Calcium in PDB 5wzm: Crystal Structure of Human Secreted Phospholipase A2 Group Iie

All present enzymatic activity of Crystal Structure of Human Secreted Phospholipase A2 Group Iie:
3.1.1.4;

The structure of Crystal Structure of Human Secreted Phospholipase A2 Group Iie, PDB code: 5wzm was solved by S.Hou, J.Xu, T.Xu, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.82 / 2.00
Space group	P 21 2 2
Cell size a, b, c (Å), α, β, γ (°)	48.510, 60.460, 63.590, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22.6

The structure of Crystal Structure of Human Secreted Phospholipase A2 Group Iie also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Calcium atom in the Crystal Structure of Human Secreted Phospholipase A2 Group Iie (pdb code 5wzm). 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 Human Secreted Phospholipase A2 Group Iie, PDB code: 5wzm:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Human Secreted Phospholipase A2 Group Iie


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 Human Secreted Phospholipase A2 Group Iie within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca209 b:41.5 occ:0.57 O A:GLY24 2.3 19.9 1.0 O A:ASP22 2.4 26.7 1.0 O A:TYR111 2.5 36.6 1.0 O A:HOH317 2.6 24.9 1.0 OD1 A:ASP22 2.7 54.0 1.0 OD1 A:ASN113 2.8 50.0 1.0 CG A:ASP22 3.4 47.1 1.0 C A:ASP22 3.4 26.4 1.0 C A:TYR111 3.5 34.1 1.0 C A:GLY24 3.5 19.4 1.0 N A:TYR111 3.6 29.4 1.0 CB A:TYR111 3.7 30.2 1.0 OD2 A:ASP22 3.7 58.4 1.0 CA A:TYR111 3.8 29.2 1.0 CG A:ASN113 3.9 52.9 1.0 C A:TYR23 3.9 18.5 1.0 N A:GLY24 3.9 17.9 1.0 O A:TYR23 4.0 18.1 1.0 O A:HOH379 4.2 42.2 1.0 CA A:GLY24 4.2 18.3 1.0 N A:TYR23 4.3 20.7 1.0 CA A:ASP22 4.3 33.8 1.0 CB A:ASP22 4.4 39.3 1.0 CA A:TYR23 4.4 19.9 1.0 ND2 A:ASN113 4.4 56.8 1.0 C A:HIS110 4.5 29.1 1.0 N A:CYS25 4.6 18.8 1.0 N A:PRO112 4.7 38.3 1.0 CG A:TYR111 4.7 27.5 1.0 CA A:CYS25 4.7 19.3 1.0 CD2 A:TYR111 4.8 28.1 1.0 N A:ASN113 4.8 42.8 1.0 O A:CYS27 4.9 29.8 1.0 CA A:HIS110 5.0 26.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Human Secreted Phospholipase A2 Group Iie


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 Human Secreted Phospholipase A2 Group Iie within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca210 b:19.8 occ:0.54 O A:GLY28 2.2 38.6 1.0 O A:TYR26 2.2 16.6 1.0 O A:GLY30 2.3 28.5 1.0 OD2 A:ASP47 2.4 27.3 1.0 OD1 A:ASP47 2.6 27.2 1.0 CG A:ASP47 2.8 26.0 1.0 C A:TYR26 3.4 18.9 1.0 C A:GLY28 3.4 39.9 1.0 C A:GLY30 3.5 33.6 1.0 O A:HOH308 3.6 46.1 1.0 N A:GLY30 3.8 39.3 1.0 O A:HOH316 3.8 42.0 1.0 C A:ILE29 4.1 42.4 1.0 CA A:TYR26 4.1 19.2 1.0 N A:GLY28 4.2 29.9 1.0 CA A:GLY30 4.2 36.9 1.0 N A:ILE29 4.3 44.5 1.0 CA A:GLY28 4.3 36.2 1.0 CA A:ILE29 4.3 46.8 1.0 CB A:ASP47 4.4 22.2 1.0 N A:CYS27 4.4 20.8 1.0 C A:CYS27 4.4 27.5 1.0 N A:GLY31 4.5 34.9 1.0 CA A:CYS27 4.6 23.0 1.0 O A:HOH307 4.6 33.5 1.0 O A:ILE29 4.6 45.6 1.0 CB A:TYR26 4.6 18.8 1.0 O A:HOH302 4.6 32.8 1.0 CA A:GLY31 4.7 37.2 1.0 O A:CYS43 4.8 19.8 1.0 CD2 A:TYR26 5.0 21.9 1.0

S.Hou, T.Xu, J.Xu, L.Qu, Y.Xu, L.Chen, J.Liu. Structural Basis For Functional Selectivity and Ligand Recognition Revealed By Crystal Structures of Human Secreted Phospholipase A2 Group Iie Sci Rep V. 7 10815 2017.
ISSN: ESSN 2045-2322
PubMed: 28883454
DOI: 10.1038/S41598-017-11219-8