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Fluorine in PDB 6fet: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439, PDB code: 6fet was solved by A.K.Singh, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.35 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.190, 110.710, 161.480, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 19.9

Other elements in 6fet:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 4 atoms
Zinc (Zn) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 (pdb code 6fet). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 16 binding sites of Fluorine where determined in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439, PDB code: 6fet:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 16 in 6fet

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Fluorine binding site 1 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F517

b:42.3
occ:1.00
 F1 A:D68517 0.0 42.3 1.0
C16 A:D68517 1.4 40.9 1.0
F2 A:D68517 2.1 40.2 1.0
O3 A:D68517 2.2 42.5 1.0
C15 A:D68517 2.8 39.6 1.0
C14 A:D68517 3.0 39.7 1.0
CB A:ASN321 3.4 33.2 1.0
CG A:PRO322 3.6 37.6 1.0
CE1 A:TYR329 3.6 39.0 1.0
ND2 A:ASN321 3.6 30.8 1.0
CE2 A:PHE372 3.7 43.6 1.0
OE1 A:GLN369 3.7 37.9 1.0
CD A:PRO322 3.7 35.7 1.0
CG A:ASN321 4.1 36.2 1.0
C17 A:D68517 4.1 41.9 1.0
CD1 A:TYR329 4.2 39.0 1.0
O A:HOH691 4.2 35.9 1.0
CD2 A:PHE372 4.3 42.5 1.0
N A:PRO322 4.3 36.4 1.0
OG1 A:THR333 4.3 37.9 1.0
C13 A:D68517 4.3 39.6 1.0
O4 A:D68517 4.5 43.1 1.0
CD A:GLN369 4.5 37.3 1.0
CA A:ASN321 4.5 34.3 1.0
C A:ASN321 4.6 36.1 1.0
CZ A:TYR329 4.6 35.7 1.0
NE2 A:GLN369 4.7 34.0 1.0
CZ A:PHE372 4.8 42.1 1.0
OH A:TYR329 4.8 38.9 1.0
CB A:PRO322 4.8 38.3 1.0
CA A:PRO322 5.0 39.0 1.0

Fluorine binding site 2 out of 16 in 6fet

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Fluorine binding site 2 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F517

b:40.2
occ:1.00
 F2 A:D68517 0.0 40.2 1.0
C16 A:D68517 1.3 40.9 1.0
F1 A:D68517 2.1 42.3 1.0
O3 A:D68517 2.2 42.5 1.0
C15 A:D68517 2.8 39.6 1.0
C14 A:D68517 2.9 39.7 1.0
ND2 A:ASN321 3.5 30.8 1.0
O A:TRP332 3.5 34.3 1.0
N A:THR333 3.5 39.8 1.0
C A:TRP332 3.5 38.2 1.0
CG2 A:ILE336 3.6 37.2 1.0
CA A:THR333 3.6 35.5 1.0
OG1 A:THR333 3.7 37.9 1.0
CB A:TRP332 3.9 30.7 1.0
C17 A:D68517 4.1 41.9 1.0
CB A:ILE336 4.2 36.4 1.0
CB A:ASN321 4.2 33.2 1.0
C13 A:D68517 4.2 39.6 1.0
CB A:THR333 4.3 35.7 1.0
CE2 A:TYR159 4.3 31.9 1.0
CG A:ASN321 4.3 36.2 1.0
CA A:TRP332 4.3 35.1 1.0
O4 A:D68517 4.6 43.1 1.0
CE1 A:TYR329 4.6 39.0 1.0
OE1 A:GLN369 4.6 37.9 1.0
NE2 A:GLN369 4.7 34.0 1.0
O A:TYR329 4.8 35.6 1.0
C A:THR333 4.8 35.8 1.0
CD1 A:TYR329 4.8 39.0 1.0
CD A:GLN369 4.9 37.3 1.0
CD2 A:TYR159 5.0 32.5 1.0
CG2 A:THR333 5.0 36.7 1.0

Fluorine binding site 3 out of 16 in 6fet

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Fluorine binding site 3 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F517

