Calcium in PDB 1gp7: Acidic Phospholipase A2 From Venom of Ophiophagus Hannah

All present enzymatic activity of Acidic Phospholipase A2 From Venom of Ophiophagus Hannah:
3.1.1.4;

The structure of Acidic Phospholipase A2 From Venom of Ophiophagus Hannah, PDB code: 1gp7 was solved by H.Zhang, Z.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8 / 2.6
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.920, 62.940, 57.160, 90.00, 100.93, 90.00
R / Rfree (%)	20.5 / 23.3

The binding sites of Calcium atom in the Acidic Phospholipase A2 From Venom of Ophiophagus Hannah (pdb code 1gp7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Acidic Phospholipase A2 From Venom of Ophiophagus Hannah, PDB code: 1gp7:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Acidic Phospholipase A2 From Venom of Ophiophagus Hannah


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Acidic Phospholipase A2 From Venom of Ophiophagus Hannah within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1125 b:23.6 occ:1.00 O A:GLY32 2.4 25.6 1.0 O A:TYR28 2.6 22.1 1.0 OD1 A:ASP49 2.7 23.2 1.0 OD2 A:ASP49 2.8 23.9 1.0 O A:GLY30 2.8 31.1 1.0 O A:HOH2008 2.8 31.3 1.0 CG A:ASP49 3.0 22.8 1.0 C A:GLY32 3.4 25.8 1.0 C A:TYR28 3.7 21.6 1.0 C A:GLY30 3.8 27.3 1.0 N A:GLY32 3.9 25.0 1.0 N A:GLY30 4.0 28.8 1.0 CA A:GLY32 4.1 24.4 1.0 OD1 B:ASP66 4.1 30.8 1.0 C A:ALA31 4.2 24.6 1.0 N A:GLY33 4.4 25.7 1.0 CA A:TYR28 4.4 20.0 1.0 CB A:ASP49 4.5 22.2 1.0 O A:HOH2012 4.5 31.1 1.0 O A:HOH2013 4.5 22.7 1.0 O A:ALA31 4.5 23.8 1.0 CA A:GLY33 4.6 24.7 1.0 CA A:GLY30 4.6 28.3 1.0 N A:ALA31 4.6 26.6 1.0 O A:HOH2014 4.7 22.1 1.0 CA A:ALA31 4.7 24.7 1.0 N A:CYS29 4.8 22.8 1.0 CB A:TYR28 4.9 20.9 1.0 C A:CYS29 4.9 27.4 1.0 CA A:CYS29 5.0 23.8 1.0

Calcium binding site 2 out of 3 in the Acidic Phospholipase A2 From Venom of Ophiophagus Hannah


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Acidic Phospholipase A2 From Venom of Ophiophagus Hannah within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1125 b:26.5 occ:1.00 O B:TYR28 2.5 30.1 1.0 O B:GLY32 2.7 29.3 1.0 OD2 B:ASP49 2.7 22.9 1.0 O B:GLY30 2.7 30.3 1.0 OD1 B:ASP49 2.8 19.6 1.0 CG B:ASP49 3.1 22.4 1.0 C B:GLY32 3.7 28.6 1.0 C B:GLY30 3.7 28.8 1.0 C B:TYR28 3.7 28.0 1.0 N B:GLY30 3.9 28.7 1.0 N B:GLY32 4.0 26.3 1.0 OD1 A:ASP66 4.1 26.1 1.0 C B:ALA31 4.3 27.3 1.0 CA B:GLY32 4.3 27.1 1.0 CA B:GLY30 4.4 28.8 1.0 CA B:TYR28 4.4 27.4 1.0 CB B:ASP49 4.6 23.0 1.0 N B:ALA31 4.6 28.2 1.0 O B:HOH2012 4.6 26.4 1.0 N B:GLY33 4.7 28.5 1.0 O B:ALA31 4.7 27.6 1.0 N B:CYS29 4.7 27.8 1.0 CA B:ALA31 4.7 27.9 1.0 C B:CYS29 4.8 28.3 1.0 CA B:CYS29 4.8 27.6 1.0 CA B:GLY33 4.9 27.0 1.0 CB B:TYR28 4.9 27.5 1.0

Calcium binding site 3 out of 3 in the Acidic Phospholipase A2 From Venom of Ophiophagus Hannah


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Acidic Phospholipase A2 From Venom of Ophiophagus Hannah within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1125 b:36.2 occ:1.00 O C:GLY32 2.7 46.0 1.0 O C:TYR28 2.7 39.8 1.0 O C:GLY30 2.7 41.1 1.0 OD2 C:ASP49 2.7 40.2 1.0 OD1 C:ASP49 2.8 38.0 1.0 CG C:ASP49 3.1 38.8 1.0 C C:GLY32 3.6 46.1 1.0 C C:GLY30 3.7 42.3 1.0 C C:TYR28 3.9 40.0 1.0 N C:GLY32 3.9 44.4 1.0 N C:GLY30 4.0 40.0 1.0 CA C:GLY32 4.2 45.4 1.0 C C:ALA31 4.2 44.6 1.0 CA C:GLY30 4.5 41.0 1.0 CB C:ASP49 4.6 39.5 1.0 N C:ALA31 4.6 43.1 1.0 CA C:TYR28 4.6 41.3 1.0 N C:GLY33 4.6 46.2 1.0 O C:ALA31 4.7 44.9 1.0 CA C:ALA31 4.7 44.8 1.0 CA C:GLY33 4.8 46.3 1.0 N C:CYS29 4.9 39.1 1.0 C C:CYS29 4.9 39.5 1.0 CA C:CYS29 5.0 38.8 1.0

H.Zhang, S.Xu, Q.Wang, S.Song, Y.Shu, Z.Lin. Structure of A Cardiotoxic Phospholipase A(2) From Ophiophagus Hannah with the "Pancreatic Loop" J.Struct.Biol. V. 138 207 2002.
ISSN: ISSN 1047-8477
PubMed: 12217659
DOI: 10.1016/S1047-8477(02)00022-9