Zinc in PDB 2fm0: Crystal Structure of PDE4D in Complex with L-869298

All present enzymatic activity of Crystal Structure of PDE4D in Complex with L-869298:
3.1.4.17;

The structure of Crystal Structure of PDE4D in Complex with L-869298, PDB code: 2fm0 was solved by Q.Huai, Y.Sun, H.Wang, D.Macdonald, R.Aspiotis, H.Robinson, Z.Huang, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.511, 112.176, 160.174, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 24.5

The structure of Crystal Structure of PDE4D in Complex with L-869298 also contains other interesting chemical elements:

Fluorine	(F)	32 atoms
Magnesium	(Mg)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4D in Complex with L-869298 (pdb code 2fm0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of PDE4D in Complex with L-869298, PDB code: 2fm0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of PDE4D in Complex with L-869298


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of PDE4D in Complex with L-869298 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:24.0 occ:1.00 OD2 A:ASP201 2.0 21.8 1.0 OD1 A:ASP318 2.0 22.4 1.0 NE2 A:HIS200 2.1 21.3 1.0 NE2 A:HIS164 2.1 19.2 1.0 O A:HOH607 2.2 22.1 1.0 O A:HOH602 2.2 24.1 1.0 CD2 A:HIS200 2.9 20.3 1.0 CG A:ASP318 3.0 22.2 1.0 CE1 A:HIS164 3.1 18.3 1.0 CD2 A:HIS164 3.1 18.7 1.0 CG A:ASP201 3.1 20.2 1.0 CE1 A:HIS200 3.1 20.7 1.0 OD2 A:ASP318 3.3 23.3 1.0 OD1 A:ASP201 3.6 21.0 1.0 O A:HOH603 3.9 24.4 1.0 MG A:MG502 4.0 21.3 1.0 CG A:HIS200 4.1 20.4 1.0 ND1 A:HIS200 4.2 21.0 1.0 ND1 A:HIS164 4.2 17.8 1.0 CD2 A:HIS160 4.2 18.6 1.0 CG A:HIS164 4.2 18.9 1.0 O A:HOH636 4.2 22.8 1.0 CB A:ASP201 4.3 19.0 1.0 CB A:ASP318 4.3 22.0 1.0 NE2 A:HIS160 4.4 18.5 1.0 CG2 A:VAL168 4.6 21.9 1.0 C20 A:M98601 4.9 29.2 1.0 CA A:ASP318 5.0 21.7 1.0 C21 A:M98601 5.0 29.8 1.0 O A:HOH605 5.0 20.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of PDE4D in Complex with L-869298


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of PDE4D in Complex with L-869298 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:30.1 occ:1.00 OD2 B:ASP201 2.0 27.1 1.0 OD1 B:ASP318 2.0 28.7 1.0 NE2 B:HIS164 2.1 25.6 1.0 NE2 B:HIS200 2.1 25.7 1.0 O B:HOH608 2.1 28.1 1.0 O B:HOH603 2.2 28.6 1.0 CD2 B:HIS200 3.0 25.2 1.0 CE1 B:HIS164 3.0 25.2 1.0 CG B:ASP318 3.0 28.7 1.0 CD2 B:HIS164 3.1 25.6 1.0 CG B:ASP201 3.1 25.2 1.0 CE1 B:HIS200 3.1 25.7 1.0 OD2 B:ASP318 3.4 28.0 1.0 OD1 B:ASP201 3.6 25.6 1.0 MG B:MG504 3.9 26.1 1.0 O B:HOH604 4.1 24.2 1.0 CG B:HIS200 4.1 24.3 1.0 ND1 B:HIS164 4.1 24.3 1.0 ND1 B:HIS200 4.1 25.0 1.0 CD2 B:HIS160 4.2 23.8 1.0 CG B:HIS164 4.2 25.6 1.0 O B:HOH619 4.3 24.2 1.0 CB B:ASP201 4.3 24.6 1.0 CB B:ASP318 4.4 28.4 1.0 NE2 B:HIS160 4.5 24.4 1.0 CG2 B:VAL168 4.7 32.1 1.0 C20 B:M98602 4.7 32.5 1.0 C21 B:M98602 4.8 33.6 1.0 CA B:ASP318 4.9 28.7 1.0 O B:HOH606 5.0 25.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of PDE4D in Complex with L-869298


