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Fluorine in PDB 3q11: Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Streptococcus Pneumoniae with Nadp and Aspartyl Beta- Difluorophosphonate

Enzymatic activity of Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Streptococcus Pneumoniae with Nadp and Aspartyl Beta- Difluorophosphonate

All present enzymatic activity of Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Streptococcus Pneumoniae with Nadp and Aspartyl Beta- Difluorophosphonate:
1.2.1.11;

Protein crystallography data

The structure of Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Streptococcus Pneumoniae with Nadp and Aspartyl Beta- Difluorophosphonate, PDB code: 3q11 was solved by A.G.Pavlovsky, R.E.Viola, C.R.Faehnle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.80 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.014, 98.702, 64.528, 90.00, 100.79, 90.00
R / Rfree (%) 20.3 / 24.2

Other elements in 3q11:

The structure of Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Streptococcus Pneumoniae with Nadp and Aspartyl Beta- Difluorophosphonate also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Streptococcus Pneumoniae with Nadp and Aspartyl Beta- Difluorophosphonate (pdb code 3q11). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Streptococcus Pneumoniae with Nadp and Aspartyl Beta- Difluorophosphonate, PDB code: 3q11:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3q11

Go back to Fluorine Binding Sites List in 3q11
Fluorine binding site 1 out of 4 in the Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Streptococcus Pneumoniae with Nadp and Aspartyl Beta- Difluorophosphonate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Streptococcus Pneumoniae with Nadp and Aspartyl Beta- Difluorophosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F368

b:70.8
occ:1.00
FAA A:P4F368 0.0 70.8 1.0
CD1 A:P4F368 1.3 70.6 1.0
FAN A:P4F368 2.2 71.1 1.0
CG A:P4F368 2.3 70.7 1.0
PAI A:P4F368 2.6 70.2 1.0
OAJ A:P4F368 2.9 69.7 1.0
CB A:P4F368 2.9 70.3 1.0
OAB A:P4F368 3.0 70.2 1.0
CA A:P4F368 3.2 70.3 1.0
OD2 A:P4F368 3.3 71.5 1.0
OAO A:P4F368 3.8 70.3 1.0
N A:P4F368 3.8 70.4 1.0
O A:HOH648 3.8 39.3 1.0
O A:GLY159 4.0 24.5 1.0
O A:HOH792 4.2 45.0 1.0
C A:P4F368 4.5 70.0 1.0
O A:HOH752 4.7 33.5 1.0
OXT A:P4F368 4.8 69.8 1.0

Fluorine binding site 2 out of 4 in 3q11

Go back to Fluorine Binding Sites List in 3q11
Fluorine binding site 2 out of 4 in the Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Streptococcus Pneumoniae with Nadp and Aspartyl Beta- Difluorophosphonate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Streptococcus Pneumoniae with Nadp and Aspartyl Beta- Difluorophosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F368

b:71.1
occ:1.00
FAN A:P4F368 0.0 71.1 1.0
CD1 A:P4F368 1.3 70.6 1.0
FAA A:P4F368 2.2 70.8 1.0
CG A:P4F368 2.3 70.7 1.0
OD2 A:P4F368 2.6 71.5 1.0
PAI A:P4F368 2.6 70.2 1.0
OAB A:P4F368 2.8 70.2 1.0
OAO A:P4F368 3.1 70.3 1.0
O A:HOH752 3.1 33.5 1.0
O A:HOH639 3.2 39.7 1.0
NZ A:LYS223 3.4 31.5 1.0
CB A:P4F368 3.7 70.3 1.0
OAJ A:P4F368 3.8 69.7 1.0
O A:HOH792 3.8 45.0 1.0
CA A:P4F368 4.4 70.3 1.0
N A:P4F368 4.5 70.4 1.0
CE A:LYS223 4.8 29.3 1.0

Fluorine binding site 3 out of 4 in 3q11

Go back to Fluorine Binding Sites List in 3q11
Fluorine binding site 3 out of 4 in the Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Streptococcus Pneumoniae with Nadp and Aspartyl Beta- Difluorophosphonate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Streptococcus Pneumoniae with Nadp and Aspartyl Beta- Difluorophosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F368

b:67.4
occ:1.00
FAA B:P4F368 0.0 67.4 1.0
CD1 B:P4F368 1.3 67.6 1.0
FAN B:P4F368 2.1 68.5 1.0
CG B:P4F368 2.3 67.4 1.0
PAI B:P4F368 2.6 66.8 1.0
CB B:P4F368 3.0 66.8 1.0
OAJ B:P4F368 3.0 66.1 1.0
OAB B:P4F368 3.0 67.4 1.0
OD2 B:P4F368 3.3 68.4 1.0
CA B:P4F368 3.4 66.7 1.0
O B:HOH663 3.5 31.3 1.0
OAO B:P4F368 3.8 66.8 1.0
O B:GLY159 3.9 28.9 1.0
N B:P4F368 4.0 67.1 1.0
O B:HOH795 4.4 36.1 1.0
C B:P4F368 4.7 66.1 1.0
OXT B:P4F368 4.9 65.8 1.0

Fluorine binding site 4 out of 4 in 3q11

Go back to Fluorine Binding Sites List in 3q11
Fluorine binding site 4 out of 4 in the Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Streptococcus Pneumoniae with Nadp and Aspartyl Beta- Difluorophosphonate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Streptococcus Pneumoniae with Nadp and Aspartyl Beta- Difluorophosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F368

b:68.5
occ:1.00
FAN B:P4F368 0.0 68.5 1.0
CD1 B:P4F368 1.3 67.6 1.0
FAA B:P4F368 2.1 67.4 1.0
CG B:P4F368 2.3 67.4 1.0
OD2 B:P4F368 2.6 68.4 1.0
PAI B:P4F368 2.6 66.8 1.0
OAB B:P4F368 2.9 67.4 1.0
OAO B:P4F368 3.0 66.8 1.0
NZ B:LYS223 3.4 34.1 1.0
O B:HOH630 3.5 28.6 0.5
CB B:P4F368 3.7 66.8 1.0
OAJ B:P4F368 3.8 66.1 1.0
CA B:P4F368 4.5 66.7 1.0
N B:P4F368 4.6 67.1 1.0
O B:HOH633 4.8 26.3 0.5
CE B:LYS223 4.8 32.8 1.0

Reference:

A.G.Pavlovsky, X.Liu, C.R.Faehnle, N.Potente, R.E.Viola. Structural Characterization of Inhibitors with Selectivity Against Members of A Homologous Enzyme Family. Chem.Biol.Drug Des. V. 79 128 2012.
ISSN: ISSN 1747-0277
PubMed: 22039970
DOI: 10.1111/J.1747-0285.2011.01267.X
Page generated: Sun Dec 13 11:53:34 2020

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