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Fluorine in PDB 4xja: Crystal Structure of the Nanb Sialidase From Streptococcus Pneumoniae in Complex with 5-Acetamido-2,3-Difluoro-3-Hydroxy-6-[1,2,3- Trihydroxypropyl]Oxane-2-Carboxylic Acid

Enzymatic activity of Crystal Structure of the Nanb Sialidase From Streptococcus Pneumoniae in Complex with 5-Acetamido-2,3-Difluoro-3-Hydroxy-6-[1,2,3- Trihydroxypropyl]Oxane-2-Carboxylic Acid

All present enzymatic activity of Crystal Structure of the Nanb Sialidase From Streptococcus Pneumoniae in Complex with 5-Acetamido-2,3-Difluoro-3-Hydroxy-6-[1,2,3- Trihydroxypropyl]Oxane-2-Carboxylic Acid:
3.2.1.18;

Protein crystallography data

The structure of Crystal Structure of the Nanb Sialidase From Streptococcus Pneumoniae in Complex with 5-Acetamido-2,3-Difluoro-3-Hydroxy-6-[1,2,3- Trihydroxypropyl]Oxane-2-Carboxylic Acid, PDB code: 4xja was solved by P.Brear, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.586, 82.556, 116.654, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Nanb Sialidase From Streptococcus Pneumoniae in Complex with 5-Acetamido-2,3-Difluoro-3-Hydroxy-6-[1,2,3- Trihydroxypropyl]Oxane-2-Carboxylic Acid (pdb code 4xja). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the Nanb Sialidase From Streptococcus Pneumoniae in Complex with 5-Acetamido-2,3-Difluoro-3-Hydroxy-6-[1,2,3- Trihydroxypropyl]Oxane-2-Carboxylic Acid, PDB code: 4xja:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4xja

Go back to Fluorine Binding Sites List in 4xja
Fluorine binding site 1 out of 2 in the Crystal Structure of the Nanb Sialidase From Streptococcus Pneumoniae in Complex with 5-Acetamido-2,3-Difluoro-3-Hydroxy-6-[1,2,3- Trihydroxypropyl]Oxane-2-Carboxylic Acid


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 the Nanb Sialidase From Streptococcus Pneumoniae in Complex with 5-Acetamido-2,3-Difluoro-3-Hydroxy-6-[1,2,3- Trihydroxypropyl]Oxane-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F705

b:21.1
occ:0.66
FAI A:SFJ705 0.0 21.1 0.7
CAS A:SFJ705 1.1 19.6 0.8
CAR A:SFJ705 2.2 18.5 1.0
CAV A:SFJ705 2.3 21.2 0.3
OAH A:SFJ705 2.6 18.5 0.9
FAJ A:SFJ705 2.7 26.9 0.6
OD1 A:ASP270 2.8 20.5 0.4
OD2 A:ASP270 2.9 24.9 0.4
CAT A:SFJ705 3.0 18.6 1.0
NH1 A:ARG245 3.1 19.2 1.0
CG A:ASP270 3.1 20.4 0.4
OAC A:SFJ705 3.1 20.1 1.0
CAO A:SFJ705 3.2 19.2 0.9
OAM A:SFJ705 3.3 22.4 0.8
CZ A:ARG245 3.5 20.2 1.0
CAU A:SFJ705 3.6 21.6 0.9
NH2 A:ARG245 3.7 16.5 1.0
NH2 A:ARG264 3.7 14.3 1.0
CD1 A:ILE246 4.0 15.5 1.0
NH1 A:ARG264 4.0 14.2 1.0
OAG A:SFJ705 4.0 30.0 0.3
CAQ A:SFJ705 4.3 28.4 0.3
NAL A:SFJ705 4.3 19.2 1.0
OH A:TYR653 4.3 15.2 1.0
CZ A:ARG264 4.3 17.0 1.0
CB A:ASP270 4.4 19.5 0.6
CB A:ASP270 4.4 19.5 0.4
OAE A:SFJ705 4.4 19.1 1.0
NE A:ARG245 4.4 16.9 1.0
CZ A:TYR653 4.6 19.4 1.0
CG1 A:ILE246 5.0 14.8 1.0
CE2 A:TYR653 5.0 17.0 1.0

Fluorine binding site 2 out of 2 in 4xja

Go back to Fluorine Binding Sites List in 4xja
Fluorine binding site 2 out of 2 in the Crystal Structure of the Nanb Sialidase From Streptococcus Pneumoniae in Complex with 5-Acetamido-2,3-Difluoro-3-Hydroxy-6-[1,2,3- Trihydroxypropyl]Oxane-2-Carboxylic Acid


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 the Nanb Sialidase From Streptococcus Pneumoniae in Complex with 5-Acetamido-2,3-Difluoro-3-Hydroxy-6-[1,2,3- Trihydroxypropyl]Oxane-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F705

b:26.9
occ:0.55
FAJ A:SFJ705 0.0 26.9 0.6
CAV A:SFJ705 1.3 21.2 0.3
CAO A:SFJ705 2.1 19.2 0.9
OAM A:SFJ705 2.1 22.4 0.8
CAS A:SFJ705 2.5 19.6 0.8
OAF A:SFJ705 2.6 38.9 0.6
OD2 A:ASP270 2.6 24.9 0.4
CAU A:SFJ705 2.7 21.6 0.9
FAI A:SFJ705 2.7 21.1 0.7
CAQ A:SFJ705 2.7 28.4 0.3
OAG A:SFJ705 2.7 30.0 0.3
OAC A:SFJ705 2.7 20.1 1.0
OAE A:SFJ705 2.9 19.1 1.0
CAP A:SFJ705 2.9 32.9 0.9
CAT A:SFJ705 3.3 18.6 1.0
CAR A:SFJ705 3.5 18.5 1.0
CG A:ASP270 3.7 20.4 0.4
OD1 A:ASP270 4.1 20.5 0.4
CAK A:SFJ705 4.3 38.4 0.8
NH1 A:ARG245 4.4 19.2 1.0
OH A:TYR653 4.5 15.2 1.0
OAH A:SFJ705 4.6 18.5 0.9
NAL A:SFJ705 4.7 19.2 1.0
CG A:ASP270 4.8 21.5 0.6
O A:HOH811 4.8 41.2 1.0
OD2 A:ASP270 4.9 22.4 0.6
CB A:ASP270 4.9 19.5 0.6
CB A:ASP270 4.9 19.5 0.4
OAD A:SFJ705 5.0 41.9 0.4
CZ3 A:TRP674 5.0 18.1 1.0

Reference:

G.W.Rogers, P.Brear, L.Yang, A.S.Chen, J.B.O.Mitchell, G.L.Taylor, N.J.Westwood. `the Hunt For Serendipitous Allosteric Sites: Discovery of A Novel Allosteric Inhibitor of the Bacterial Sialidase Nanb To Be Published.
Page generated: Tue Jul 15 01:29:27 2025

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