Calcium in PDB 4q1u: Serum Paraoxonase-1 By Directed Evolution with the K192Q Mutation

All present enzymatic activity of Serum Paraoxonase-1 By Directed Evolution with the K192Q Mutation:
3.1.1.2; 3.1.1.81; 3.1.8.1;

The structure of Serum Paraoxonase-1 By Directed Evolution with the K192Q Mutation, PDB code: 4q1u was solved by M.Ben-David, J.L.Sussman, D.S.Tawfik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.47 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.514, 93.514, 144.007, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.2

The structure of Serum Paraoxonase-1 By Directed Evolution with the K192Q Mutation also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Serum Paraoxonase-1 By Directed Evolution with the K192Q Mutation (pdb code 4q1u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Serum Paraoxonase-1 By Directed Evolution with the K192Q Mutation, PDB code: 4q1u:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Serum Paraoxonase-1 By Directed Evolution with the K192Q Mutation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Serum Paraoxonase-1 By Directed Evolution with the K192Q Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:22.4 occ:1.00 OD2 A:ASP54 2.3 20.3 1.0 O A:ILE117 2.4 22.9 1.0 O A:HOH508 2.4 17.7 1.0 OD1 A:ASP169 2.5 22.2 1.0 O A:HOH512 2.5 21.5 1.0 OD2 A:ASP169 2.6 26.8 1.0 O A:HOH511 2.8 17.6 1.0 CG A:ASP169 2.9 24.4 1.0 CG A:ASP54 3.3 23.9 1.0 C A:ILE117 3.5 20.2 1.0 OD1 A:ASP54 3.6 26.4 1.0 N A:ILE117 3.7 20.0 1.0 O A:ILE170 3.8 22.2 1.0 O A:HOH510 4.0 22.6 1.0 CA A:ILE117 4.2 19.2 1.0 O A:HOH509 4.3 20.3 1.0 CB A:ASP169 4.4 20.2 1.0 N A:SER118 4.6 19.1 1.0 C A:GLY116 4.6 21.8 1.0 CG1 A:ILE117 4.6 20.1 1.0 CA A:GLY116 4.7 18.4 1.0 OE2 A:GLU56 4.7 28.7 1.0 CB A:ASP54 4.8 19.6 1.0 CA A:SER118 4.8 22.9 1.0 N A:ILE170 4.8 20.7 1.0 O A:ILE226 4.8 18.3 1.0 CB A:SER118 4.9 19.8 1.0 C A:ILE170 5.0 21.0 1.0

Calcium binding site 2 out of 2 in the Serum Paraoxonase-1 By Directed Evolution with the K192Q Mutation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Serum Paraoxonase-1 By Directed Evolution with the K192Q Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:35.0 occ:1.00 O3 A:PO4404 2.3 47.8 1.0 OD1 A:ASN270 2.3 24.7 1.0 OD1 A:ASN224 2.4 45.0 1.0 OE2 A:GLU53 2.5 33.4 1.0 O A:HOH507 2.5 23.7 1.0 OD2 A:ASP269 2.6 27.6 1.0 OD1 A:ASN168 2.7 26.1 1.0 CG A:ASN270 3.2 21.4 1.0 ND2 A:ASN270 3.4 21.2 1.0 CG A:ASN224 3.5 38.5 1.0 P A:PO4404 3.6 62.2 1.0 CG A:ASN168 3.6 24.5 1.0 CD A:GLU53 3.6 30.1 1.0 CG A:ASP269 3.7 30.0 1.0 ND2 A:ASN168 3.8 21.4 1.0 O2 A:PO4404 3.8 48.2 1.0 ND2 A:ASN224 3.9 34.8 1.0 OE1 A:GLU53 4.0 33.3 1.0 O1 A:PO4404 4.1 59.4 1.0 NE2 A:HIS115 4.1 45.7 1.0 OD1 A:ASP269 4.3 34.6 1.0 CD2 A:HIS115 4.5 46.3 1.0 CB A:ASN270 4.5 19.5 1.0 N A:ASN270 4.6 21.9 1.0 C A:ASP269 4.6 24.3 1.0 C A:ASN224 4.7 23.5 1.0 N A:GLY225 4.7 19.5 1.0 CB A:ASN224 4.7 29.9 1.0 O4 A:PO4404 4.8 62.0 1.0 O A:ASN168 4.8 23.8 1.0 CA A:ASN270 4.8 19.9 1.0 O A:ASP269 4.9 23.3 1.0 CA A:ASN224 4.9 23.6 1.0 CG A:GLU53 4.9 29.1 1.0 CB A:ASP169 4.9 20.2 1.0 CB A:ASP269 4.9 23.6 1.0

M.Ben-David, J.L.Sussman, C.I.Maxwell, K.Szeler, S.C.Kamerlin, D.S.Tawfik. Catalytic Stimulation By Restrained Active-Site Floppiness - the Case of High-Density Lipoprotein Bound Serum Paraoxonase-1. J.Mol.Biol. 2015.
ISSN: ESSN 1089-8638
PubMed: 25644661
DOI: 10.1016/J.JMB.2015.01.013