Zinc in PDB 6nji: Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49:
3.1.4.53;

The structure of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49, PDB code: 6nji was solved by D.Fox Iii, J.W.Fairman, M.E.Gurney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.87 / 2.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	124.040, 85.660, 83.450, 90.00, 110.41, 90.00
R / Rfree (%)	18.4 / 23

The structure of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49 (pdb code 6nji). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49, PDB code: 6nji:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49


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 the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn700 b:38.2 occ:1.00 NE2 A:HIS366 2.1 37.7 1.0 OD2 A:ASP367 2.2 34.7 1.0 NE2 A:HIS330 2.2 34.0 1.0 OD1 A:ASP484 2.2 40.1 1.0 O A:HOH805 2.3 29.5 1.0 O A:HOH822 2.4 41.8 1.0 CE1 A:HIS330 3.0 32.3 1.0 CD2 A:HIS366 3.0 35.5 1.0 CG A:ASP367 3.1 35.9 1.0 CG A:ASP484 3.1 41.2 1.0 CE1 A:HIS366 3.1 34.9 1.0 CD2 A:HIS330 3.3 36.1 1.0 OD2 A:ASP484 3.3 41.0 1.0 OD1 A:ASP367 3.5 37.1 1.0 MG A:MG701 3.6 36.5 1.0 CG A:HIS366 4.1 32.6 1.0 O A:HOH846 4.2 32.9 1.0 ND1 A:HIS330 4.2 32.8 1.0 CD2 A:HIS326 4.2 39.3 1.0 ND1 A:HIS366 4.2 33.7 1.0 CB A:ASP367 4.3 36.9 1.0 CG A:HIS330 4.3 34.7 1.0 NE2 A:HIS326 4.4 40.3 1.0 CB A:ASP484 4.5 38.6 1.0 O A:HOH807 4.6 38.0 1.0 CG2 A:VAL334 4.7 33.7 1.0 O A:HOH802 4.7 39.3 1.0 CA A:ASP484 5.0 38.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49


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 the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn700 b:44.9 occ:1.00 NE2 B:HIS366 2.1 42.3 1.0 OD1 B:ASP484 2.1 48.1 1.0 O B:HOH805 2.2 40.7 1.0 OD2 B:ASP367 2.2 47.3 1.0 NE2 B:HIS330 2.2 47.2 1.0 O B:HOH810 2.4 40.7 1.0 CD2 B:HIS366 3.0 45.5 1.0 CE1 B:HIS330 3.0 41.2 1.0 CG B:ASP484 3.1 48.7 1.0 CE1 B:HIS366 3.1 44.5 1.0 CG B:ASP367 3.1 44.2 1.0 OD2 B:ASP484 3.3 54.8 1.0 CD2 B:HIS330 3.3 44.7 1.0 OD1 B:ASP367 3.6 40.2 1.0 MG B:MG701 3.9 42.1 1.0 CG B:HIS366 4.1 43.2 1.0 ND1 B:HIS366 4.2 44.7 1.0 ND1 B:HIS330 4.2 41.8 1.0 CD2 B:HIS326 4.2 40.5 1.0 O B:HOH822 4.3 45.5 1.0 CB B:ASP367 4.3 41.3 1.0 CG B:HIS330 4.4 43.0 1.0 O B:HOH812 4.4 46.4 1.0 NE2 B:HIS326 4.5 36.4 1.0 CB B:ASP484 4.5 52.0 1.0 O B:HOH807 4.6 48.7 1.0 CG2 B:VAL334 4.7 43.7 1.0 CA B:ASP484 4.9 50.8 1.0

M.E.Gurney, R.A.Nugent, X.Mo, J.A.Sindac, T.J.Hagen, D.Fox Iii, J.M.O'donnell, C.Zhang, Y.Xu, H.T.Zhang, V.E.Groppi, M.Bailie, R.E.White, D.L.Romero, A.S.Vellekoop, J.R.Walker, M.D.Surman, L.Zhu, R.F.Campbell. Design and Synthesis of Selective Phosphodiesterase 4D (PDE4D) Allosteric Inhibitors For the Treatment of Fragile X Syndrome and Other Brain Disorders. J.Med.Chem. V. 62 4884 2019.
ISSN: ISSN 0022-2623
PubMed: 31013090
DOI: 10.1021/ACS.JMEDCHEM.9B00193