Fluorine in PDB 6f8u: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B

Enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B, PDB code: 6f8u 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) 49.33 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.672, 98.669, 119.644, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 21.9

Other elements in 6f8u:

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B 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- 20B (pdb code 6f8u). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B, PDB code: 6f8u:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6f8u

Go back to Fluorine Binding Sites List in 6f8u
Fluorine binding site 1 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B


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- 20B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F606

b:23.7
occ:0.78
F01 A:CZQ606 0.0 23.7 0.8
C17 A:CZQ606 1.3 19.4 0.8
H17 A:CZQ606 1.9 23.2 0.8
F02 A:CZQ606 2.0 18.6 0.8
O03 A:CZQ606 2.2 18.9 0.8
H18 A:CZQ606 2.6 21.1 0.8
C16 A:CZQ606 2.9 19.4 0.8
C18 A:CZQ606 3.0 17.6 0.8
CE1 A:TYR495 3.2 19.1 1.0
CB A:ASN487 3.3 13.7 1.0
ND2 A:ASN487 3.6 13.5 1.0
CG A:PRO488 3.7 19.9 1.0
OE1 A:GLN535 3.7 19.7 1.0
CD1 A:TYR495 3.8 15.7 1.0
CD A:PRO488 3.8 15.2 1.0
CG A:ASN487 4.0 20.4 1.0
CE2 A:PHE538 4.0 17.5 1.0
OG1 A:THR499 4.2 17.0 1.0
C09 A:CZQ606 4.2 21.2 0.8
N A:PRO488 4.2 17.9 1.0
C19 A:CZQ606 4.3 17.7 0.8
CZ A:TYR495 4.4 21.1 1.0
CD A:GLN535 4.4 20.1 1.0
CA A:ASN487 4.4 21.3 1.0
NE2 A:GLN535 4.4 19.2 1.0
CD2 A:PHE538 4.4 16.9 1.0
C A:ASN487 4.5 16.2 1.0
OH A:TYR495 4.6 19.4 1.0
O A:HOH819 4.7 16.0 1.0
CB A:TRP498 4.7 9.2 1.0
O02 A:CZQ606 4.8 18.0 0.8
H20 A:CZQ606 4.8 21.2 0.8
CB A:PRO488 4.8 16.6 1.0
N A:THR499 4.8 15.5 1.0
CA A:PRO488 4.9 16.9 1.0
CA A:THR499 5.0 15.0 1.0

Fluorine binding site 2 out of 6 in 6f8u

Go back to Fluorine Binding Sites List in 6f8u
Fluorine binding site 2 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B


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- 20B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F606

b:18.6
occ:0.78
F02 A:CZQ606 0.0 18.6 0.8
C17 A:CZQ606 1.0 19.4 0.8
H17 A:CZQ606 1.6 23.2 0.8
F01 A:CZQ606 2.0 23.7 0.8
O03 A:CZQ606 2.0 18.9 0.8
H18 A:CZQ606 2.4 21.1 0.8
C16 A:CZQ606 2.7 19.4 0.8
C18 A:CZQ606 2.9 17.6 0.8
N A:THR499 3.4 15.5 1.0
C A:TRP498 3.4 18.0 1.0
ND2 A:ASN487 3.4 13.5 1.0
O A:TRP498 3.5 16.2 1.0
CA A:THR499 3.5 15.0 1.0
CB A:TRP498 3.7 9.2 1.0
OG1 A:THR499 3.7 17.0 1.0
CG2 A:ILE502 3.8 15.8 1.0
C09 A:CZQ606 4.0 21.2 0.8
CB A:ASN487 4.0 13.7 1.0
CA A:TRP498 4.2 17.0 1.0
CG A:ASN487 4.2 20.4 1.0
C19 A:CZQ606 4.2 17.7 0.8
CB A:THR499 4.3 19.4 1.0
CB A:ILE502 4.3 19.4 1.0
CE1 A:TYR495 4.4 19.1 1.0
CE2 A:TYR325 4.4 19.5 1.0
NE2 A:GLN535 4.4 19.2 1.0
CD1 A:TYR495 4.6 15.7 1.0
O02 A:CZQ606 4.6 18.0 0.8
OE1 A:GLN535 4.6 19.7 1.0
H20 A:CZQ606 4.7 21.2 0.8
O A:TYR495 4.7 15.4 1.0
C A:THR499 4.8 19.4 1.0
CD A:GLN535 4.8 20.1 1.0
CG A:TRP498 4.9 13.3 1.0
CD2 A:TYR325 5.0 10.5 1.0

