Calcium in PDB 1db4: Human S-PLA2 in Complex with Indole 8

All present enzymatic activity of Human S-PLA2 in Complex with Indole 8:
3.1.1.4;

The structure of Human S-PLA2 in Complex with Indole 8, PDB code: 1db4 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 / 2.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	77.012, 77.012, 91.620, 90.00, 90.00, 120.00
R / Rfree (%)	22.6 / 25.6

The binding sites of Calcium atom in the Human S-PLA2 in Complex with Indole 8 (pdb code 1db4). 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 8, PDB code: 1db4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human S-PLA2 in Complex with Indole 8


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 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca198 b:16.7 occ:1.00 O A:HIS27 2.4 16.4 1.0 O29 A:8IN200 2.4 17.2 1.0 O A:GLY29 2.4 18.5 1.0 OD1 A:ASP48 2.4 21.2 1.0 O A:GLY31 2.5 19.8 1.0 OD2 A:ASP48 2.6 19.9 1.0 O12 A:8IN200 2.6 21.4 1.0 CG A:ASP48 2.8 21.2 1.0 C A:HIS27 3.6 17.0 1.0 C A:GLY31 3.6 22.9 1.0 C11 A:8IN200 3.6 19.9 1.0 C A:GLY29 3.6 17.2 1.0 N A:GLY31 3.7 19.9 1.0 P26 A:8IN200 3.8 22.7 1.0 N13 A:8IN200 3.8 17.7 1.0 N A:GLY29 4.1 15.7 1.0 O28 A:8IN200 4.2 17.6 1.0 CA A:GLY31 4.2 21.7 1.0 C25 A:8IN200 4.2 20.4 1.0 C A:CYS28 4.3 18.4 1.0 C A:VAL30 4.3 18.0 1.0 CB A:ASP48 4.4 18.1 1.0 CA A:HIS27 4.4 19.0 1.0 CA A:CYS28 4.5 17.5 1.0 N A:CYS28 4.5 17.4 1.0 CA A:GLY29 4.5 16.1 1.0 CA A:VAL30 4.5 15.4 1.0 N A:VAL30 4.5 15.5 1.0 O A:HOH259 4.6 35.8 1.0 N A:GLY32 4.6 22.5 1.0 O A:CYS44 4.7 17.3 1.0 C24 A:8IN200 4.8 20.6 1.0 CB A:HIS27 4.8 20.0 1.0 O27 A:8IN200 4.8 18.8 1.0 CA A:GLY32 4.9 26.6 1.0 O A:CYS28 4.9 19.4 1.0 O A:HOH217 4.9 22.4 1.0 O A:HOH206 4.9 34.3 1.0 C10 A:8IN200 5.0 17.9 1.0

Calcium binding site 2 out of 2 in the Human S-PLA2 in Complex with Indole 8


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 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca199 b:27.7 occ:1.00 O A:GLY25 2.4 22.6 1.0 O A:TYR112 2.4 20.6 1.0 OD1 A:ASN114 2.5 19.5 1.0 O A:PHE23 2.5 17.4 1.0 C A:PHE23 3.3 19.1 1.0 C A:GLY25 3.5 20.5 1.0 C A:TYR112 3.5 21.9 1.0 CG A:ASN114 3.6 24.0 1.0 O A:TYR24 3.9 15.5 1.0 C A:TYR24 4.0 19.8 1.0 CA A:PHE23 4.0 18.1 1.0 N A:GLY25 4.1 18.5 1.0 ND2 A:ASN114 4.2 23.0 1.0 CB A:TYR112 4.2 24.3 1.0 CA A:TYR112 4.2 21.3 1.0 N A:TYR24 4.3 19.1 1.0 O A:HOH207 4.3 19.2 1.0 CA A:GLY25 4.3 20.7 1.0 N A:ASN114 4.3 22.4 1.0 N A:CYS26 4.4 17.7 1.0 CB A:PHE23 4.4 15.3 1.0 N A:TYR112 4.4 23.6 1.0 CA A:CYS26 4.4 18.7 1.0 CA A:TYR24 4.6 18.4 1.0 N A:SER113 4.6 20.4 1.0 C A:SER113 4.7 23.1 1.0 O A:CYS28 4.8 19.4 1.0 CB A:ASN114 4.8 23.0 1.0 CA A:ASN114 4.8 23.8 1.0 CA A:SER113 4.8 21.3 1.0 O A:HOH206 4.9 34.3 1.0 C A:CYS26 4.9 18.3 1.0 CD1 A:TYR112 5.0 26.3 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