Calcium in PDB 4hho: Serum Paraoxonase-1 By Directed Evolution with the H115W Mutation

All present enzymatic activity of Serum Paraoxonase-1 By Directed Evolution with the H115W Mutation:
3.1.1.2; 3.1.1.25; 3.1.8.1;

The structure of Serum Paraoxonase-1 By Directed Evolution with the H115W Mutation, PDB code: 4hho 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)	46.89 / 2.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.782, 93.782, 145.158, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.2

The structure of Serum Paraoxonase-1 By Directed Evolution with the H115W Mutation also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Calcium atom in the Serum Paraoxonase-1 By Directed Evolution with the H115W Mutation (pdb code 4hho). 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 H115W Mutation, PDB code: 4hho:
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 H115W 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 H115W Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:21.5 occ:1.00 OD2 A:ASP54 2.3 21.9 1.0 O A:HOH573 2.3 23.4 1.0 OD1 A:ASP169 2.4 18.8 1.0 O A:HOH615 2.4 25.0 1.0 O A:ILE117 2.5 20.4 1.0 OD2 A:ASP169 2.5 24.4 1.0 O A:HOH616 2.5 19.4 1.0 CG A:ASP169 2.9 24.1 1.0 CG A:ASP54 3.3 22.6 1.0 OD1 A:ASP54 3.5 22.0 1.0 C A:ILE117 3.6 22.5 1.0 N A:ILE117 3.7 19.0 1.0 O A:ILE170 3.8 21.2 1.0 O A:HOH572 4.0 19.3 1.0 O A:HOH505 4.3 22.5 1.0 CA A:ILE117 4.3 20.9 1.0 CB A:ASP169 4.4 18.3 1.0 C A:GLY116 4.6 24.1 1.0 OE2 A:GLU56 4.6 33.4 1.0 CA A:GLY116 4.7 19.2 1.0 N A:SER118 4.7 19.1 1.0 CB A:ASP54 4.7 21.0 1.0 O A:ILE226 4.7 20.2 1.0 N A:ILE170 4.8 19.5 1.0 CG1 A:ILE117 4.8 21.6 1.0 CA A:SER118 4.9 21.9 1.0 C A:ILE170 4.9 19.4 1.0 CB A:SER118 4.9 23.3 1.0

Calcium binding site 2 out of 2 in the Serum Paraoxonase-1 By Directed Evolution with the H115W 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 H115W Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:26.8 occ:0.60 O A:HOH598 2.0 29.0 0.8 OE1 A:GLU53 2.1 24.8 0.7 O A:HOH596 2.2 20.0 1.0 O A:HOH600 2.3 25.7 1.0 OD1 A:ASP269 2.4 27.8 1.0 O A:HOH599 2.6 36.1 0.8 OE2 A:GLU53 2.8 24.4 0.3 OE1 A:GLU53 3.0 24.8 0.3 OD2 A:ASP269 3.1 29.2 1.0 CG A:ASP269 3.1 25.2 1.0 CD A:GLU53 3.2 25.1 0.3 CD A:GLU53 3.4 28.1 0.7 O A:HOH597 3.8 44.7 1.0 O A:HOH601 3.9 42.0 1.0 OD1 A:ASN224 3.9 30.1 1.0 ND2 A:ASN270 4.0 22.0 1.0 OD1 A:ASN168 4.1 22.8 1.0 OD1 A:ASN270 4.1 23.4 1.0 ND2 A:ASN168 4.1 18.2 1.0 O A:HOH617 4.2 50.8 1.0 OE2 A:GLU53 4.2 28.5 0.7 CG A:GLU53 4.3 25.9 0.7 CG A:ASN270 4.4 20.9 1.0 CG A:ASN168 4.6 23.0 1.0 CB A:ASP269 4.6 18.8 1.0 CG A:GLU53 4.6 23.9 0.3 CG2 A:THR332 4.7 21.4 1.0 CG A:ASN224 4.8 27.4 1.0 CB A:THR332 4.8 21.8 1.0 CB A:ASN224 4.9 24.7 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