Magnesium 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
Zinc	(Zn)	4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of PDE4D in Complex with L-869298, PDB code: 2fm0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg502 b:21.3 occ:1.00 OD1 A:ASP201 2.0 21.0 1.0 O A:HOH603 2.1 24.4 1.0 O A:HOH606 2.2 24.6 1.0 O A:HOH605 2.2 20.6 1.0 O A:HOH604 2.2 21.9 1.0 O A:HOH607 2.2 22.1 1.0 CG A:ASP201 3.1 20.2 1.0 OD2 A:ASP201 3.5 21.8 1.0 ZN A:ZN501 4.0 24.0 1.0 O A:HIS200 4.0 18.5 1.0 NE2 A:HIS233 4.1 20.1 1.0 CD2 A:HIS200 4.1 20.3 1.0 OG1 A:THR271 4.1 23.2 1.0 CD2 A:HIS233 4.2 19.4 1.0 C23 A:M98601 4.2 29.7 1.0 O A:HOH602 4.3 24.1 1.0 OE2 A:GLU230 4.3 22.8 1.0 O A:HOH614 4.4 35.4 1.0 CB A:ASP201 4.4 19.0 1.0 C21 A:M98601 4.5 29.8 1.0 O A:HOH609 4.6 30.5 1.0 NE2 A:HIS200 4.6 21.3 1.0 CD2 A:HIS204 4.7 18.0 1.0 CB A:THR271 4.7 23.7 1.0 OD2 A:ASP318 4.7 23.3 1.0 CA A:ASP201 4.7 18.6 1.0 O A:THR271 4.7 24.4 1.0 N2 A:M98601 4.8 30.4 1.0 C A:HIS200 4.8 18.2 1.0 CD2 A:HIS160 4.9 18.6 1.0 NE2 A:HIS160 4.9 18.5 1.0 CG A:GLU230 4.9 21.3 1.0 CD A:GLU230 5.0 22.1 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg504 b:26.1 occ:1.00 OD1 B:ASP201 2.0 25.6 1.0 O B:HOH604 2.1 24.2 1.0 O B:HOH606 2.2 25.5 1.0 O B:HOH605 2.2 25.2 1.0 O B:HOH607 2.2 26.7 1.0 O B:HOH608 2.2 28.1 1.0 CG B:ASP201 3.1 25.2 1.0 OD2 B:ASP201 3.4 27.1 1.0 ZN B:ZN503 3.9 30.1 1.0 NE2 B:HIS233 4.0 21.3 1.0 O B:HIS200 4.1 24.1 1.0 O B:HOH603 4.1 28.6 1.0 CD2 B:HIS200 4.1 25.2 1.0 OE2 B:GLU230 4.2 25.9 1.0 C23 B:M98602 4.2 33.4 1.0 CD2 B:HIS233 4.2 21.9 1.0 C21 B:M98602 4.3 33.6 1.0 O B:HOH615 4.4 31.6 1.0 CB B:ASP201 4.4 24.6 1.0 O B:HOH651 4.4 32.6 1.0 OG1 B:THR271 4.5 33.3 1.0 CD2 B:HIS204 4.5 20.8 1.0 NE2 B:HIS200 4.6 25.7 1.0 CD2 B:HIS160 4.7 23.8 1.0 CA B:ASP201 4.7 23.8 1.0 NE2 B:HIS160 4.8 24.4 1.0 OD2 B:ASP318 4.8 28.0 1.0 NE2 B:HIS204 4.8 19.8 1.0 N2 B:M98602 4.8 33.7 1.0 C B:HIS200 4.9 23.7 1.0 O B:THR271 4.9 34.1 1.0 CB B:THR271 4.9 33.5 1.0 CD B:GLU230 5.0 25.1 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg506 b:25.9 occ:1.00 OD1 C:ASP201 2.0 23.1 1.0 O C:HOH605 2.1 25.8 1.0 O C:HOH607 2.1 25.6 1.0 O C:HOH608 2.2 26.6 1.0 O C:HOH606 2.2 25.8 1.0 O C:HOH609 2.2 27.5 1.0 CG C:ASP201 3.0 23.6 1.0 OD2 C:ASP201 3.4 24.2 1.0 ZN C:ZN505 3.9 28.0 1.0 O C:HIS200 4.0 21.3 1.0 CD2 C:HIS200 4.1 24.8 1.0 NE2 C:HIS233 4.2 19.2 1.0 C23 C:M98603 4.2 37.0 1.0 O C:HOH604 4.2 26.1 1.0 OE2 C:GLU230 4.2 27.6 1.0 CD2 C:HIS233 4.3 18.8 1.0 C21 C:M98603 4.3 37.0 1.0 O C:HOH613 4.3 39.8 1.0 OG1 C:THR271 4.4 27.4 1.0 CB C:ASP201 4.4 23.1 1.0 NE2 C:HIS200 4.5 25.4 1.0 CD2 C:HIS204 4.6 18.1 1.0 O C:HOH611 4.6 32.8 1.0 CA C:ASP201 4.7 22.9 1.0 CD2 C:HIS160 4.8 21.8 1.0 O C:THR271 4.8 29.5 1.0 NE2 C:HIS160 4.8 21.7 1.0 OD2 C:ASP318 4.9 28.3 1.0 C C:HIS200 4.9 22.3 1.0 CB C:THR271 4.9 28.6 1.0 N2 C:M98603 4.9 37.5 1.0 NE2 C:HIS204 5.0 18.3 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg508 b:24.6 occ:1.00 OD1 D:ASP201 2.0 22.4 1.0 O D:HOH608 2.1 26.2 1.0 O D:HOH606 2.1 27.7 1.0 O D:HOH609 2.2 24.1 1.0 O D:HOH610 2.2 25.3 1.0 O D:HOH607 2.2 23.8 1.0 CG D:ASP201 3.1 21.0 1.0 OD2 D:ASP201 3.5 21.4 1.0 NE2 D:HIS233 4.0 18.5 1.0 O D:HIS200 4.0 20.0 1.0 ZN D:ZN507 4.0 24.4 1.0 CD2 D:HIS200 4.1 20.0 1.0 CD2 D:HIS233 4.1 18.6 1.0 OG1 D:THR271 4.2 23.9 1.0 C23 D:M98604 4.2 31.7 1.0 OE2 D:GLU230 4.3 23.6 1.0 O D:HOH605 4.4 25.6 1.0 CB D:ASP201 4.4 20.0 1.0 O D:HOH612 4.4 45.6 1.0 O D:HOH665 4.5 32.6 1.0 C21 D:M98604 4.5 31.4 1.0 NE2 D:HIS200 4.6 21.6 1.0 CD2 D:HIS204 4.6 22.1 1.0 CA D:ASP201 4.7 19.5 1.0 CB D:THR271 4.7 24.9 1.0 OD2 D:ASP318 4.7 23.6 1.0 C D:HIS200 4.8 19.5 1.0 N2 D:M98604 4.8 32.8 1.0 O D:THR271 4.8 24.4 1.0 CG D:GLU230 4.8 22.1 1.0 CD2 D:HIS160 4.9 20.7 1.0 NE2 D:HIS160 4.9 21.3 1.0 NE2 D:HIS204 4.9 22.4 1.0 CD D:GLU230 5.0 23.0 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