Fluorine binding site 3 out of 6 in 6f8u

Go back to Fluorine Binding Sites List in 6f8u
Fluorine binding site 3 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B


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- 20B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F603

b:25.9
occ:0.35
F01 B:CZQ603 0.0 25.9 0.3
F01 B:CZQ604 0.1 25.7 0.5
C17 B:CZQ604 1.3 27.2 0.5
C17 B:CZQ603 1.4 27.1 0.3
F02 B:CZQ604 1.8 25.0 0.5
H17 B:CZQ604 1.9 32.6 0.5
H17 B:CZQ603 1.9 32.5 0.3
F02 B:CZQ603 2.0 24.7 0.3
O03 B:CZQ604 2.2 25.4 0.5
O03 B:CZQ603 2.2 25.5 0.3
H18 B:CZQ604 2.4 29.1 0.5
H18 B:CZQ603 2.6 29.2 0.3
C16 B:CZQ604 2.8 26.1 0.5
C16 B:CZQ603 2.8 26.1 0.3
C18 B:CZQ604 2.9 24.3 0.5
C18 B:CZQ603 2.9 24.3 0.3
CB B:ASN487 3.1 16.5 1.0
CE1 B:TYR495 3.3 17.6 1.0
OD1 B:ASN487 3.5 17.0 1.0
CG B:PRO488 3.7 15.9 1.0
CD B:PRO488 3.8 11.9 1.0
CG B:ASN487 3.8 20.6 1.0
OE1 B:GLN535 3.8 21.8 1.0
CD1 B:TYR495 3.9 20.8 1.0
CE2 B:PHE538 4.0 22.0 1.0
C09 B:CZQ603 4.0 26.1 0.3
C09 B:CZQ604 4.0 26.1 0.5
C19 B:CZQ604 4.2 27.9 0.5
OG1 B:THR499 4.2 17.4 1.0
C19 B:CZQ603 4.2 27.9 0.3
N B:PRO488 4.3 13.3 1.0
CA B:ASN487 4.4 15.8 1.0
CZ B:TYR495 4.4 20.7 1.0
C B:ASN487 4.5 16.4 1.0
CD2 B:PHE538 4.5 18.6 1.0
CB B:TRP498 4.5 13.9 1.0
CD B:GLN535 4.5 20.8 1.0
O02 B:CZQ603 4.6 27.0 0.3
H20 B:CZQ604 4.6 33.5 0.5
O B:HOH773 4.6 18.9 1.0
NE2 B:GLN535 4.6 28.6 1.0
O02 B:CZQ604 4.6 27.0 0.5
H20 B:CZQ603 4.7 33.5 0.3
OH B:TYR495 4.7 18.4 1.0
N B:THR499 4.8 18.6 1.0
CB B:PRO488 4.9 13.7 1.0
CA B:THR499 4.9 17.9 1.0
C B:TRP498 5.0 17.4 1.0
CA B:PRO488 5.0 13.1 1.0

Fluorine binding site 4 out of 6 in 6f8u

Go back to Fluorine Binding Sites List in 6f8u
Fluorine binding site 4 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B


