Zinc in PDB 5gz5: Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp

The structure of Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp, PDB code: 5gz5 was solved by C.C.Lin, B.S.Wu, W.G.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.88 / 2.09
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	171.207, 65.612, 88.675, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.9

The structure of Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp (pdb code 5gz5). 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 Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp, PDB code: 5gz5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp


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 Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1013 b:22.4 occ:1.00 O1P A:AMP1016 1.9 46.8 1.0 NE2 A:HIS309 2.0 28.0 1.0 OD1 A:ASP305 2.0 20.8 1.0 NE2 A:HIS462 2.0 17.4 1.0 OD2 A:ASP305 2.6 24.1 1.0 CG A:ASP305 2.6 25.4 1.0 P A:AMP1016 2.7 47.4 1.0 O3P A:AMP1016 2.8 50.9 1.0 CE1 A:HIS309 2.9 23.7 1.0 CD2 A:HIS309 3.0 22.7 1.0 CD2 A:HIS462 3.0 18.1 1.0 CE1 A:HIS462 3.1 16.4 1.0 O2P A:AMP1016 3.7 46.6 1.0 O A:HOH1102 3.9 28.4 1.0 CE1 A:HIS353 4.0 16.6 1.0 ND1 A:HIS309 4.1 24.1 1.0 O5' A:AMP1016 4.1 43.1 1.0 CG A:HIS309 4.1 24.4 1.0 CG A:HIS462 4.1 21.4 1.0 ND1 A:HIS462 4.2 23.8 1.0 CB A:ASP305 4.2 22.3 1.0 CE A:MET355 4.2 19.3 1.0 OG1 A:THR185 4.2 23.8 1.0 NE2 A:HIS353 4.2 23.4 1.0 O A:HOH1103 4.3 31.3 1.0 C5' A:AMP1016 4.4 41.2 1.0 ZN A:ZN1014 4.4 20.2 1.0 OD1 A:ASP147 4.5 20.4 1.0 O A:HOH1690 4.6 33.5 1.0 O A:ASP305 4.9 24.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp


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 Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1014 b:20.2 occ:1.00 OG1 A:THR185 1.8 23.8 1.0 OD2 A:ASP352 1.9 21.4 1.0 NE2 A:HIS353 2.0 23.4 1.0 OD1 A:ASP147 2.0 20.4 1.0 CG A:ASP147 2.6 25.5 1.0 OD2 A:ASP147 2.7 23.6 1.0 CG A:ASP352 2.8 21.7 1.0 CD2 A:HIS353 2.9 17.3 1.0 CB A:THR185 2.9 20.9 1.0 CE1 A:HIS353 3.0 16.6 1.0 OD1 A:ASP352 3.1 22.4 1.0 CA A:THR185 3.4 21.9 1.0 O3P A:AMP1016 3.4 50.9 1.0 CG2 A:THR185 3.4 17.3 1.0 OD1 A:ASP305 3.9 20.8 1.0 N A:THR185 4.0 20.7 1.0 CG A:HIS353 4.0 18.9 1.0 ND1 A:HIS353 4.0 18.3 1.0 CB A:ASP147 4.0 24.1 1.0 CB A:ASP352 4.2 15.0 1.0 CE1 A:HIS462 4.2 16.4 1.0 N A:GLY148 4.2 17.9 1.0 CG A:ASP305 4.3 25.4 1.0 ZN A:ZN1013 4.4 22.4 1.0 NE2 A:HIS462 4.4 17.4 1.0 CA A:ASP147 4.5 24.7 1.0 NE2 A:HIS189 4.5 19.8 1.0 P A:AMP1016 4.6 47.4 1.0 C5' A:AMP1016 4.6 41.2 1.0 C A:ASP147 4.7 19.9 1.0 C A:THR185 4.7 20.2 1.0 C A:LYS184 4.7 19.2 1.0 CB A:ASP305 4.8 22.3 1.0 CD2 A:HIS189 4.8 16.9 1.0 O5' A:AMP1016 4.8 43.1 1.0 O1P A:AMP1016 4.9 46.8 1.0 CA A:GLY148 4.9 19.3 1.0 OD2 A:ASP305 4.9 24.1 1.0

C.C.Lin, B.S.Wu, W.G.Wu. Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp To Be Published.