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Fluorine in PDB 6fdc: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A

Enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A, PDB code: 6fdc was solved by T.Prosdocimi, S.Donini, E.Parisini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.32 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.692, 98.608, 120.165, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 19.9

Other elements in 6fdc:

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A (pdb code 6fdc). 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 the PDE4D Catalytic Domain in Complex with Gebr- 32A, PDB code: 6fdc:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6fdc

Go back to Fluorine Binding Sites List in 6fdc
Fluorine binding site 1 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A


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 PDE4D Catalytic Domain in Complex with Gebr- 32A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F606

b:19.4
occ:0.70
 F01 A:DD5606 0.0 19.4 0.7
C01 A:DD5606 1.4 17.3 0.7
H02 A:DD5606 2.0 20.8 0.7
F02 A:DD5606 2.2 20.4 0.7
O01 A:DD5606 2.2 18.8 0.7
H14 A:DD5606 2.6 23.1 0.7
C02 A:DD5606 2.9 18.2 0.7
C12 A:DD5606 3.1 19.2 0.7
CB A:ASN487 3.2 14.7 1.0
CE1 A:TYR495 3.4 14.9 1.0
CG A:PRO488 3.6 16.5 1.0
OD1 A:ASN487 3.6 16.3 1.0
CD A:PRO488 3.7 14.8 1.0
OE1 A:GLN535 3.7 18.2 1.0
CE2 A:PHE538 3.8 19.4 1.0
CD1 A:TYR495 3.9 14.5 1.0
CG A:ASN487 3.9 16.6 1.0
C03 A:DD5606 4.2 19.3 0.7
N A:PRO488 4.2 14.8 1.0
CD2 A:PHE538 4.3 17.8 1.0
OG1 A:THR499 4.3 15.7 1.0
O A:HOH843 4.3 17.3 1.0
C11 A:DD5606 4.4 18.7 0.7
CA A:ASN487 4.4 15.7 1.0
CD A:GLN535 4.5 19.0 1.0
C A:ASN487 4.5 15.1 1.0
CZ A:TYR495 4.5 15.4 1.0
NE2 A:GLN535 4.6 18.0 1.0
O02 A:DD5606 4.6 18.1 0.7
CB A:PRO488 4.8 15.9 1.0
OH A:TYR495 4.8 16.9 1.0
CB A:TRP498 4.8 14.4 1.0
CZ A:PHE538 4.8 17.7 1.0
CA A:PRO488 4.9 16.3 1.0
H13 A:DD5606 4.9 22.4 0.7

Fluorine binding site 2 out of 4 in 6fdc

Go back to Fluorine Binding Sites List in 6fdc
Fluorine binding site 2 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A


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 PDE4D Catalytic Domain in Complex with Gebr- 32A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F606

b:20.4
occ:0.70
 F02 A:DD5606 0.0 20.4 0.7
C01 A:DD5606 1.4 17.3 0.7
H02 A:DD5606 2.0 20.8 0.7
F01 A:DD5606 2.2 19.4 0.7
O01 A:DD5606 2.3 18.8 0.7
H14 A:DD5606 2.5 23.1 0.7
C02 A:DD5606 2.8 18.2 0.7
C12 A:DD5606 2.9 19.2 0.7
C A:TRP498 3.3 15.7 1.0
O A:TRP498 3.3 15.2 1.0
N A:THR499 3.4 15.1 1.0
OD1 A:ASN487 3.5 16.3 1.0
CA A:THR499 3.5 16.5 1.0
CB A:TRP498 3.6 14.4 1.0
OG1 A:THR499 3.7 15.7 1.0
CG2 A:ILE502 3.7 16.0 1.0
C03 A:DD5606 4.1 19.3 0.7
CA A:TRP498 4.1 13.8 1.0
CB A:ASN487 4.1 14.7 1.0
CG A:ASN487 4.2 16.6 1.0
CB A:THR499 4.2 16.1 1.0
C11 A:DD5606 4.2 18.7 0.7
CB A:ILE502 4.3 14.7 1.0
CE2 A:TYR325 4.3 14.9 1.0
CE1 A:TYR495 4.5 14.9 1.0
O02 A:DD5606 4.6 18.1 0.7
OE1 A:GLN535 4.7 18.2 1.0
NE2 A:GLN535 4.7 18.0 1.0
CD1 A:TYR495 4.7 14.5 1.0
C A:THR499 4.7 16.0 1.0
H13 A:DD5606 4.7 22.4 0.7
O A:TYR495 4.8 16.4 1.0
CG A:TRP498 4.9 13.6 1.0
CD A:GLN535 4.9 19.0 1.0
CD2 A:TYR325 4.9 13.1 1.0

Fluorine binding site 3 out of 4 in 6fdc

Go back to Fluorine Binding Sites List in 6fdc
Fluorine binding site 3 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A


