Zinc in PDB 4ojv: Crystal Structure of Unliganded Yeast PDE1

All present enzymatic activity of Crystal Structure of Unliganded Yeast PDE1:
3.1.4.17;

The structure of Crystal Structure of Unliganded Yeast PDE1, PDB code: 4ojv was solved by Y.Tian, W.Cui, M.Huang, H.Robinson, Y.Wan, Y.Wang, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.81 / 1.31
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	73.478, 85.151, 130.565, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 18.4

The binding sites of Zinc atom in the Crystal Structure of Unliganded Yeast PDE1 (pdb code 4ojv). 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 Unliganded Yeast PDE1, PDB code: 4ojv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Unliganded Yeast PDE1


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 Unliganded Yeast PDE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:14.3 occ:1.00 O A:HOH501 1.9 13.3 1.0 NE2 A:HIS213 2.1 11.9 1.0 NE2 A:HIS128 2.2 11.6 1.0 ND1 A:HIS130 2.2 11.3 1.0 OD2 A:ASP244 2.2 12.9 1.0 O3 A:SO4401 2.2 16.9 1.0 CE1 A:HIS213 3.1 12.2 1.0 CE1 A:HIS130 3.1 11.5 1.0 CD2 A:HIS128 3.1 11.0 1.0 CD2 A:HIS213 3.1 11.1 1.0 CE1 A:HIS128 3.2 11.1 1.0 CG A:HIS130 3.3 10.3 1.0 S A:SO4401 3.3 17.2 1.0 ZN A:ZN404 3.3 12.8 1.0 CG A:ASP244 3.3 10.5 1.0 O4 A:SO4401 3.6 19.2 1.0 CB A:HIS130 3.6 9.6 1.0 O1 A:SO4401 3.8 18.0 1.0 CB A:ASP244 3.9 11.1 1.0 NE2 A:HIS133 4.1 10.7 1.0 ND1 A:HIS213 4.2 11.2 1.0 CG A:HIS213 4.3 11.6 1.0 NE2 A:HIS130 4.3 11.7 1.0 CG A:HIS128 4.3 10.3 1.0 CD2 A:HIS133 4.3 9.9 1.0 ND1 A:HIS128 4.3 10.8 1.0 CD2 A:HIS130 4.4 11.2 1.0 OD1 A:ASP244 4.4 11.0 1.0 O A:HOH701 4.4 25.7 1.0 OD1 A:ASP132 4.4 11.1 1.0 CE1 A:HIS294 4.6 11.4 1.0 O2 A:SO4401 4.6 18.0 1.0 OD2 A:ASP132 4.8 11.4 1.0 NE2 A:HIS294 5.0 12.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Unliganded Yeast PDE1


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 Unliganded Yeast PDE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:12.8 occ:1.00 O A:HOH501 2.0 13.3 1.0 OD2 A:ASP244 2.1 12.9 1.0 NE2 A:HIS326 2.1 11.3 1.0 NE2 A:HIS133 2.1 10.7 1.0 OD2 A:ASP132 2.1 11.4 1.0 O4 A:SO4401 2.3 19.2 1.0 CG A:ASP244 3.0 10.5 1.0 CD2 A:HIS133 3.0 9.9 1.0 CE1 A:HIS326 3.0 11.2 1.0 CD2 A:HIS326 3.1 11.2 1.0 OD1 A:ASP244 3.2 11.0 1.0 CG A:ASP132 3.2 10.6 1.0 CE1 A:HIS133 3.2 10.0 1.0 ZN A:ZN403 3.3 14.3 1.0 S A:SO4401 3.4 17.2 1.0 OD1 A:ASP132 3.5 11.1 1.0 O3 A:SO4401 3.7 16.9 1.0 O1 A:SO4401 3.9 18.0 1.0 O A:HOH510 3.9 11.8 1.0 NE2 A:HIS128 4.1 11.6 1.0 ND1 A:HIS326 4.1 12.0 1.0 CE1 A:HIS128 4.2 11.1 1.0 CG A:HIS133 4.2 9.2 1.0 CG A:HIS326 4.2 10.9 1.0 ND1 A:HIS133 4.3 10.1 1.0 O A:HOH518 4.4 15.6 1.0 CB A:ASP244 4.4 11.1 1.0 CE1 A:HIS294 4.6 11.4 1.0 CB A:ASP132 4.6 11.2 1.0 O2 A:SO4401 4.7 18.0 1.0 O A:GLY13 4.9 12.1 1.0

Y.Tian, W.Cui, M.Huang, H.Robinson, Y.Wan, Y.Wang, H.Ke. Dual Specificity and Novel Structural Folding of Yeast Phosphodiesterase-1 For Hydrolysis of Second Messengers Camp and Cgmp To Be Published.