b:43.6
occ:1.00
 F3 A:D68517 0.0 43.6 1.0
C18 A:D68517 1.3 54.2 1.0
F4 A:D68517 2.1 51.2 1.0
O4 A:D68517 2.2 43.1 1.0
C17 A:D68517 2.8 41.9 1.0
C19 A:D68517 2.9 39.1 1.0
CE A:MET357 2.9 86.7 1.0
O1 A:D68517 3.4 65.6 1.0
CE2 A:PHE340 3.5 49.4 1.0
SD A:MET357 3.8 83.8 1.0
C15 A:D68517 4.2 39.6 1.0
C5 A:D68517 4.2 77.3 1.0
C12 A:D68517 4.3 37.9 1.0
CZ A:PHE340 4.3 50.8 1.0
CD2 A:PHE340 4.3 53.7 1.0
NE2 A:GLN369 4.5 34.0 1.0
N4 A:D68517 4.5 40.2 1.0
CG A:PHE372 4.6 43.7 1.0
CD1 A:PHE372 4.6 41.5 1.0
O3 A:D68517 4.6 42.5 1.0
C6 A:D68517 4.8 54.7 1.0
O A:HOH679 4.8 52.6 1.0
CB A:PHE372 4.8 43.4 1.0
N1 A:D68517 4.9 80.0 1.0
CD2 A:PHE372 4.9 42.5 1.0
C27 A:D68517 4.9 46.7 1.0
C11 A:D68517 4.9 41.3 1.0

Fluorine binding site 4 out of 16 in 6fet

Go back to Fluorine Binding Sites List in 6fet
Fluorine binding site 4 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F517

b:51.2
occ:1.00
 F4 A:D68517 0.0 51.2 1.0
C18 A:D68517 1.3 54.2 1.0
F3 A:D68517 2.1 43.6 1.0
O4 A:D68517 2.1 43.1 1.0
CB A:PHE372 3.2 43.4 1.0
NE2 A:GLN369 3.2 34.0 1.0
O1 A:D68517 3.3 65.6 1.0
C17 A:D68517 3.3 41.9 1.0
CG A:PHE372 3.5 43.7 1.0
O A:SER368 3.6 48.3 1.0
CD2 A:PHE372 3.8 42.5 1.0
O A:HOH679 3.9 52.6 1.0
C A:SER368 4.0 47.4 1.0
C19 A:D68517 4.0 39.1 1.0
C5 A:D68517 4.0 77.3 1.0
CE A:MET357 4.0 86.7 1.0
SD A:MET357 4.0 83.8 1.0
CD1 A:PHE372 4.1 41.5 1.0
CD A:GLN369 4.1 37.3 1.0
C4 A:D68517 4.3 68.6 1.0
CB A:SER368 4.3 55.1 1.0
O3 A:D68517 4.4 42.5 1.0
C15 A:D68517 4.4 39.6 1.0
N A:GLN369 4.4 39.9 1.0
CA A:GLN369 4.5 37.7 1.0
CA A:PHE372 4.5 42.3 1.0
OE1 A:GLN369 4.6 37.9 1.0
CE2 A:PHE372 4.7 43.6 1.0
CA A:SER368 4.8 52.0 1.0
N A:PHE372 4.9 42.6 1.0
CE1 A:PHE372 4.9 46.0 1.0
CG A:GLN369 5.0 40.5 1.0

Fluorine binding site 5 out of 16 in 6fet

Go back to Fluorine Binding Sites List in 6fet
Fluorine binding site 5 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F514

b:34.4
occ:1.00
 F1 B:D68514 0.0 34.4 1.0
C16 B:D68514 1.4 33.1 1.0
F2 B:D68514 2.1 37.6 1.0
O3 B:D68514 2.2 33.0 1.0
C15 B:D68514 2.7 32.6 1.0
C14 B:D68514 2.9 31.5 1.0
CB B:ASN321 3.4 34.6 1.0
OD1 B:ASN321 3.5 35.3 1.0
CE1 B:TYR329 3.6 35.3 1.0
OE1 B:GLN369 3.7 37.3 1.0
CG B:PRO322 3.7 37.5 1.0
CE2 B:PHE372 3.7 37.9 1.0
CD B:PRO322 3.8 34.9 1.0
CG B:ASN321 4.0 35.5 1.0
C17 B:D68514 4.0 35.2 1.0
O B:HOH675 4.2 30.8 1.0
CD1 B:TYR329 4.2 39.3 1.0
C13 B:D68514 4.2 32.6 1.0
CD2 B:PHE372 4.3 35.1 1.0
N B:PRO322 4.3 32.4 1.0
OG1 B:THR333 4.4 35.9 1.0
O4 B:D68514 4.5 34.5 1.0
CD B:GLN369 4.5 37.3 1.0
NE2 B:GLN369 4.6 39.8 1.0
CA B:ASN321 4.6 32.4 1.0
CZ B:TYR329 4.7 35.8 1.0
C B:ASN321 4.7 32.3 1.0
CZ B:PHE372 4.8 31.6 1.0
OH B:TYR329 4.8 32.0 1.0
CB B:PRO322 4.9 33.7 1.0
CB B:TRP332 5.0 33.4 1.0