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of PDE4D in Complex with L-869298 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn505 b:28.0 occ:1.00 OD2 C:ASP201 2.0 24.2 1.0 OD1 C:ASP318 2.0 28.0 1.0 NE2 C:HIS200 2.1 25.4 1.0 NE2 C:HIS164 2.1 25.5 1.0 O C:HOH604 2.1 26.1 1.0 O C:HOH609 2.2 27.5 1.0 CD2 C:HIS200 3.0 24.8 1.0 CE1 C:HIS164 3.0 25.5 1.0 CG C:ASP318 3.0 28.5 1.0 CE1 C:HIS200 3.1 25.1 1.0 CD2 C:HIS164 3.1 25.2 1.0 CG C:ASP201 3.1 23.6 1.0 OD2 C:ASP318 3.4 28.3 1.0 OD1 C:ASP201 3.6 23.1 1.0 MG C:MG506 3.9 25.9 1.0 O C:HOH605 4.0 25.8 1.0 ND1 C:HIS164 4.1 25.3 1.0 CG C:HIS200 4.1 23.8 1.0 CD2 C:HIS160 4.1 21.8 1.0 ND1 C:HIS200 4.1 25.2 1.0 CG C:HIS164 4.2 25.2 1.0 O C:HOH633 4.3 25.0 1.0 CB C:ASP201 4.3 23.1 1.0 CB C:ASP318 4.4 28.4 1.0 NE2 C:HIS160 4.4 21.7 1.0 CG2 C:VAL168 4.6 24.0 1.0 C20 C:M98603 4.7 36.6 1.0 C21 C:M98603 4.8 37.0 1.0 CA C:ASP318 4.9 28.6 1.0 O C:HOH607 4.9 25.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of PDE4D in Complex with L-869298


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of PDE4D in Complex with L-869298 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn507 b:24.4 occ:1.00 OD2 D:ASP201 2.0 21.4 1.0 OD1 D:ASP318 2.0 21.6 1.0 NE2 D:HIS200 2.1 21.6 1.0 NE2 D:HIS164 2.1 20.8 1.0 O D:HOH605 2.1 25.6 1.0 O D:HOH610 2.2 25.3 1.0 CD2 D:HIS200 2.9 20.0 1.0 CG D:ASP318 3.0 21.7 1.0 CE1 D:HIS164 3.0 20.0 1.0 CG D:ASP201 3.1 21.0 1.0 CE1 D:HIS200 3.1 20.5 1.0 CD2 D:HIS164 3.1 20.4 1.0 OD2 D:ASP318 3.2 23.6 1.0 OD1 D:ASP201 3.6 22.4 1.0 O D:HOH606 3.8 27.7 1.0 MG D:MG508 4.0 24.6 1.0 CG D:HIS200 4.1 19.4 1.0 CD2 D:HIS160 4.1 20.7 1.0 ND1 D:HIS164 4.1 19.9 1.0 O D:HOH653 4.2 22.9 1.0 ND1 D:HIS200 4.2 20.4 1.0 CG D:HIS164 4.2 19.7 1.0 CB D:ASP201 4.3 20.0 1.0 CB D:ASP318 4.3 21.0 1.0 NE2 D:HIS160 4.3 21.3 1.0 CG2 D:VAL168 4.7 17.0 1.0 C21 D:M98604 4.8 31.4 1.0 C20 D:M98604 4.8 31.0 1.0 CA D:ASP318 4.9 20.6 1.0

Q.Huai, Y.Sun, H.Wang, D.Macdonald, R.Aspiotis, H.Robinson, Z.Huang, H.Ke. Enantiomer Discrimination Illustrated By the High Resolution Crystal Structures of Type 4 Phosphodiesterase J.Med.Chem. V. 49 1867 2006.
ISSN: ISSN 0022-2623
PubMed: 16539372
DOI: 10.1021/JM051273D