Calcium in PDB 6g5j: Secreted Phospholipase A2 Type X in Complex with Ligand

All present enzymatic activity of Secreted Phospholipase A2 Type X in Complex with Ligand:
3.1.1.4;

The structure of Secreted Phospholipase A2 Type X in Complex with Ligand, PDB code: 6g5j was solved by J.Sandmark, L.Oster, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.76 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	27.962, 85.501, 103.079, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.8

The structure of Secreted Phospholipase A2 Type X in Complex with Ligand also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

The binding sites of Calcium atom in the Secreted Phospholipase A2 Type X in Complex with Ligand (pdb code 6g5j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Secreted Phospholipase A2 Type X in Complex with Ligand, PDB code: 6g5j:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Secreted Phospholipase A2 Type X in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Secreted Phospholipase A2 Type X in Complex with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:19.4 occ:1.00 O6 A:EM8202 2.3 22.8 0.5 O6 A:EM8202 2.3 23.4 0.5 O A:GLY28 2.3 21.4 1.0 O A:PHE26 2.3 18.6 1.0 O A:GLY30 2.4 22.8 1.0 O23 A:EM8202 2.4 16.8 0.5 O23 A:EM8202 2.5 17.3 0.5 OD2 A:ASP47 2.5 18.5 1.0 OD1 A:ASP47 2.5 18.7 1.0 CG A:ASP47 2.9 18.4 1.0 C22 A:EM8202 3.4 17.6 0.5 C22 A:EM8202 3.5 16.7 0.5 C A:GLY30 3.5 23.4 1.0 C4 A:EM8202 3.5 22.6 0.5 C A:GLY28 3.5 20.8 1.0 C4 A:EM8202 3.5 23.3 0.5 C A:PHE26 3.5 18.8 1.0 N24 A:EM8202 3.7 16.8 0.5 N A:GLY28 3.8 18.7 1.0 N24 A:EM8202 3.9 15.9 0.5 N A:GLY30 4.1 22.1 1.0 CA A:GLY30 4.2 22.7 1.0 O5 A:EM8202 4.2 22.8 0.5 O5 A:EM8202 4.2 23.6 0.5 O A:HOH356 4.3 34.4 1.0 CA A:GLY28 4.3 20.1 1.0 CA A:PHE26 4.4 18.9 1.0 CB A:ASP47 4.4 17.9 1.0 C A:LEU29 4.4 23.6 1.0 C3 A:EM8202 4.4 21.7 0.5 C3 A:EM8202 4.4 22.5 0.5 N A:CYS27 4.5 18.5 1.0 C A:CYS27 4.5 18.9 1.0 CA A:CYS27 4.5 18.8 1.0 N A:LEU29 4.5 22.9 1.0 N A:GLY31 4.6 23.9 1.0 C1 A:DMS205 4.6 29.8 1.0 C12 A:EM8202 4.7 18.8 0.5 O A:HOH314 4.7 23.7 1.0 CA A:LEU29 4.7 24.2 1.0 C12 A:EM8202 4.7 19.7 0.5 C21 A:EM8202 4.8 16.6 0.5 C21 A:EM8202 4.8 17.6 0.5 CA A:GLY31 4.8 24.6 1.0 CB A:PHE26 4.8 19.3 1.0 C7 A:EM8202 4.9 19.8 0.5 C11 A:EM8202 4.9 18.2 0.5 O A:CYS43 4.9 17.1 1.0 O A:LEU29 4.9 24.2 1.0 C7 A:EM8202 5.0 20.6 0.5

Calcium binding site 2 out of 2 in the Secreted Phospholipase A2 Type X in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Secreted Phospholipase A2 Type X in Complex with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:17.9 occ:1.00 O6 B:EM8202 2.2 23.4 1.0 O B:PHE26 2.3 19.3 1.0 O B:GLY28 2.3 22.1 1.0 O B:GLY30 2.4 20.5 1.0 OD2 B:ASP47 2.4 16.8 1.0 O23 B:EM8202 2.5 16.7 1.0 OD1 B:ASP47 2.5 17.2 1.0 CG B:ASP47 2.8 17.8 1.0 C22 B:EM8202 3.5 17.2 1.0 C B:GLY30 3.5 22.4 1.0 C4 B:EM8202 3.5 22.2 1.0 C B:PHE26 3.5 19.6 1.0 C B:GLY28 3.6 23.0 1.0 N24 B:EM8202 3.7 15.7 1.0 N B:GLY28 3.9 20.4 1.0 N B:GLY30 3.9 22.8 1.0 O5 B:EM8202 4.1 22.4 1.0 CA B:GLY30 4.2 22.7 1.0 C B:LEU29 4.3 23.7 1.0 CA B:PHE26 4.3 19.0 1.0 CB B:ASP47 4.4 16.9 1.0 CA B:GLY28 4.4 21.7 1.0 N B:CYS27 4.5 19.2 1.0 C3 B:EM8202 4.5 20.6 1.0 CA B:CYS27 4.5 20.2 1.0 C B:CYS27 4.5 20.1 1.0 N B:LEU29 4.6 24.2 1.0 N B:GLY31 4.6 22.6 1.0 CA B:LEU29 4.7 24.4 0.5 O B:LEU29 4.7 22.9 1.0 O B:HOH325 4.7 22.0 1.0 CA B:LEU29 4.8 24.7 0.5 C12 B:EM8202 4.8 18.5 1.0 C21 B:EM8202 4.8 17.3 1.0 CB B:PHE26 4.8 19.4 1.0 CA B:GLY31 4.9 22.4 1.0 C7 B:EM8202 5.0 19.3 1.0

F.Giordanetto, L.Knerr, P.Nordberg, D.Pettersen, N.Selmi, H.G.Beisel, H.De La Motte, A.Mansson, M.Dahlstrom, J.Broddefalk, G.Saarinen, F.Klingegard, E.Hurt-Camejo, B.Rosengren, J.Wikstrom, M.Wagberg, J.Brengdahl, M.Rohman, J.Sandmark, T.Akerud, R.G.Roth, F.Jansen, M.Ahlqvist. Design of Selective SPLA2-X Inhibitor (-)-2-{2-[Carbamoyl-6-(Trifluoromethoxy) -1H-Indol-1-Yl]Pyridine-2-Yl}Propanoic Acid. Acs Med Chem Lett V. 9 600 2018.
ISSN: ISSN 1948-5875
PubMed: 30034586
DOI: 10.1021/ACSMEDCHEMLETT.7B00507