Fluorine binding site 6 out of 16 in 6fet

Go back to Fluorine Binding Sites List in 6fet
Fluorine binding site 6 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F514

b:37.6
occ:1.00
 F2 B:D68514 0.0 37.6 1.0
C16 B:D68514 1.3 33.1 1.0
F1 B:D68514 2.1 34.4 1.0
O3 B:D68514 2.2 33.0 1.0
C15 B:D68514 2.8 32.6 1.0
C14 B:D68514 2.9 31.5 1.0
O B:TRP332 3.4 36.5 1.0
OD1 B:ASN321 3.4 35.3 1.0
C B:TRP332 3.5 34.8 1.0
N B:THR333 3.5 32.5 1.0
CG2 B:ILE336 3.6 35.5 1.0
CA B:THR333 3.6 32.8 1.0
OG1 B:THR333 3.8 35.9 1.0
CB B:TRP332 3.8 33.4 1.0
CB B:ILE336 4.1 34.4 1.0
C17 B:D68514 4.1 35.2 1.0
CE2 B:TYR159 4.2 31.0 1.0
CB B:ASN321 4.2 34.6 1.0
CG B:ASN321 4.2 35.5 1.0
C13 B:D68514 4.2 32.6 1.0
CA B:TRP332 4.3 35.0 1.0
CB B:THR333 4.4 35.6 1.0
OE1 B:GLN369 4.6 37.3 1.0
O4 B:D68514 4.6 34.5 1.0
CE1 B:TYR329 4.6 35.3 1.0
NE2 B:GLN369 4.6 39.8 1.0
C B:THR333 4.8 33.8 1.0
CD2 B:TYR159 4.8 35.9 1.0
CD1 B:TYR329 4.9 39.3 1.0
CD B:GLN369 4.9 37.3 1.0
CG1 B:ILE336 4.9 35.1 1.0
O B:TYR329 4.9 38.4 1.0
CZ B:TYR159 5.0 31.4 1.0
OH B:TYR159 5.0 28.2 1.0

Fluorine binding site 7 out of 16 in 6fet

Go back to Fluorine Binding Sites List in 6fet
Fluorine binding site 7 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F514

b:41.7
occ:1.00
 F3 B:D68514 0.0 41.7 1.0
C18 B:D68514 1.3 44.7 1.0
F4 B:D68514 2.1 38.2 1.0
O4 B:D68514 2.3 34.5 1.0
C17 B:D68514 2.9 35.2 1.0
C19 B:D68514 2.9 31.0 1.0
CE B:MET357 3.1 73.8 1.0
O6 B:D68514 3.2 55.7 1.0
CE2 B:PHE340 3.5 37.9 1.0
SD B:MET357 3.6 53.4 1.0
C29 B:D68514 4.0 60.9 1.0
CZ B:PHE340 4.2 40.6 1.0
C15 B:D68514 4.2 32.6 1.0
C12 B:D68514 4.3 32.5 1.0
N4 B:D68514 4.3 36.8 1.0
CD2 B:PHE340 4.5 42.6 1.0
CD1 B:PHE372 4.5 38.3 1.0
CG B:PHE372 4.5 34.6 1.0
C6 B:D68514 4.6 49.0 1.0
NE2 B:GLN369 4.7 39.8 1.0
C27 B:D68514 4.7 35.2 1.0
O3 B:D68514 4.7 33.0 1.0
N1 B:D68514 4.7 58.1 1.0
CB B:PHE372 4.8 33.5 1.0
C11 B:D68514 4.8 36.2 1.0
CE1 B:PHE372 4.8 37.3 1.0
CD2 B:PHE372 4.9 35.1 1.0
C30 B:D68514 5.0 63.3 1.0
O B:HOH686 5.0 39.0 1.0

Fluorine binding site 8 out of 16 in 6fet

Go back to Fluorine Binding Sites List in 6fet
Fluorine binding site 8 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F514

b:38.2
occ:1.00
 F4 B:D68514 0.0 38.2 1.0
C18 B:D68514 1.3 44.7 1.0
F3 B:D68514 2.1 41.7 1.0
O4 B:D68514 2.1 34.5 1.0
CB B:PHE372 3.2 33.5 1.0
O6 B:D68514 3.2 55.7 1.0
NE2 B:GLN369 3.3 39.8 1.0
C17 B:D68514 3.3 35.2 1.0
CG B:PHE372 3.4 34.6 1.0
O B:SER368 3.6 32.5 1.0
CD2 B:PHE372 3.8 35.1 1.0
C B:SER368 4.0 38.7 1.0
CD1 B:PHE372 4.0 38.3 1.0
C29 B:D68514 4.0 60.9 1.0
SD B:MET357 4.0 53.4 1.0
C19 B:D68514 4.0 31.0 1.0
O B:HOH686 4.0 39.0 1.0
CD B:GLN369 4.2 37.3 1.0
CB B:SER368 4.3 41.8 1.0
C30 B:D68514 4.3 63.3 1.0
O3 B:D68514 4.3 33.0 1.0
CE B:MET357 4.3 73.8 1.0
N B:GLN369 4.4 36.2 1.0
C15 B:D68514 4.4 32.6 1.0
CA B:GLN369 4.5 34.5 1.0
CA B:PHE372 4.5 33.9 1.0
OE1 B:GLN369 4.6 37.3 1.0
CE2 B:PHE372 4.6 37.9 1.0
CA B:SER368 4.7 42.1 1.0
CE1 B:PHE372 4.8 37.3 1.0
N B:PHE372 4.9 34.3 1.0

