Calcium in PDB 2wg8: Structure of Oryza Sativa (Rice) PLA2, Orthorhombic Crystal Form

All present enzymatic activity of Structure of Oryza Sativa (Rice) PLA2, Orthorhombic Crystal Form:
3.1.1.4;

The structure of Structure of Oryza Sativa (Rice) PLA2, Orthorhombic Crystal Form, PDB code: 2wg8 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)	30.00 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	169.094, 41.491, 53.124, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 24.5

The structure of Structure of Oryza Sativa (Rice) PLA2, Orthorhombic Crystal Form also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Structure of Oryza Sativa (Rice) PLA2, Orthorhombic Crystal Form (pdb code 2wg8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Oryza Sativa (Rice) PLA2, Orthorhombic Crystal Form, PDB code: 2wg8:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of Oryza Sativa (Rice) PLA2, Orthorhombic Crystal Form


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, Orthorhombic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:42.3 occ:1.00 O A:TYR42 2.2 27.2 1.0 O A:TYR37 2.4 24.4 1.0 O A:GLY39 2.4 25.2 1.0 O A:HOH2026 2.7 18.6 1.0 OD2 A:ASP62 2.8 29.5 1.0 OD1 A:ASP62 3.1 27.3 1.0 CG A:ASP62 3.3 25.5 1.0 C A:TYR42 3.3 26.6 1.0 O A:HOH2024 3.5 27.7 1.0 C A:TYR37 3.6 24.0 1.0 C A:GLY39 3.6 25.4 1.0 N A:GLY39 3.7 25.8 1.0 N A:TYR42 3.9 26.8 1.0 CA A:TYR42 4.1 26.4 1.0 CA A:GLY39 4.2 25.1 1.0 N A:SER43 4.3 26.7 1.0 CA A:SER43 4.4 26.8 1.0 C A:CYS38 4.4 25.1 1.0 N A:CYS38 4.5 24.5 1.0 CA A:TYR37 4.5 23.6 1.0 OG A:SER43 4.5 28.3 1.0 CA A:CYS38 4.5 24.9 1.0 O A:HOH2027 4.5 22.4 1.0 CB A:TYR42 4.5 26.3 1.0 CB A:SER43 4.6 27.0 1.0 N A:ILE40 4.7 25.3 1.0 N A:LEU41 4.7 26.0 1.0 CB A:ASP62 4.7 23.8 1.0 CD2 A:TYR42 4.9 24.4 1.0 O A:HOH2015 4.9 39.9 1.0 O A:HOH2018 5.0 38.8 1.0

Calcium binding site 2 out of 3 in the Structure of Oryza Sativa (Rice) PLA2, Orthorhombic Crystal Form


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, Orthorhombic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:28.2 occ:0.70 O B:TYR42 2.2 27.1 1.0 O B:TYR37 2.3 25.0 1.0 O B:GLY39 2.6 24.9 1.0 O B:HOH2037 2.6 21.1 1.0 OD1 B:ASP62 2.6 27.6 1.0 OD2 B:ASP62 2.7 29.6 1.0 CG B:ASP62 3.0 27.2 1.0 O B:HOH2038 3.3 27.1 1.0 C B:TYR42 3.4 26.7 1.0 C B:TYR37 3.4 24.1 1.0 C B:GLY39 3.7 25.4 1.0 N B:GLY39 3.7 24.8 1.0 N B:TYR42 4.1 27.8 1.0 CA B:TYR42 4.3 26.9 1.0 CA B:TYR37 4.3 23.8 1.0 CA B:GLY39 4.3 24.8 1.0 N B:SER43 4.3 26.4 1.0 C B:CYS38 4.3 24.6 1.0 OG B:SER43 4.3 28.2 1.0 CA B:SER43 4.3 26.1 1.0 N B:CYS38 4.4 24.3 1.0 CB B:SER43 4.4 26.4 1.0 CA B:CYS38 4.4 24.6 1.0 CB B:ASP62 4.5 24.8 1.0 CB B:TYR42 4.6 26.0 1.0 N B:ILE40 4.8 25.9 1.0 O B:HOH2022 4.8 47.3 1.0 CB B:TYR37 4.8 23.2 1.0 CD2 B:TYR42 4.9 22.8 1.0 O B:CYS58 4.9 24.6 1.0 N B:LEU41 5.0 27.3 1.0

Calcium binding site 3 out of 3 in the Structure of Oryza Sativa (Rice) PLA2, Orthorhombic Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Oryza Sativa (Rice) PLA2, Orthorhombic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:36.7 occ:1.00 O C:TYR42 2.3 23.4 1.0 O C:TYR37 2.4 23.8 1.0 O C:GLY39 2.4 25.1 1.0 OD2 C:ASP62 2.9 31.2 1.0 C C:TYR42 3.5 23.0 1.0 C C:TYR37 3.5 23.5 1.0 OD1 C:ASP62 3.5 33.2 1.0 N C:GLY39 3.6 24.7 1.0 C C:GLY39 3.6 25.4 1.0 CG C:ASP62 3.6 30.2 1.0 O C:HOH2032 3.7 28.3 1.0 CA C:GLY39 4.2 24.8 1.0 C C:CYS38 4.2 24.5 1.0 CA C:CYS38 4.3 24.5 1.0 N C:CYS38 4.4 23.8 1.0 N C:TYR42 4.4 23.9 1.0 N C:SER43 4.4 22.4 1.0 CA C:TYR42 4.5 23.6 1.0 CA C:SER43 4.5 21.9 1.0 CA C:TYR37 4.5 23.4 1.0 CB C:SER43 4.5 21.9 1.0 O C:HOH2015 4.5 39.6 1.0 OG C:SER43 4.6 22.7 1.0 N C:ILE40 4.7 25.6 1.0 CB C:TYR42 4.7 23.4 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