Calcium in PDB 1v04: Serum Paraoxonase By Directed Evolution

All present enzymatic activity of Serum Paraoxonase By Directed Evolution:
3.1.1.2; 3.1.8.1;

The structure of Serum Paraoxonase By Directed Evolution, PDB code: 1v04 was solved by M.Harel, A.Aharoni, L.Gaidukov, B.Brumshtein, O.Khersonsky, S.Yagur, R.Meged, H.Dvir, R.B.G.Ravelli, A.Mccarthy, L.Toker, 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)	20.00 / 2.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.440, 98.440, 139.170, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 21.7

The binding sites of Calcium atom in the Serum Paraoxonase By Directed Evolution (pdb code 1v04). 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 By Directed Evolution, PDB code: 1v04:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Serum Paraoxonase By Directed Evolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Serum Paraoxonase By Directed Evolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1356 b:37.9 occ:1.00 OD2 A:ASP54 2.2 37.5 1.0 O A:HOH2011 2.3 38.2 1.0 O A:HOH2010 2.4 36.3 1.0 O A:HOH2053 2.4 36.3 1.0 O A:ILE117 2.4 35.9 1.0 OD2 A:ASP169 2.5 35.6 1.0 OD1 A:ASP169 2.9 33.5 1.0 CG A:ASP169 3.0 37.4 1.0 CG A:ASP54 3.3 38.4 1.0 C A:ILE117 3.6 36.6 1.0 OD1 A:ASP54 3.6 39.8 1.0 N A:ILE117 3.8 35.2 1.0 O A:HOH2052 3.8 34.9 1.0 O A:ILE170 3.8 33.3 1.0 O A:HOH2032 4.3 38.8 1.0 CA A:ILE117 4.4 35.7 1.0 CB A:ASP169 4.5 31.4 1.0 N A:SER118 4.6 37.8 1.0 OE2 A:GLU56 4.6 43.0 1.0 O A:ILE226 4.6 35.0 1.0 O A:HOH2083 4.7 47.7 1.0 CB A:ASP54 4.7 34.2 1.0 C A:GLY116 4.7 35.0 1.0 CG1 A:ILE117 4.7 33.1 1.0 CA A:SER118 4.8 37.4 1.0 CA A:GLY116 4.8 33.5 1.0 N A:ILE170 4.9 33.7 1.0 CB A:SER118 4.9 35.6 1.0 O A:ILE271 5.0 35.7 1.0 C A:ILE170 5.0 34.1 1.0

Calcium binding site 2 out of 2 in the Serum Paraoxonase By Directed Evolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Serum Paraoxonase By Directed Evolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1357 b:37.8 occ:1.00 O1 A:PO41358 2.2 41.4 1.0 OD1 A:ASN270 2.3 37.7 1.0 OD1 A:ASN224 2.3 42.2 1.0 OE2 A:GLU53 2.4 42.0 1.0 OD2 A:ASP269 2.5 41.0 1.0 O A:HOH2009 2.5 37.7 1.0 OD1 A:ASN168 2.6 36.7 1.0 CG A:ASN270 3.2 37.6 1.0 CG A:ASN224 3.4 40.6 1.0 P A:PO41358 3.5 47.3 1.0 ND2 A:ASN270 3.5 40.2 1.0 CD A:GLU53 3.5 45.3 1.0 CG A:ASN168 3.5 34.9 1.0 CG A:ASP269 3.7 42.5 1.0 ND2 A:ASN224 3.8 36.5 1.0 ND2 A:ASN168 3.8 31.9 1.0 OE1 A:GLU53 3.9 44.5 1.0 O4 A:PO41358 3.9 49.3 1.0 O2 A:PO41358 4.1 44.0 1.0 NE2 A:HIS115 4.1 42.8 1.0 OD1 A:ASP269 4.2 42.4 1.0 N A:ASN270 4.6 35.8 1.0 CB A:ASN270 4.6 33.2 1.0 CD2 A:HIS115 4.6 41.1 1.0 C A:ASP269 4.6 36.6 1.0 O3 A:PO41358 4.7 43.6 1.0 CB A:ASN224 4.7 36.2 1.0 C A:ASN224 4.7 36.1 1.0 N A:GLY225 4.7 35.8 1.0 O A:ASN168 4.8 34.5 1.0 CB A:ASP269 4.8 36.0 1.0 CA A:ASN270 4.9 34.1 1.0 CG A:GLU53 4.9 39.0 1.0 CA A:ASN224 4.9 35.7 1.0 CB A:ASN168 5.0 34.3 1.0 O A:ASP269 5.0 35.9 1.0

M.Harel, A.Aharoni, L.Gaidukov, B.Brumshtein, O.Khersonsky, R.Meged, H.Dvir, R.B.G.Ravelli, A.Mccarthy, L.Toker, I.Silman, J.L.Sussman, D.S.Tawfik. Structure and Evolution of the Serum Paraoxonase Family of Detoxifying and Anti-Atherosclerotic Enzymes Nat.Struct.Mol.Biol. V. 11 412 2004.
ISSN: ISSN 1545-9993
PubMed: 15098021
DOI: 10.1038/NSMB767