Zinc in PDB 7cba: Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Isorhamnetin and Citrate

The structure of Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Isorhamnetin and Citrate, PDB code: 7cba was solved by I.J.Lin, C.C.Lin, W.G.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.30 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.186, 168.619, 93.715, 90, 105.93, 90
R / Rfree (%)	18.7 / 24.2

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

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Isorhamnetin and Citrate (pdb code 7cba). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Isorhamnetin and Citrate, PDB code: 7cba:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Isorhamnetin and Citrate


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 Isorhamnetin and Citrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn905 b:37.3 occ:1.00 NE2 A:HIS462 2.1 39.0 1.0 NE2 A:HIS309 2.1 40.6 1.0 O7 A:CIT909 2.2 54.2 1.0 OD2 A:ASP305 2.5 40.8 1.0 O5 A:CIT909 2.7 59.2 1.0 OD1 A:ASP305 2.7 36.8 1.0 O2 A:CIT909 2.8 54.6 1.0 CD2 A:HIS309 2.9 46.5 1.0 CG A:ASP305 2.9 37.5 1.0 CE1 A:HIS462 3.0 39.5 1.0 CD2 A:HIS462 3.1 37.9 1.0 C3 A:CIT909 3.2 53.9 1.0 CE1 A:HIS309 3.3 44.3 1.0 C6 A:CIT909 3.3 60.1 1.0 C1 A:CIT909 3.4 57.3 1.0 C2 A:CIT909 3.9 52.4 1.0 O3 A:CIT909 3.9 61.8 1.0 ND1 A:HIS462 4.1 42.5 1.0 CG A:HIS309 4.1 47.8 1.0 O1 A:CIT909 4.2 62.9 1.0 CG A:HIS462 4.2 38.8 1.0 ND1 A:HIS309 4.3 47.3 1.0 NE2 A:HIS353 4.4 42.3 1.0 CE1 A:HIS353 4.4 37.6 1.0 CB A:ASP305 4.5 41.9 1.0 O6 A:CIT909 4.5 67.7 1.0 C4 A:CIT909 4.5 56.1 1.0 ZN A:ZN906 4.6 51.1 1.0 O24 A:IRH908 4.7 53.0 1.0 OD1 A:ASP147 4.7 43.3 1.0 C5 A:CIT909 4.7 59.0 1.0 OG1 A:THR185 4.8 32.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Isorhamnetin and Citrate


