Calcium in PDB 2wg9: Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid

All present enzymatic activity of Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid:
3.1.1.4;

The structure of Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid, PDB code: 2wg9 was solved by J.E.Guy, U.Stahl, Y.Lindqvist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.05 / 2.00
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	109.159, 109.159, 41.394, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 22

The structure of Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid (pdb code 2wg9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid, PDB code: 2wg9:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:14.1 occ:0.70 O A:TYR42 2.2 16.8 1.0 O A:TYR37 2.3 10.3 1.0 O A:HOH2023 2.4 21.5 1.0 OD2 A:ASP62 2.4 17.1 1.0 O1 A:OCA301 2.5 18.1 1.0 O A:GLY39 2.5 15.8 1.0 OD1 A:ASP62 3.0 18.4 1.0 CG A:ASP62 3.0 15.6 1.0 C A:TYR42 3.4 16.5 1.0 C A:TYR37 3.5 10.6 1.0 C1 A:OCA301 3.5 20.5 1.0 N A:GLY39 3.6 13.4 1.0 C A:GLY39 3.6 15.6 1.0 O2 A:OCA301 4.0 21.8 1.0 N A:TYR42 4.2 17.7 1.0 CA A:GLY39 4.2 14.6 1.0 C A:CYS38 4.2 12.4 1.0 CA A:TYR42 4.3 16.5 1.0 N A:CYS38 4.3 11.2 1.0 CA A:CYS38 4.3 11.6 1.0 N A:SER43 4.3 16.4 1.0 CA A:TYR37 4.4 10.4 1.0 CA A:SER43 4.4 15.8 1.0 CB A:SER43 4.4 16.4 1.0 CB A:ASP62 4.5 13.7 1.0 OG A:SER43 4.6 17.5 1.0 CB A:TYR42 4.6 15.7 1.0 N A:ILE40 4.8 16.6 1.0 C2 A:OCA301 4.8 21.5 1.0 CD2 A:TYR42 4.9 13.7 1.0 CB A:TYR37 5.0 10.2 1.0

Calcium binding site 2 out of 2 in the Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:17.6 occ:0.70 O B:TYR37 2.3 11.3 1.0 O B:TYR42 2.3 16.7 1.0 O1 B:OCA301 2.4 18.7 1.0 OD2 B:ASP62 2.5 18.0 1.0 O B:GLY39 2.6 15.4 1.0 OD1 B:ASP62 3.0 17.3 1.0 CG B:ASP62 3.1 15.3 1.0 C1 B:OCA301 3.5 20.3 1.0 N B:GLY39 3.5 13.2 1.0 C B:TYR37 3.5 10.8 1.0 C B:TYR42 3.5 16.6 1.0 C B:GLY39 3.6 15.7 1.0 O2 B:OCA301 3.9 21.4 1.0 CA B:GLY39 4.1 14.5 1.0 C B:CYS38 4.2 12.2 1.0 N B:TYR42 4.3 17.5 1.0 CA B:CYS38 4.3 11.4 1.0 N B:CYS38 4.3 11.0 1.0 CA B:TYR42 4.4 16.4 1.0 N B:SER43 4.4 16.3 1.0 CA B:SER43 4.4 16.1 1.0 CB B:SER43 4.5 16.6 1.0 CA B:TYR37 4.5 10.8 1.0 OG B:SER43 4.5 18.9 1.0 CB B:ASP62 4.5 13.7 1.0 CB B:TYR42 4.7 15.8 1.0 O B:HOH2022 4.7 38.2 1.0 C2 B:OCA301 4.8 20.4 1.0 N B:ILE40 4.8 16.8 1.0 O B:HOH2047 4.9 37.1 1.0 CD2 B:TYR42 4.9 13.6 1.0

J.E.Guy, U.Stahl, Y.Lindqvist. Crystal Structure of A Class Xib Phospholipase A2 (PLA2): Rice (Oryza Sativa) Isoform-2 PLA2 and An Octanoate Complex. J.Biol.Chem. V. 284 19371 2009.
ISSN: ISSN 0021-9258
PubMed: 19457861
DOI: 10.1074/JBC.M109.008466