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 the PDE4D Catalytic Domain in Complex with Gebr- 32A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F605

b:24.1
occ:0.65
 F01 B:D5N605 0.0 24.1 0.7
C01 B:D5N605 1.3 15.6 0.7
H01 B:D5N605 2.0 18.8 0.7
F02 B:D5N605 2.2 19.4 0.7
O01 B:D5N605 2.3 19.6 0.7
H13 B:D5N605 2.5 27.3 0.7
C02 B:D5N605 2.8 18.9 0.7
C12 B:D5N605 3.0 22.7 0.7
C B:TRP498 3.4 18.2 1.0
O B:TRP498 3.4 17.7 1.0
OD1 B:ASN487 3.4 17.6 1.0
N B:THR499 3.4 16.1 1.0
CA B:THR499 3.6 16.1 1.0
CB B:TRP498 3.6 16.6 1.0
OG1 B:THR499 3.7 20.4 1.0
CG2 B:ILE502 3.8 19.2 1.0
CB B:ASN487 4.1 13.6 1.0
C03 B:D5N605 4.1 20.1 0.7
CA B:TRP498 4.1 19.2 1.0
CG B:ASN487 4.1 15.0 1.0
CE2 B:TYR325 4.2 14.0 1.0
CB B:THR499 4.3 18.5 1.0
CB B:ILE502 4.3 17.9 1.0
C11 B:D5N605 4.3 23.9 0.7
O02 B:D5N605 4.5 17.6 0.7
CE1 B:TYR495 4.5 15.1 1.0
OE1 B:GLN535 4.6 18.0 1.0
CD1 B:TYR495 4.7 15.8 1.0
NE2 B:GLN535 4.8 21.3 1.0
C B:THR499 4.8 20.0 1.0
O B:TYR495 4.8 19.7 1.0
CD2 B:TYR325 4.8 14.8 1.0
H12 B:D5N605 4.8 28.6 0.7
CG B:TRP498 4.9 15.5 1.0
CD B:GLN535 5.0 18.4 1.0
CZ B:TYR325 5.0 14.5 1.0

Fluorine binding site 4 out of 4 in 6fdc

Go back to Fluorine Binding Sites List in 6fdc
Fluorine binding site 4 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A


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 the PDE4D Catalytic Domain in Complex with Gebr- 32A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F605

b:19.4
occ:0.65
 F02 B:D5N605 0.0 19.4 0.7
C01 B:D5N605 1.4 15.6 0.7
H01 B:D5N605 2.0 18.8 0.7
F01 B:D5N605 2.2 24.1 0.7
O01 B:D5N605 2.2 19.6 0.7
H13 B:D5N605 2.6 27.3 0.7
C02 B:D5N605 2.9 18.9 0.7
C12 B:D5N605 3.0 22.7 0.7
CB B:ASN487 3.2 13.6 1.0
CE1 B:TYR495 3.4 15.1 1.0
CG B:PRO488 3.6 12.8 1.0
CE2 B:PHE538 3.6 17.0 1.0
OD1 B:ASN487 3.6 17.6 1.0
CD B:PRO488 3.6 13.7 1.0
OE1 B:GLN535 3.7 18.0 1.0
CG B:ASN487 3.9 15.0 1.0
CD1 B:TYR495 4.0 15.8 1.0
C03 B:D5N605 4.1 20.1 0.7
CD2 B:PHE538 4.1 15.5 1.0
N B:PRO488 4.2 13.2 1.0
O B:HOH846 4.2 17.2 1.0
OG1 B:THR499 4.3 20.4 1.0
C11 B:D5N605 4.4 23.9 0.7
CA B:ASN487 4.4 13.9 1.0
O02 B:D5N605 4.5 17.6 0.7
C B:ASN487 4.5 15.1 1.0
CZ B:TYR495 4.5 18.0 1.0
CD B:GLN535 4.5 18.4 1.0
CZ B:PHE538 4.6 17.4 1.0
NE2 B:GLN535 4.7 21.3 1.0
OH B:TYR495 4.7 18.2 1.0
CB B:PRO488 4.8 14.3 1.0
CB B:TRP498 4.8 16.6 1.0
CA B:PRO488 4.9 13.4 1.0
H12 B:D5N605 4.9 28.6 0.7
N B:ASN487 5.0 13.4 1.0

Reference:

T.Prosdocimi, L.Mollica, S.Donini, M.S.Semrau, A.P.Lucarelli, E.Aiolfi, A.Cavalli, P.Storici, S.Alfei, C.Brullo, O.Bruno, E.Parisini. Molecular Bases of PDE4D Inhibition By Memory-Enhancing Gebr Library Compounds. Biochemistry V. 57 2876 2018.
ISSN: ISSN 1520-4995
PubMed: 29652483
DOI: 10.1021/ACS.BIOCHEM.8B00288
Page generated: Thu Aug 1 19:53:09 2024

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