Fluorine binding site 9 out of 16 in 6fet

Go back to Fluorine Binding Sites List in 6fet
Fluorine binding site 9 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F515

b:34.7
occ:1.00
 F1 C:D68515 0.0 34.7 1.0
C16 C:D68515 1.3 36.6 1.0
F2 C:D68515 2.0 40.0 1.0
O3 C:D68515 2.2 41.0 1.0
C15 C:D68515 2.7 39.2 1.0
C14 C:D68515 2.9 35.6 1.0
CB C:ASN321 3.4 34.2 1.0
ND2 C:ASN321 3.5 29.7 1.0
CG C:PRO322 3.6 43.4 1.0
CE2 C:PHE372 3.6 43.1 1.0
CE1 C:TYR329 3.7 44.0 1.0
CD C:PRO322 3.8 42.3 1.0
OE1 C:GLN369 3.8 35.9 1.0
C17 C:D68515 4.0 40.7 1.0
O C:HOH673 4.0 37.3 1.0
CG C:ASN321 4.0 36.9 1.0
CD2 C:PHE372 4.1 44.0 1.0
C13 C:D68515 4.2 36.9 1.0
CD1 C:TYR329 4.3 43.3 1.0
N C:PRO322 4.3 38.8 1.0
OG1 C:THR333 4.4 35.9 1.0
O4 C:D68515 4.5 40.2 1.0
CD C:GLN369 4.5 42.0 1.0
CA C:ASN321 4.5 33.9 1.0
NE2 C:GLN369 4.6 36.1 1.0
CZ C:PHE372 4.6 44.7 1.0
C C:ASN321 4.7 40.4 1.0
CZ C:TYR329 4.7 44.9 1.0
CB C:PRO322 4.9 42.5 1.0
OH C:TYR329 4.9 37.7 1.0
C19 C:D68515 5.0 35.5 1.0

Fluorine binding site 10 out of 16 in 6fet

Go back to Fluorine Binding Sites List in 6fet
Fluorine binding site 10 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F515

b:40.0
occ:1.00
 F2 C:D68515 0.0 40.0 1.0
C16 C:D68515 1.3 36.6 1.0
F1 C:D68515 2.0 34.7 1.0
O3 C:D68515 2.2 41.0 1.0
C15 C:D68515 2.8 39.2 1.0
C14 C:D68515 2.9 35.6 1.0
ND2 C:ASN321 3.2 29.7 1.0
C C:TRP332 3.5 37.2 1.0
O C:TRP332 3.5 33.9 1.0
N C:THR333 3.6 35.7 1.0
CG2 C:ILE336 3.7 35.6 1.0
CA C:THR333 3.7 35.2 1.0
CB C:TRP332 3.8 33.7 1.0
OG1 C:THR333 3.8 35.9 1.0
CB C:ASN321 4.0 34.2 1.0
CG C:ASN321 4.1 36.9 1.0
C17 C:D68515 4.1 40.7 1.0
C13 C:D68515 4.2 36.9 1.0
CE2 C:TYR159 4.2 31.5 1.0
CB C:ILE336 4.3 32.4 1.0
CA C:TRP332 4.3 35.6 1.0
CB C:THR333 4.4 34.7 1.0
CE1 C:TYR329 4.6 44.0 1.0
OE1 C:GLN369 4.7 35.9 1.0
O4 C:D68515 4.7 40.2 1.0
NE2 C:GLN369 4.7 36.1 1.0
CD1 C:TYR329 4.8 43.3 1.0
O C:TYR329 4.9 37.6 1.0
OH C:TYR159 4.9 32.2 1.0
C C:THR333 4.9 34.2 1.0
O C:HOH673 4.9 37.3 1.0
CZ C:TYR159 5.0 32.2 1.0
CD2 C:TYR159 5.0 30.2 1.0
CD C:GLN369 5.0 42.0 1.0

Reference:

I.G.Salado, C.Moreno, G.Sakaine, A.K.Singh, A.R.Blaazer, M.Siderius, A.Matheeussen, S.Gul, L.Maes, R.Leurs, D.G.Brown, K.Augustyns. HPDE4D2 Structure with Inhibitor Npd-1439 To Be Published.
Page generated: Thu Aug 1 19:55:40 2024

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