Calcium in PDB 1dcy: Crystal Structure of Human S-PLA2 in Complex with Indole 3 Active Site Inhibitor

All present enzymatic activity of Crystal Structure of Human S-PLA2 in Complex with Indole 3 Active Site Inhibitor:
3.1.1.4;

The structure of Crystal Structure of Human S-PLA2 in Complex with Indole 3 Active Site Inhibitor, PDB code: 1dcy was solved by N.Y.Chirgadze, R.W.Schevitz, J.-P.Wery, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.70
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	76.254, 76.254, 91.465, 90.00, 90.00, 120.00
R / Rfree (%)	21.8 / 26.9

The binding sites of Calcium atom in the Crystal Structure of Human S-PLA2 in Complex with Indole 3 Active Site Inhibitor (pdb code 1dcy). 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 S-PLA2 in Complex with Indole 3 Active Site Inhibitor, PDB code: 1dcy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Human S-PLA2 in Complex with Indole 3 Active Site Inhibitor


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 S-PLA2 in Complex with Indole 3 Active Site Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca198 b:31.4 occ:1.00 O A:HIS27 2.4 21.3 1.0 O A:GLY29 2.4 15.4 1.0 O A:GLY31 2.5 15.9 1.0 OD1 A:ASP48 2.6 29.8 1.0 OD2 A:ASP48 2.6 27.2 1.0 O14 A:I3N1201 2.6 22.2 1.0 CG A:ASP48 2.9 25.9 1.0 C A:HIS27 3.6 19.0 1.0 C13 A:I3N1201 3.6 22.0 1.0 C A:GLY31 3.7 21.3 1.0 C A:GLY29 3.7 16.1 1.0 N A:GLY31 3.8 16.5 1.0 O15 A:I3N1201 3.9 26.2 1.0 N A:GLY29 4.1 15.1 1.0 CA A:GLY31 4.3 18.0 1.0 C A:VAL30 4.3 16.4 1.0 C A:CYS28 4.4 15.2 1.0 CB A:ASP48 4.4 23.6 1.0 CA A:HIS27 4.4 20.1 1.0 CA A:CYS28 4.5 15.2 1.0 N A:CYS28 4.5 15.2 1.0 CA A:GLY29 4.5 14.1 1.0 CA A:VAL30 4.5 15.6 1.0 N A:VAL30 4.6 16.7 1.0 O A:CYS44 4.7 19.9 1.0 N A:GLY32 4.7 22.5 1.0 CB A:HIS27 4.8 22.2 1.0 C4 A:I3N1201 4.9 17.5 1.0 CA A:GLY32 5.0 24.6 1.0 O A:VAL30 5.0 21.6 1.0 C12 A:I3N1201 5.0 21.5 1.0 O A:CYS28 5.0 17.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Human S-PLA2 in Complex with Indole 3 Active Site Inhibitor


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 S-PLA2 in Complex with Indole 3 Active Site Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca199 b:26.3 occ:1.00 OD1 A:ASN114 2.5 22.9 1.0 O A:TYR112 2.5 18.4 1.0 O A:PHE23 2.6 18.1 1.0 O A:GLY25 2.7 21.1 1.0 C A:PHE23 3.4 18.5 1.0 CG A:ASN114 3.6 26.1 1.0 C A:TYR112 3.6 20.2 1.0 C A:GLY25 3.7 16.8 1.0 CA A:PHE23 3.9 18.9 1.0 O A:HOH202 4.1 32.5 1.0 O A:TYR24 4.1 17.1 1.0 C A:TYR24 4.1 17.8 1.0 CB A:PHE23 4.3 14.6 1.0 ND2 A:ASN114 4.3 20.7 1.0 N A:ASN114 4.3 26.2 1.0 N A:TYR24 4.3 18.5 1.0 N A:GLY25 4.3 14.8 1.0 CA A:TYR112 4.4 20.6 1.0 CB A:TYR112 4.4 21.1 1.0 N A:CYS26 4.5 17.3 1.0 N A:TYR112 4.5 19.3 1.0 CA A:GLY25 4.6 16.0 1.0 CA A:CYS26 4.6 18.1 1.0 N A:SER113 4.6 21.7 1.0 O A:CYS28 4.6 17.8 1.0 C A:SER113 4.6 25.9 1.0 CA A:TYR24 4.7 15.6 1.0 CB A:ASN114 4.7 24.8 1.0 CA A:SER113 4.8 25.0 1.0 CA A:ASN114 4.8 26.0 1.0 C A:CYS26 5.0 18.9 1.0

R.W.Schevitz, N.J.Bach, D.G.Carlson, N.Y.Chirgadze, D.K.Clawson, R.D Dillard, S.D.Draheim, L.W.Hartley, N.D.Jones, E.D.Mihelich, J.L Olkowski, D.W.Snyder, S.C.Dand, J.-P.Wery. Structure-Based Design of the First Potent and Selective Inhibitor of Human Non-Pancreatic Secretory Phospholipase A2. Nat.Struct.Biol. V. 2 458 1995.
ISSN: ISSN 1072-8368
PubMed: 7664108
DOI: 10.1038/NSB0695-458