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- 20B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F603

b:24.7
occ:0.35
F02 B:CZQ603 0.0 24.7 0.3
F02 B:CZQ604 0.2 25.0 0.5
C17 B:CZQ603 1.0 27.1 0.3
C17 B:CZQ604 1.1 27.2 0.5
H17 B:CZQ603 1.6 32.5 0.3
H17 B:CZQ604 1.7 32.6 0.5
F01 B:CZQ603 2.0 25.9 0.3
O03 B:CZQ603 2.0 25.5 0.3
O03 B:CZQ604 2.1 25.4 0.5
F01 B:CZQ604 2.1 25.7 0.5
H18 B:CZQ604 2.4 29.1 0.5
H18 B:CZQ603 2.5 29.2 0.3
C16 B:CZQ603 2.8 26.1 0.3
C16 B:CZQ604 2.8 26.1 0.5
C18 B:CZQ604 2.9 24.3 0.5
C18 B:CZQ603 3.0 24.3 0.3
C B:TRP498 3.2 17.4 1.0
O B:TRP498 3.3 17.8 1.0
N B:THR499 3.3 18.6 1.0
CA B:THR499 3.4 17.9 1.0
CB B:TRP498 3.5 13.9 1.0
OD1 B:ASN487 3.6 17.0 1.0
OG1 B:THR499 3.6 17.4 1.0
CG2 B:ILE502 3.9 20.9 1.0
CA B:TRP498 4.0 20.1 1.0
CB B:ASN487 4.1 16.5 1.0
C09 B:CZQ603 4.1 26.1 0.3
C09 B:CZQ604 4.1 26.1 0.5
CB B:THR499 4.2 20.5 1.0
CG B:ASN487 4.2 20.6 1.0
CE2 B:TYR325 4.3 11.9 1.0
C19 B:CZQ604 4.3 27.9 0.5
CB B:ILE502 4.3 22.0 1.0
C19 B:CZQ603 4.3 27.9 0.3
CE1 B:TYR495 4.3 17.6 1.0
O02 B:CZQ603 4.6 27.0 0.3
NE2 B:GLN535 4.6 28.6 1.0
CD1 B:TYR495 4.6 20.8 1.0
O B:TYR495 4.6 19.3 1.0
O02 B:CZQ604 4.6 27.0 0.5
C B:THR499 4.7 22.2 1.0
OE1 B:GLN535 4.7 21.8 1.0
H20 B:CZQ604 4.7 33.5 0.5
H20 B:CZQ603 4.8 33.5 0.3
CG B:TRP498 4.8 11.7 1.0
CD2 B:TYR325 4.9 14.9 1.0
CD B:GLN535 4.9 20.8 1.0

Fluorine binding site 5 out of 6 in 6f8u

Go back to Fluorine Binding Sites List in 6f8u
Fluorine binding site 5 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B


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 the PDE4D Catalytic Domain in Complex with Gebr- 20B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F604

b:25.7
occ:0.48
F01 B:CZQ604 0.0 25.7 0.5
F01 B:CZQ603 0.1 25.9 0.3
C17 B:CZQ604 1.4 27.2 0.5
C17 B:CZQ603 1.5 27.1 0.3
H17 B:CZQ604 1.9 32.6 0.5
F02 B:CZQ604 2.0 25.0 0.5
H17 B:CZQ603 2.0 32.5 0.3
F02 B:CZQ603 2.1 24.7 0.3
O03 B:CZQ604 2.2 25.4 0.5
O03 B:CZQ603 2.3 25.5 0.3
H18 B:CZQ604 2.5 29.1 0.5
H18 B:CZQ603 2.6 29.2 0.3
C16 B:CZQ604 2.8 26.1 0.5
C16 B:CZQ603 2.8 26.1 0.3
C18 B:CZQ604 2.9 24.3 0.5
C18 B:CZQ603 3.0 24.3 0.3
CB B:ASN487 3.2 16.5 1.0
CE1 B:TYR495 3.3 17.6 1.0
OD1 B:ASN487 3.6 17.0 1.0
CG B:PRO488 3.6 15.9 1.0
CD B:PRO488 3.7 11.9 1.0
OE1 B:GLN535 3.8 21.8 1.0
CG B:ASN487 3.9 20.6 1.0
CD1 B:TYR495 3.9 20.8 1.0
CE2 B:PHE538 3.9 22.0 1.0
C09 B:CZQ603 4.0 26.1 0.3
C09 B:CZQ604 4.0 26.1 0.5
C19 B:CZQ604 4.2 27.9 0.5
N B:PRO488 4.2 13.3 1.0
C19 B:CZQ603 4.2 27.9 0.3
OG1 B:THR499 4.3 17.4 1.0
CA B:ASN487 4.4 15.8 1.0
CZ B:TYR495 4.4 20.7 1.0
CD2 B:PHE538 4.4 18.6 1.0
C B:ASN487 4.5 16.4 1.0
CD B:GLN535 4.5 20.8 1.0
O02 B:CZQ603 4.6 27.0 0.3
O B:HOH773 4.6 18.9 1.0
OH B:TYR495 4.6 18.4 1.0
H20 B:CZQ604 4.6 33.5 0.5
O02 B:CZQ604 4.6 27.0 0.5
NE2 B:GLN535 4.6 28.6 1.0
CB B:TRP498 4.7 13.9 1.0
H20 B:CZQ603 4.7 33.5 0.3
CB B:PRO488 4.8 13.7 1.0
CA B:PRO488 4.9 13.1 1.0
N B:THR499 5.0 18.6 1.0
N B:ASN487 5.0 13.3 1.0
CZ B:PHE538 5.0 19.3 1.0

