Calcium in PDB 1db5: Human S-PLA2 in Complex with Indole 6

All present enzymatic activity of Human S-PLA2 in Complex with Indole 6:
3.1.1.4;

The structure of Human S-PLA2 in Complex with Indole 6, PDB code: 1db5 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)	30.00 / 2.80
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	76.360, 76.360, 91.530, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 24

The binding sites of Calcium atom in the Human S-PLA2 in Complex with Indole 6 (pdb code 1db5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Human S-PLA2 in Complex with Indole 6, PDB code: 1db5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human S-PLA2 in Complex with Indole 6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human S-PLA2 in Complex with Indole 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca198 b:24.2 occ:1.00 O A:HIS27 2.4 24.7 1.0 O A:GLY31 2.4 25.3 1.0 O A:GLY29 2.4 24.6 1.0 OD1 A:ASP48 2.5 22.7 1.0 O54 A:6IN200 2.6 35.5 1.0 O40 A:6IN200 2.6 20.9 1.0 OD2 A:ASP48 2.8 22.5 1.0 CG A:ASP48 3.0 23.3 1.0 C49 A:6IN200 3.5 35.5 1.0 C A:GLY31 3.5 26.6 1.0 C A:HIS27 3.5 23.9 1.0 C34 A:6IN200 3.6 21.3 1.0 C A:GLY29 3.7 22.4 1.0 N A:GLY31 3.7 24.1 1.0 N A:GLY29 4.0 21.2 1.0 N37 A:6IN200 4.1 21.6 1.0 CA A:GLY31 4.2 25.0 1.0 O52 A:6IN200 4.2 37.3 1.0 C A:VAL30 4.3 23.9 1.0 CA A:HIS27 4.4 23.9 1.0 C A:CYS28 4.4 21.1 1.0 O A:HOH236 4.4 25.3 1.0 N A:CYS28 4.5 22.1 1.0 C46 A:6IN200 4.5 32.5 1.0 CA A:CYS28 4.5 21.1 1.0 CB A:ASP48 4.5 23.4 1.0 CA A:VAL30 4.5 23.4 1.0 N A:VAL30 4.5 21.9 1.0 CA A:GLY29 4.6 21.7 1.0 N A:GLY32 4.6 27.9 1.0 O A:CYS44 4.7 21.3 1.0 C43 A:6IN200 4.7 28.4 1.0 CB A:HIS27 4.8 24.4 1.0 O A:HOH205 4.8 33.5 1.0 CA A:GLY32 4.9 29.1 1.0 C32 A:6IN200 4.9 21.3 1.0 O A:HOH214 5.0 27.9 1.0

Calcium binding site 2 out of 2 in the Human S-PLA2 in Complex with Indole 6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human S-PLA2 in Complex with Indole 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca199 b:40.5 occ:1.00 O A:TYR112 2.5 22.4 1.0 OD1 A:ASN114 2.6 31.5 1.0 O A:PHE23 2.6 26.2 1.0 O A:GLY25 2.9 27.7 1.0 C A:PHE23 3.2 23.7 1.0 CA A:PHE23 3.5 22.6 1.0 C A:TYR112 3.7 24.7 1.0 CG A:ASN114 3.8 33.2 1.0 O A:TYR24 3.8 23.4 1.0 CB A:PHE23 3.9 20.8 1.0 C A:GLY25 4.0 25.0 1.0 O A:HOH206 4.1 20.6 1.0 C A:TYR24 4.1 22.3 1.0 N A:TYR24 4.1 22.6 1.0 ND2 A:ASN114 4.4 33.0 1.0 O A:CYS28 4.4 21.1 1.0 N A:ASN114 4.5 29.8 1.0 CA A:TYR112 4.5 25.2 1.0 N A:GLY25 4.5 21.7 1.0 N A:TYR112 4.6 24.5 1.0 CB A:TYR112 4.6 25.8 1.0 CA A:TYR24 4.6 21.5 1.0 O A:HOH205 4.7 33.5 1.0 C A:SER113 4.7 28.6 1.0 N A:SER113 4.7 26.5 1.0 CA A:GLY25 4.8 23.6 1.0 N A:CYS26 4.8 24.6 1.0 CB A:ASN114 4.8 31.2 1.0 CA A:CYS26 4.9 24.1 1.0 CA A:SER113 4.9 28.5 1.0 CA A:ASN114 4.9 30.3 1.0 N A:PHE23 4.9 20.8 1.0

R.W.Schevitz, N.J.Bach, D.G.Carlson, N.Y.Chirgadze, D.K.Clawson, R.D.Dillard, S.E.Draheim, L.W.Hartley, N.D.Jones, E.D.Mihelich, J.L.Olkowski, D.W.Snyder, C.Sommers, 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