Calcium in PDB 3sre: Serum Paraoxonase-1 By Directed Evolution at pH 6.5

All present enzymatic activity of Serum Paraoxonase-1 By Directed Evolution at pH 6.5:
3.1.1.2;

The structure of Serum Paraoxonase-1 By Directed Evolution at pH 6.5, PDB code: 3sre was solved by M.Ben David, M.Elias, I.Silman, 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)	33.54 / 1.99
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.653, 93.653, 143.705, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 22

The structure of Serum Paraoxonase-1 By Directed Evolution at pH 6.5 also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Calcium atom in the Serum Paraoxonase-1 By Directed Evolution at pH 6.5 (pdb code 3sre). 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 at pH 6.5, PDB code: 3sre:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Serum Paraoxonase-1 By Directed Evolution at pH 6.5


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 at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1356 b:20.6 occ:1.00 OD2 A:ASP54 2.3 19.5 1.0 O A:HOH379 2.4 22.1 1.0 O A:HOH361 2.4 21.7 1.0 O A:ILE117 2.4 18.6 1.0 OD2 A:ASP169 2.5 24.8 1.0 OD1 A:ASP169 2.5 19.9 1.0 O A:HOH360 2.5 19.5 1.0 CG A:ASP169 2.9 26.6 1.0 CG A:ASP54 3.3 24.9 1.0 C A:ILE117 3.6 19.6 1.0 OD1 A:ASP54 3.7 21.4 1.0 N A:ILE117 3.7 17.8 1.0 O A:ILE170 3.8 19.6 1.0 O A:HOH378 4.0 18.5 1.0 CA A:ILE117 4.3 17.1 1.0 O A:HOH370 4.3 21.3 1.0 CB A:ASP169 4.4 16.4 1.0 OE2 A:GLU56 4.6 30.0 1.0 C A:GLY116 4.6 21.9 1.0 N A:SER118 4.6 18.1 1.0 CG1 A:ILE117 4.7 19.4 1.0 CB A:ASP54 4.7 18.9 1.0 CA A:GLY116 4.7 19.1 1.0 CA A:SER118 4.8 19.9 1.0 O A:ILE226 4.8 19.3 1.0 N A:ILE170 4.8 19.2 1.0 CB A:SER118 4.9 19.8 1.0 C A:ILE170 5.0 19.3 1.0

Calcium binding site 2 out of 2 in the Serum Paraoxonase-1 By Directed Evolution at pH 6.5


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 at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1357 b:27.2 occ:1.00 OD1 A:ASN224 2.2 30.2 1.0 O1 A:PO41358 2.3 30.8 0.8 OD1 A:ASN270 2.3 21.6 1.0 OD1 A:ASN168 2.5 19.2 1.0 O A:HOH359 2.5 22.9 1.0 OD2 A:ASP269 2.6 24.6 1.0 OE2 A:GLU53 2.6 30.1 1.0 CG A:ASN270 3.2 19.3 1.0 CG A:ASN224 3.4 30.6 1.0 ND2 A:ASN270 3.5 21.1 1.0 CG A:ASN168 3.5 22.4 1.0 P A:PO41358 3.5 45.5 0.8 CD A:GLU53 3.7 28.2 1.0 CG A:ASP269 3.8 28.4 1.0 ND2 A:ASN168 3.8 20.9 1.0 O3 A:PO41358 3.8 36.1 0.8 ND2 A:ASN224 3.9 31.1 1.0 OE1 A:GLU53 4.1 30.4 1.0 O2 A:PO41358 4.2 47.1 0.8 NE2 A:HIS115 4.2 40.5 1.0 OD1 A:ASP269 4.3 33.3 1.0 CB A:ASN270 4.6 17.1 1.0 C A:ASN224 4.6 21.2 1.0 N A:ASN270 4.6 17.6 1.0 C A:ASP269 4.6 19.9 1.0 CB A:ASN224 4.6 23.1 1.0 N A:GLY225 4.7 18.4 1.0 O4 A:PO41358 4.7 46.5 0.8 CD2 A:HIS115 4.7 40.4 1.0 O A:ASN168 4.8 19.4 1.0 CA A:ASN270 4.9 15.8 1.0 CB A:ASN168 4.9 17.4 1.0 O A:ASP269 4.9 20.7 1.0 CA A:ASN224 4.9 21.1 1.0 CB A:ASP269 4.9 16.6 1.0 CB A:ASP169 4.9 16.4 1.0 CG A:GLU53 4.9 26.9 1.0 C A:ASN168 5.0 18.0 1.0

M.Ben-David, M.Elias, J.J.Filippi, E.Dunach, I.Silman, J.L.Sussman, D.S.Tawfik. Catalytic Versatility and Backups in Enzyme Active Sites: the Case of Serum Paraoxonase 1. J.Mol.Biol. V. 418 181 2012.
ISSN: ISSN 0022-2836
PubMed: 22387469
DOI: 10.1016/J.JMB.2012.02.042