Calcium in PDB 4dbk: Crystal Structure of Porcine Pancreatic Phospholipase A2 Complexed with Berberine

All present enzymatic activity of Crystal Structure of Porcine Pancreatic Phospholipase A2 Complexed with Berberine:
3.1.1.4;

The structure of Crystal Structure of Porcine Pancreatic Phospholipase A2 Complexed with Berberine, PDB code: 4dbk was solved by C.D.Naveen, J.Abhilash, G.K.Prasanth, C.Sadasivan, M.Haridas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.90 / 2.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	68.600, 68.600, 70.080, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 25.3

The binding sites of Calcium atom in the Crystal Structure of Porcine Pancreatic Phospholipase A2 Complexed with Berberine (pdb code 4dbk). 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 Porcine Pancreatic Phospholipase A2 Complexed with Berberine, PDB code: 4dbk:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Porcine Pancreatic Phospholipase A2 Complexed with Berberine


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 Porcine Pancreatic Phospholipase A2 Complexed with Berberine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:29.8 occ:0.50 OE2 A:GLU71 2.0 28.5 1.0 O A:SER72 2.3 26.3 1.0 OE1 A:GLU92 2.5 25.6 1.0 CD A:GLU71 3.2 30.4 1.0 C A:SER72 3.3 26.0 1.0 N A:SER72 3.4 25.4 1.0 CD A:GLU92 3.5 24.7 1.0 CG A:GLU92 3.7 19.9 1.0 CA A:SER72 3.8 25.4 1.0 CG A:GLU71 4.0 25.7 1.0 OE1 A:GLU71 4.0 32.3 1.0 O A:HOH302 4.1 22.5 1.0 CB A:SER72 4.1 27.0 1.0 C A:GLU71 4.2 25.3 1.0 CA A:GLU71 4.5 24.7 1.0 N A:TYR73 4.5 27.0 1.0 OE2 A:GLU92 4.6 20.0 1.0 CB A:GLU71 4.7 25.1 1.0 OG A:SER72 4.8 28.2 1.0 CA A:TYR73 4.9 27.1 1.0 CB A:GLU92 5.0 23.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Porcine Pancreatic Phospholipase A2 Complexed with Berberine


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 Porcine Pancreatic Phospholipase A2 Complexed with Berberine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:36.2 occ:1.00 O A:HOH369 2.2 20.4 1.0 O A:TYR28 2.3 31.6 1.0 O A:GLY30 2.4 40.4 1.0 OD1 A:ASP49 2.5 31.6 1.0 OD2 A:ASP49 2.5 38.7 1.0 O A:GLY32 2.5 40.6 1.0 O A:HOH400 2.7 25.4 1.0 CG A:ASP49 2.8 33.7 1.0 C A:TYR28 3.5 32.4 1.0 C A:GLY30 3.6 41.9 1.0 C A:GLY32 3.7 41.9 1.0 N A:GLY32 4.0 44.0 1.0 N A:GLY30 4.1 38.8 1.0 CA A:TYR28 4.2 32.4 1.0 O A:HOH372 4.2 30.9 1.0 CA A:GLY32 4.3 43.3 1.0 C A:LEU31 4.3 44.8 1.0 CB A:ASP49 4.3 35.7 1.0 CA A:GLY30 4.5 40.3 1.0 N A:CYS29 4.5 33.7 1.0 O A:HOH307 4.5 24.5 1.0 N A:LEU31 4.6 43.4 1.0 CB A:TYR28 4.6 30.6 1.0 CA A:LEU31 4.7 44.6 1.0 CA A:CYS29 4.7 36.8 1.0 N A:GLY33 4.7 40.7 1.0 C A:CYS29 4.8 38.0 1.0 CD1 A:TYR28 4.8 35.6 1.0 O A:LEU31 4.8 47.3 1.0 O A:CYS45 4.8 31.7 1.0 C10 A:BER203 4.9 66.0 0.6 C7 A:BER203 4.9 68.1 0.6

C.D.Naveen, J.Abhilash, G.K.Prasanth, C.Sadasivan, M.Haridas. Crystal Structure of Porcine Pancreatic Phospholipase A2 Complexed with Berberine To Be Published.