Calcium 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:

Zinc

(Zn)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium 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 Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca907 b:64.1 occ:1.00 OD1 A:ASP732 2.3 55.1 1.0 O A:HIS734 2.4 41.9 1.0 OD1 A:ASP736 2.6 54.6 1.0 OD1 A:ASN730 2.9 50.9 1.0 OD1 A:ASP728 3.0 40.0 1.0 CG A:ASP732 3.1 47.6 1.0 OD2 A:ASP732 3.1 54.0 1.0 C A:HIS734 3.3 42.2 1.0 O A:PHE735 3.5 43.7 1.0 C A:PHE735 3.6 42.5 1.0 CG A:ASP736 3.6 49.8 1.0 N A:ASP736 3.7 42.3 1.0 CG A:ASN730 3.8 47.5 1.0 CA A:ASP736 3.9 42.3 1.0 ND2 A:ASN730 4.0 45.4 1.0 CA A:HIS734 4.1 39.2 1.0 CG A:ASP728 4.1 37.2 1.0 N A:HIS734 4.2 42.1 1.0 N A:PHE735 4.2 42.5 1.0 CB A:HIS734 4.2 43.5 1.0 CA A:PHE735 4.3 43.1 1.0 CB A:ASP736 4.4 48.0 1.0 OD2 A:ASP736 4.4 48.2 1.0 CA A:ASP728 4.4 40.3 1.0 O A:PHE727 4.4 42.3 1.0 CB A:ASP732 4.5 38.5 1.0 N A:ASP732 4.7 38.9 1.0 CB A:ASP728 4.7 39.9 1.0

Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca 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 B:Ca906 b:57.5 occ:1.00 OD1 B:ASP732 2.4 46.4 1.0 OD1 B:ASP736 2.5 42.5 1.0 OD1 B:ASN730 2.6 38.1 1.0 O B:HIS734 2.6 47.8 1.0 OD1 B:ASP728 2.9 36.8 1.0 CG B:ASP732 3.1 45.0 1.0 OD2 B:ASP732 3.2 48.0 1.0 CG B:ASN730 3.5 34.3 1.0 C B:HIS734 3.6 42.2 1.0 O B:PHE735 3.6 41.4 1.0 CG B:ASP736 3.6 43.9 1.0 C B:PHE735 3.7 36.2 1.0 ND2 B:ASN730 3.7 35.1 1.0 N B:ASP736 3.8 34.9 1.0 CA B:ASP736 3.8 34.6 1.0 CG B:ASP728 4.1 41.2 1.0 CA B:HIS734 4.3 41.6 1.0 CB B:ASP736 4.3 40.9 1.0 N B:HIS734 4.3 39.6 1.0 CB B:HIS734 4.4 35.1 1.0 N B:PHE735 4.5 31.9 1.0 CA B:ASP728 4.5 35.1 1.0 OD2 B:ASP736 4.5 42.0 1.0 CB B:ASP732 4.5 37.0 1.0 CA B:PHE735 4.6 34.0 1.0 O B:PHE727 4.7 44.2 1.0 N B:ASP732 4.7 37.1 1.0 CB B:ASP728 4.8 30.2 1.0 CB B:ASN730 4.9 33.0 1.0 N B:ASN730 4.9 33.0 1.0 OD2 B:ASP728 5.0 42.1 1.0 CD B:PRO737 5.0 41.2 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.