Calcium in PDB 4hhq: Serum Paraoxonase-1 By Directed Evolution with the H115Q and H134Q Mutations

All present enzymatic activity of Serum Paraoxonase-1 By Directed Evolution with the H115Q and H134Q Mutations:
3.1.1.2; 3.1.1.25; 3.1.8.1;

The structure of Serum Paraoxonase-1 By Directed Evolution with the H115Q and H134Q Mutations, PDB code: 4hhq was solved by B.-D.Moshe, W.Grzegorz, E.Mikael, S.Israel, L.S.Joel, S.T.Dan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.34 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.789, 93.789, 144.602, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.8

The structure of Serum Paraoxonase-1 By Directed Evolution with the H115Q and H134Q Mutations also contains other interesting chemical elements:

Bromine

(Br)

3 atoms

The binding sites of Calcium atom in the Serum Paraoxonase-1 By Directed Evolution with the H115Q and H134Q Mutations (pdb code 4hhq). 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 H115Q and H134Q Mutations, PDB code: 4hhq:
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 H115Q and H134Q Mutations


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 H115Q and H134Q Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:18.9 occ:1.00 OD2 A:ASP54 2.3 18.4 1.0 OD1 A:ASP169 2.4 16.6 1.0 O A:HOH560 2.4 16.4 1.0 O A:ILE117 2.5 17.5 1.0 O A:HOH581 2.5 20.7 1.0 OD2 A:ASP169 2.5 19.6 1.0 O A:HOH582 2.7 12.4 1.0 CG A:ASP169 2.8 18.9 1.0 CG A:ASP54 3.2 18.7 1.0 OD1 A:ASP54 3.4 18.6 1.0 C A:ILE117 3.6 17.1 1.0 N A:ILE117 3.7 16.1 1.0 O A:ILE170 3.8 18.9 1.0 O A:HOH559 4.0 17.2 1.0 CA A:ILE117 4.3 17.3 1.0 O A:HOH504 4.3 15.8 1.0 CB A:ASP169 4.4 16.1 1.0 C A:GLY116 4.6 19.3 1.0 CA A:GLY116 4.6 16.2 1.0 OE2 A:GLU56 4.6 23.2 1.0 N A:SER118 4.7 17.2 1.0 CB A:ASP54 4.7 17.1 1.0 CG1 A:ILE117 4.7 19.0 1.0 O A:ILE226 4.8 15.8 1.0 N A:ILE170 4.8 16.6 1.0 CA A:SER118 4.9 18.0 1.0 C A:ILE170 5.0 18.6 1.0 CB A:SER118 5.0 18.1 1.0

Calcium binding site 2 out of 2 in the Serum Paraoxonase-1 By Directed Evolution with the H115Q and H134Q Mutations


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 H115Q and H134Q Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:34.9 occ:0.60 OE2 A:GLU53 2.1 39.6 0.8 O A:HOH573 2.2 19.3 1.0 O A:HOH574 2.3 27.1 1.0 O A:HOH592 2.4 33.8 1.0 O A:HOH610 2.5 63.2 1.0 OD1 A:ASP269 2.6 23.9 1.0 OE2 A:GLU53 2.6 17.1 0.2 OD2 A:ASP269 3.1 26.1 1.0 CD A:GLU53 3.1 39.1 0.8 CG A:ASP269 3.2 22.2 1.0 OE1 A:GLU53 3.5 44.7 0.8 CD A:GLU53 3.6 17.8 0.2 O A:HOH605 3.7 38.7 1.0 OD1 A:ASN224 3.9 31.5 1.0 OD1 A:ASN168 4.0 23.3 1.0 ND2 A:ASN168 4.0 18.3 1.0 OD1 A:ASN270 4.0 24.3 1.0 ND2 A:ASN270 4.1 17.5 1.0 O A:HOH584 4.1 50.6 1.0 CG A:GLU53 4.2 18.3 0.2 CG A:ASN270 4.4 19.2 1.0 CG A:GLU53 4.4 34.4 0.8 CG A:ASN168 4.4 20.9 1.0 OE1 A:GLU53 4.4 17.6 0.2 CB A:ASP269 4.7 17.0 1.0 CG A:ASN224 4.8 24.3 1.0 CG2 A:THR332 4.8 18.0 1.0 CB A:THR332 4.9 18.3 1.0 CB A:ASN224 4.9 21.9 1.0

M.Ben-David, G.Wieczorek, M.Elias, I.Silman, J.L.Sussman, D.S.Tawfik. Catalytic Metal Ion Rearrangements Underline Promiscuity and Evolvability of A Metalloenzyme. J.Mol.Biol. V. 425 1028 2013.
ISSN: ISSN 0022-2836
PubMed: 23318950
DOI: 10.1016/J.JMB.2013.01.009