Fluorine binding site 6 out of 6 in 6f8u

Go back to Fluorine Binding Sites List in 6f8u
Fluorine binding site 6 out of 6 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B


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 the PDE4D Catalytic Domain in Complex with Gebr- 20B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F604

b:25.0
occ:0.48
F02 B:CZQ604 0.0 25.0 0.5
F02 B:CZQ603 0.2 24.7 0.3
C17 B:CZQ603 0.8 27.1 0.3
C17 B:CZQ604 1.0 27.2 0.5
H17 B:CZQ603 1.5 32.5 0.3
H17 B:CZQ604 1.6 32.6 0.5
F01 B:CZQ603 1.8 25.9 0.3
O03 B:CZQ603 1.9 25.5 0.3
F01 B:CZQ604 2.0 25.7 0.5
O03 B:CZQ604 2.0 25.4 0.5
H18 B:CZQ604 2.5 29.1 0.5
H18 B:CZQ603 2.5 29.2 0.3
C16 B:CZQ603 2.7 26.1 0.3
C16 B:CZQ604 2.7 26.1 0.5
C18 B:CZQ604 2.9 24.3 0.5
C18 B:CZQ603 3.0 24.3 0.3
C B:TRP498 3.3 17.4 1.0
N B:THR499 3.4 18.6 1.0
O B:TRP498 3.4 17.8 1.0
CA B:THR499 3.5 17.9 1.0
OG1 B:THR499 3.6 17.4 1.0
OD1 B:ASN487 3.6 17.0 1.0
CB B:TRP498 3.6 13.9 1.0
CG2 B:ILE502 3.9 20.9 1.0
C09 B:CZQ603 4.0 26.1 0.3
CB B:ASN487 4.0 16.5 1.0
C09 B:CZQ604 4.1 26.1 0.5
CA B:TRP498 4.1 20.1 1.0
CB B:THR499 4.1 20.5 1.0
CE1 B:TYR495 4.2 17.6 1.0
CG B:ASN487 4.2 20.6 1.0
C19 B:CZQ604 4.3 27.9 0.5
C19 B:CZQ603 4.3 27.9 0.3
CE2 B:TYR325 4.4 11.9 1.0
CB B:ILE502 4.4 22.0 1.0
NE2 B:GLN535 4.5 28.6 1.0
CD1 B:TYR495 4.5 20.8 1.0
O02 B:CZQ603 4.5 27.0 0.3
OE1 B:GLN535 4.5 21.8 1.0
O02 B:CZQ604 4.6 27.0 0.5
O B:TYR495 4.6 19.3 1.0
C B:THR499 4.7 22.2 1.0
H20 B:CZQ604 4.8 33.5 0.5
CD B:GLN535 4.8 20.8 1.0
H20 B:CZQ603 4.8 33.5 0.3
CG B:TRP498 4.9 11.7 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: Sun Dec 13 12:50:02 2020

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