Zinc in PDB 4ojx: Crystal Structure of Yeast Phosphodiesterase-1 in Complex with Gmp

All present enzymatic activity of Crystal Structure of Yeast Phosphodiesterase-1 in Complex with Gmp:
3.1.4.17;

The structure of Crystal Structure of Yeast Phosphodiesterase-1 in Complex with Gmp, PDB code: 4ojx 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)	34.34 / 1.31
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	73.674, 85.162, 130.836, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 17.9

The binding sites of Zinc atom in the Crystal Structure of Yeast Phosphodiesterase-1 in Complex with Gmp (pdb code 4ojx). 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 Yeast Phosphodiesterase-1 in Complex with Gmp, PDB code: 4ojx:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Yeast Phosphodiesterase-1 in Complex with Gmp


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 Yeast Phosphodiesterase-1 in Complex with Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:14.1 occ:1.00 O A:HOH501 2.0 14.3 1.0 NE2 A:HIS213 2.1 11.2 1.0 ND1 A:HIS130 2.2 11.1 1.0 NE2 A:HIS128 2.2 10.2 1.0 OP2 A:G402 2.2 15.9 1.0 OD2 A:ASP244 2.2 13.1 1.0 CE1 A:HIS130 3.1 11.3 1.0 CE1 A:HIS213 3.1 11.1 1.0 CD2 A:HIS128 3.1 10.3 1.0 CD2 A:HIS213 3.1 10.8 1.0 CE1 A:HIS128 3.2 9.9 1.0 CG A:HIS130 3.2 9.9 1.0 CG A:ASP244 3.3 11.0 1.0 P A:G402 3.4 17.8 1.0 ZN A:ZN404 3.4 12.3 1.0 CB A:HIS130 3.6 9.8 1.0 OP3 A:G402 3.6 20.8 1.0 CB A:ASP244 3.8 11.3 1.0 O5' A:G402 4.1 24.3 1.0 NE2 A:HIS133 4.2 9.8 1.0 ND1 A:HIS213 4.2 10.9 1.0 NE2 A:HIS130 4.3 12.0 1.0 CG A:HIS213 4.3 10.9 1.0 CG A:HIS128 4.3 9.3 1.0 ND1 A:HIS128 4.3 9.8 1.0 CD2 A:HIS130 4.3 11.6 1.0 CD2 A:HIS133 4.4 9.6 1.0 O A:HOH706 4.4 22.7 1.0 OD1 A:ASP244 4.4 10.6 1.0 OD1 A:ASP132 4.5 10.3 1.0 CE1 A:HIS294 4.6 12.1 1.0 OP1 A:G402 4.6 18.8 1.0 C5' A:G402 4.7 30.1 1.0 OD2 A:ASP132 4.9 11.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Yeast Phosphodiesterase-1 in Complex with Gmp


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 Yeast Phosphodiesterase-1 in Complex with Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:12.3 occ:1.00 O A:HOH501 2.0 14.3 1.0 NE2 A:HIS326 2.1 9.9 1.0 NE2 A:HIS133 2.1 9.8 1.0 OD2 A:ASP244 2.1 13.1 1.0 OD2 A:ASP132 2.1 11.0 1.0 OP3 A:G402 2.3 20.8 1.0 CD2 A:HIS133 3.0 9.6 1.0 CG A:ASP244 3.0 11.0 1.0 CE1 A:HIS326 3.0 10.9 1.0 CD2 A:HIS326 3.1 10.5 1.0 OD1 A:ASP244 3.2 10.6 1.0 CG A:ASP132 3.2 10.5 1.0 CE1 A:HIS133 3.2 9.3 1.0 ZN A:ZN403 3.4 14.1 1.0 OD1 A:ASP132 3.5 10.3 1.0 P A:G402 3.5 17.8 1.0 OP2 A:G402 3.8 15.9 1.0 O A:HOH507 3.9 11.3 1.0 ND1 A:HIS326 4.1 11.3 1.0 CE1 A:HIS128 4.1 9.9 1.0 CG A:HIS133 4.2 9.6 1.0 NE2 A:HIS128 4.2 10.2 1.0 CG A:HIS326 4.2 10.6 1.0 ND1 A:HIS133 4.3 9.3 1.0 O A:HOH515 4.4 14.3 1.0 O5' A:G402 4.4 24.3 1.0 CB A:ASP244 4.5 11.3 1.0 CB A:ASP132 4.6 10.5 1.0 OP1 A:G402 4.6 18.8 1.0 CE1 A:HIS294 4.7 12.1 1.0 O A:GLY13 4.9 11.9 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.