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 Isorhamnetin and Citrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn906 b:51.1 occ:1.00 OG1 A:THR185 1.7 32.8 1.0 NE2 A:HIS353 1.9 42.3 1.0 OD1 A:ASP147 2.0 43.3 1.0 OD2 A:ASP352 2.1 39.8 1.0 CG A:ASP147 2.5 37.5 1.0 OD2 A:ASP147 2.6 38.3 1.0 CD2 A:HIS353 2.7 37.0 1.0 CE1 A:HIS353 2.7 37.6 1.0 CG A:ASP352 2.8 38.1 1.0 O2 A:CIT909 2.8 54.6 1.0 OD1 A:ASP352 3.0 37.3 1.0 CB A:THR185 3.0 40.4 1.0 CA A:THR185 3.5 39.4 1.0 ND1 A:HIS353 3.7 39.4 1.0 CG A:HIS353 3.7 37.2 1.0 C1 A:CIT909 3.9 57.3 1.0 CG2 A:THR185 3.9 44.8 1.0 N A:THR185 3.9 38.0 1.0 CB A:ASP147 4.0 34.3 1.0 N A:GLY148 4.1 37.2 1.0 CB A:ASP352 4.2 36.6 1.0 O1 A:CIT909 4.2 62.9 1.0 CE1 A:HIS462 4.3 39.5 1.0 NE2 A:HIS462 4.3 39.0 1.0 OD1 A:ASP305 4.3 36.8 1.0 CG A:ASP305 4.4 37.5 1.0 CA A:ASP147 4.4 36.5 1.0 OD2 A:ASP305 4.5 40.8 1.0 C A:ASP147 4.6 37.2 1.0 C A:LYS184 4.6 39.2 1.0 ZN A:ZN905 4.6 37.3 1.0 CA A:GLY148 4.8 38.9 1.0 CE1 A:HIS189 4.8 35.2 1.0 C A:THR185 4.9 36.6 1.0 CB A:ASP305 4.9 41.9 1.0 ND1 A:HIS189 5.0 33.7 1.0 ND1 A:HIS462 5.0 42.5 1.0 C2 A:CIT909 5.0 52.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Isorhamnetin and Citrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Isorhamnetin and Citrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn904 b:42.8 occ:1.00 OD2 B:ASP305 2.3 44.5 1.0 NE2 B:HIS309 2.3 49.6 1.0 NE2 B:HIS462 2.3 37.2 1.0 O6 B:CIT908 2.3 47.5 1.0 O7 B:CIT908 2.4 58.9 1.0 OD1 B:ASP305 2.5 41.2 1.0 O2 B:CIT908 2.6 58.2 1.0 CG B:ASP305 2.7 42.4 1.0 CD2 B:HIS309 2.9 47.2 1.0 CE1 B:HIS462 3.1 41.3 1.0 C6 B:CIT908 3.2 49.8 1.0 C3 B:CIT908 3.3 57.8 1.0 CD2 B:HIS462 3.5 42.2 1.0 C1 B:CIT908 3.5 62.0 1.0 CE1 B:HIS309 3.5 46.1 1.0 C2 B:CIT908 4.0 59.1 1.0 O3 B:CIT908 4.1 54.7 1.0 CG B:HIS309 4.1 47.8 1.0 CB B:ASP305 4.2 39.8 1.0 ND1 B:HIS462 4.3 41.3 1.0 NE2 B:HIS353 4.3 41.6 1.0 OG1 B:THR185 4.3 34.3 1.0 CE1 B:HIS353 4.4 40.1 1.0 O1 B:CIT908 4.4 54.9 1.0 O5 B:CIT908 4.4 50.5 1.0 ND1 B:HIS309 4.4 49.8 1.0 CG B:HIS462 4.5 44.3 1.0 C4 B:CIT908 4.6 58.8 1.0 ZN B:ZN905 4.6 47.8 1.0 OD1 B:ASP147 4.7 42.4 1.0 O24 B:IRH907 4.7 59.3 1.0 O B:ASP305 4.7 43.6 1.0 C5 B:CIT908 4.7 60.4 1.0 CE B:MET355 4.9 41.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Isorhamnetin and Citrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Isorhamnetin and Citrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn905 b:47.8 occ:1.00 OG1 B:THR185 1.8 34.3 1.0 OD2 B:ASP352 1.9 36.7 1.0 OD1 B:ASP147 2.0 42.4 1.0 NE2 B:HIS353 2.0 41.6 1.0 CG B:ASP147 2.6 34.3 1.0 OD2 B:ASP147 2.6 32.3 1.0 CG B:ASP352 2.7 37.3 1.0 CD2 B:HIS353 2.8 37.8 1.0 CE1 B:HIS353 2.9 40.1 1.0 OD1 B:ASP352 2.9 37.3 1.0 CB B:THR185 3.0 39.0 1.0 CA B:THR185 3.4 38.9 1.0 O2 B:CIT908 3.4 58.2 1.0 CG2 B:THR185 3.6 42.3 1.0 CG B:HIS353 3.8 37.5 1.0 ND1 B:HIS353 3.8 40.1 1.0 CB B:ASP147 4.0 32.7 1.0 N B:THR185 4.0 37.9 1.0 CB B:ASP352 4.1 35.8 1.0 N B:GLY148 4.2 39.0 1.0 OD2 B:ASP305 4.2 44.5 1.0 CG B:ASP305 4.3 42.4 1.0 OD1 B:ASP305 4.4 41.2 1.0 C1 B:CIT908 4.4 62.0 1.0 CE1 B:HIS462 4.4 41.3 1.0 CA B:ASP147 4.4 38.3 1.0 CE1 B:HIS189 4.5 35.6 1.0 NE2 B:HIS462 4.5 37.2 1.0 ZN B:ZN904 4.6 42.8 1.0 C B:LYS184 4.7 38.6 1.0 C B:ASP147 4.7 39.2 1.0 C B:THR185 4.7 35.8 1.0 ND1 B:HIS189 4.8 34.3 1.0 CB B:ASP305 4.8 39.8 1.0 CA B:GLY148 4.9 39.0 1.0 O1 B:CIT908 4.9 54.9 1.0

I.J.Lin, C.C.Lin, W.G.Wu. Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Isorhamnetin and Citrate To Be Published.