Zinc in PDB 2fm5: Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299

All present enzymatic activity of Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299:
3.1.4.17;

The structure of Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299, PDB code: 2fm5 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 / 2.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.357, 112.812, 161.079, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 26

The structure of Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299 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 PDE4D2 in Complex with Inhibitor L- 869299 (pdb code 2fm5). 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 PDE4D2 in Complex with Inhibitor L- 869299, PDB code: 2fm5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299


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 PDE4D2 in Complex with Inhibitor L- 869299 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:23.1 occ:1.00 OD2 A:ASP201 2.0 18.7 1.0 OD1 A:ASP318 2.0 19.1 1.0 NE2 A:HIS164 2.1 18.4 1.0 NE2 A:HIS200 2.1 19.5 1.0 O A:HOH607 2.2 20.1 1.0 O A:HOH602 2.2 22.3 1.0 CD2 A:HIS200 3.0 19.1 1.0 CG A:ASP318 3.0 19.0 1.0 CE1 A:HIS164 3.0 17.1 1.0 CG A:ASP201 3.1 15.8 1.0 CE1 A:HIS200 3.1 19.3 1.0 CD2 A:HIS164 3.1 17.4 1.0 OD2 A:ASP318 3.3 19.9 1.0 OD1 A:ASP201 3.6 16.4 1.0 O A:HOH603 3.9 24.0 1.0 MG A:MG502 3.9 20.1 1.0 CD2 A:HIS160 4.1 15.2 1.0 ND1 A:HIS164 4.1 17.1 1.0 CG A:HIS200 4.1 17.5 1.0 ND1 A:HIS200 4.2 19.3 1.0 O A:HOH637 4.2 20.6 1.0 CG A:HIS164 4.2 17.1 1.0 CB A:ASP201 4.3 14.9 1.0 CB A:ASP318 4.4 19.0 1.0 NE2 A:HIS160 4.4 16.2 1.0 CG2 A:VAL168 4.8 17.8 1.0 CA A:ASP318 5.0 19.3 1.0 O A:HOH605 5.0 19.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299


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 PDE4D2 in Complex with Inhibitor L- 869299 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:26.8 occ:1.00 OD2 B:ASP201 2.0 22.4 1.0 OD1 B:ASP318 2.0 26.1 1.0 NE2 B:HIS200 2.1 23.1 1.0 NE2 B:HIS164 2.1 23.0 1.0 O B:HOH608 2.1 24.9 1.0 O B:HOH603 2.2 25.7 1.0 CG B:ASP318 3.0 25.5 1.0 CE1 B:HIS164 3.0 22.2 1.0 CE1 B:HIS200 3.0 22.1 1.0 CD2 B:HIS200 3.0 22.0 1.0 CG B:ASP201 3.1 18.7 1.0 CD2 B:HIS164 3.1 22.5 1.0 OD2 B:ASP318 3.3 25.7 1.0 OD1 B:ASP201 3.6 19.5 1.0 MG B:MG504 3.8 20.9 1.0 O B:HOH604 3.9 21.1 1.0 O B:HOH635 4.0 23.4 1.0 ND1 B:HIS200 4.1 21.4 1.0 ND1 B:HIS164 4.1 21.4 1.0 CD2 B:HIS160 4.1 19.5 1.0 CG B:HIS200 4.2 20.9 1.0 CG B:HIS164 4.2 22.6 1.0 CB B:ASP201 4.3 18.5 1.0 CB B:ASP318 4.3 25.8 1.0 NE2 B:HIS160 4.5 19.5 1.0 CG2 B:VAL168 4.7 26.2 1.0 O B:HOH606 4.9 20.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299


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 PDE4D2 in Complex with Inhibitor L- 869299 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn505 b:25.8 occ:1.00 OD2 C:ASP201 2.0 20.6 1.0 OD1 C:ASP318 2.0 25.7 1.0 NE2 C:HIS200 2.1 19.3 1.0 NE2 C:HIS164 2.1 23.5 1.0 O C:HOH609 2.1 25.2 1.0 O C:HOH604 2.2 24.6 1.0 CG C:ASP318 3.0 26.3 1.0 CE1 C:HIS164 3.0 21.6 1.0 CD2 C:HIS200 3.0 18.9 1.0 CE1 C:HIS200 3.1 19.1 1.0 CD2 C:HIS164 3.1 21.9 1.0 CG C:ASP201 3.1 18.1 1.0 OD2 C:ASP318 3.3 26.9 1.0 OD1 C:ASP201 3.6 19.1 1.0 MG C:MG506 3.9 22.2 1.0 O C:HOH605 4.0 22.7 1.0 O C:HOH640 4.1 23.9 1.0 ND1 C:HIS164 4.1 22.1 1.0 ND1 C:HIS200 4.2 18.3 1.0 CD2 C:HIS160 4.2 17.3 1.0 CG C:HIS200 4.2 18.0 1.0 CG C:HIS164 4.2 21.7 1.0 CB C:ASP201 4.3 17.4 1.0 CB C:ASP318 4.3 26.8 1.0 NE2 C:HIS160 4.4 18.2 1.0 CG2 C:VAL168 4.7 18.1 1.0 O C:HOH607 4.9 22.1 1.0 CA C:ASP318 4.9 26.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299


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 PDE4D2 in Complex with Inhibitor L- 869299 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn507 b:21.4 occ:1.00 OD2 D:ASP201 2.0 17.6 1.0 OD1 D:ASP318 2.0 20.2 1.0 NE2 D:HIS200 2.1 15.4 1.0 NE2 D:HIS164 2.1 19.9 1.0 O D:HOH610 2.1 20.6 1.0 O D:HOH605 2.2 19.0 1.0 CG D:ASP318 3.0 18.6 1.0 CE1 D:HIS164 3.0 19.3 1.0 CD2 D:HIS200 3.0 14.3 1.0 CE1 D:HIS200 3.1 15.3 1.0 CG D:ASP201 3.1 16.3 1.0 CD2 D:HIS164 3.1 19.5 1.0 OD2 D:ASP318 3.3 20.2 1.0 OD1 D:ASP201 3.6 17.1 1.0 MG D:MG508 3.9 19.7 1.0 O D:HOH606 4.0 21.6 1.0 ND1 D:HIS164 4.1 18.3 1.0 CD2 D:HIS160 4.1 17.3 1.0 ND1 D:HIS200 4.2 14.0 1.0 CG D:HIS200 4.2 13.9 1.0 CG D:HIS164 4.2 18.6 1.0 O D:HOH675 4.2 26.0 1.0 CB D:ASP201 4.3 15.8 1.0 CB D:ASP318 4.3 17.8 1.0 NE2 D:HIS160 4.4 18.3 1.0 CG2 D:VAL168 4.7 14.5 1.0 C20 D:M99604 4.9 35.2 1.0 C21 D:M99604 4.9 35.3 1.0 CA D:ASP318 5.0 18.0 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