Calcium in PDB 4g5i: Crystal Structure of Porcine Pancreatic PLA2 in Complex with Dbp

All present enzymatic activity of Crystal Structure of Porcine Pancreatic PLA2 in Complex with Dbp:
3.1.1.4;

The structure of Crystal Structure of Porcine Pancreatic PLA2 in Complex with Dbp, PDB code: 4g5i was solved by G.K.Prasanth, C.D.Naveen, P.K.Mandal, P.Karthe, M.Haridas, C.Sadasivan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.94 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	68.860, 68.860, 70.180, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 24.3

The structure of Crystal Structure of Porcine Pancreatic PLA2 in Complex with Dbp also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Porcine Pancreatic PLA2 in Complex with Dbp (pdb code 4g5i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Porcine Pancreatic PLA2 in Complex with Dbp, PDB code: 4g5i:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Porcine Pancreatic PLA2 in Complex with Dbp


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 PLA2 in Complex with Dbp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:22.1 occ:1.00 O A:TYR28 2.3 28.9 1.0 O A:GLY30 2.3 37.7 1.0 OD1 A:ASP49 2.3 36.1 1.0 OD2 A:ASP49 2.3 31.4 1.0 O A:HOH301 2.4 25.4 1.0 O A:GLY32 2.5 38.2 1.0 O A:HOH335 2.6 28.3 1.0 CG A:ASP49 2.7 32.4 1.0 C A:TYR28 3.5 30.3 1.0 C A:GLY32 3.5 40.3 1.0 C A:GLY30 3.5 39.6 1.0 N A:GLY32 3.9 41.3 1.0 N A:GLY30 3.9 36.8 1.0 CA A:GLY32 4.1 41.4 1.0 CB A:ASP49 4.2 31.7 1.0 CA A:TYR28 4.3 30.5 1.0 C A:LEU31 4.3 43.0 1.0 O A:HOH352 4.3 21.0 1.0 CA A:GLY30 4.3 38.5 1.0 N A:CYS29 4.5 31.9 1.0 O A:HOH305 4.5 19.4 1.0 N A:LEU31 4.5 41.6 1.0 O A:HOH356 4.5 39.7 1.0 O A:HOH346 4.6 23.9 1.0 C A:CYS29 4.6 36.4 1.0 O A:HOH341 4.6 36.5 1.0 CA A:CYS29 4.6 33.9 1.0 N A:GLY33 4.6 40.2 1.0 CB A:TYR28 4.7 29.2 1.0 CA A:LEU31 4.7 43.5 1.0 O A:CYS45 4.8 29.1 1.0 CD1 A:TYR28 4.8 33.4 1.0 O A:LEU31 4.9 45.3 1.0 O A:HOH381 4.9 38.5 1.0 O11 A:DB7205 4.9 91.6 1.0 CA A:GLY33 5.0 38.9 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Porcine Pancreatic PLA2 in Complex with Dbp


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 PLA2 in Complex with Dbp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:16.6 occ:0.50 OE2 A:GLU92 2.3 25.6 1.0 OE1 A:GLU71 2.5 37.7 1.0 O A:SER72 2.6 21.9 1.0 CD A:GLU92 3.5 26.1 1.0 CD A:GLU71 3.7 34.3 1.0 C A:SER72 3.7 23.8 1.0 N A:SER72 3.9 25.8 1.0 CG A:GLU92 4.1 21.1 1.0 O A:HOH314 4.1 23.2 1.0 CA A:SER72 4.3 24.1 1.0 OE2 A:GLU71 4.3 38.5 1.0 CB A:SER72 4.4 25.4 1.0 OE1 A:GLU92 4.5 23.8 1.0 CG A:GLU71 4.6 30.3 1.0 C A:GLU71 4.8 26.5 1.0 N A:TYR73 4.9 23.1 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Porcine Pancreatic PLA2 in Complex with Dbp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Porcine Pancreatic PLA2 in Complex with Dbp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:66.5 occ:1.00 CL A:CL204 3.2 64.5 1.0 O A:HOH381 3.2 38.5 1.0 O A:PHE22 3.9 52.3 1.0 O A:HOH335 4.0 28.3 1.0 N A:GLY30 4.1 36.8 1.0 C A:PHE22 4.4 52.5 1.0 CE2 A:PHE5 4.5 31.1 1.0 OH A:TYR69 4.6 39.8 1.0 CA A:ASN23 4.6 52.4 1.0 C A:CYS29 4.7 36.4 1.0 N A:ASN23 4.7 53.0 1.0 O A:HOH352 4.8 21.0 1.0 CB A:PHE22 4.8 52.2 1.0 CA A:CYS29 4.8 33.9 1.0 OD1 A:ASN23 4.9 54.0 1.0 CB A:CYS29 5.0 34.9 1.0 CA A:GLY30 5.0 38.5 1.0

G.K.Prasanth, C.D.Naveen, P.K.Mandal, P.Karthe, M.Haridas, C.Sadasivan. Crystal Structure of Porcine Pancreatic PLA2 in Complex with Dbp To Be Published.