD700 1.4 12.1 1.0
C4 A:FKD700 2.3 13.3 1.0
C2 A:FKD700 2.4 11.7 1.0
O1B A:FKD700 2.7 10.2 1.0
C1 A:FKD700 2.7 13.7 1.0
O4 A:FKD700 2.7 12.3 1.0
C5 A:FKD700 2.9 12.1 1.0
OD2 A:ASP60 2.9 20.0 1.0
O6 A:FKD700 2.9 14.2 1.0
NH2 A:ARG36 3.0 12.4 1.0
O A:HOH1403 3.1 28.8 1.0
CG A:ASP60 3.4 20.7 1.0
O A:HOH1388 3.4 32.0 1.0
OD1 A:ASP60 3.4 23.5 1.0
C6 A:FKD700 3.5 11.3 1.0
OH A:TYR343 3.7 11.9 1.0
O1A A:FKD700 3.8 13.7 1.0
NH2 A:ARG54 3.8 17.2 1.0
CZ A:ARG36 3.8 9.6 1.0
NH1 A:ARG36 4.0 11.8 1.0
O5 A:FKD700 4.2 12.4 1.0
O7 A:FKD700 4.2 13.1 1.0
CZ A:TYR343 4.3 11.6 1.0
NH1 A:ARG54 4.3 15.8 1.0
O A:HOH1196 4.4 18.7 1.0
C7 A:FKD700 4.5 13.5 1.0
CD1 A:ILE37 4.5 11.3 1.0
CZ A:ARG54 4.6 14.1 1.0
CB A:ASP60 4.7 16.4 1.0
CE2 A:TYR343 4.9 10.3 1.0
CE1 A:TYR343 4.9 9.4 1.0
O A:HOH970 4.9 15.2 1.0
O A:HOH1261 5.0 26.2 1.0
NE A:ARG36 5.0 10.6 1.0

Reference:

A.G.Watts, P.Oppezzo, S.G.Withers, P.M.Alzari, A.Buschiazzo. Structural and Kinetic Analysis of Two Covalent Sialosyl-Enzyme Intermediates on Trypanosoma Rangeli Sialidase. J.Biol.Chem. V. 281 4149 2006.
ISSN: ISSN 0021-9258
PubMed: 16298994
DOI: 10.1074/JBC.M510677200
Page generated: Mon Jul 14 12:35:19 2025

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