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Calcium in PDB 3srg: Serum Paraoxonase-1 By Directed Evolution at pH 6.5 in Complex with 2- Hydroxyquinoline

Enzymatic activity of Serum Paraoxonase-1 By Directed Evolution at pH 6.5 in Complex with 2- Hydroxyquinoline

All present enzymatic activity of Serum Paraoxonase-1 By Directed Evolution at pH 6.5 in Complex with 2- Hydroxyquinoline:
3.1.1.2;

Protein crystallography data

The structure of Serum Paraoxonase-1 By Directed Evolution at pH 6.5 in Complex with 2- Hydroxyquinoline, PDB code: 3srg 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) 46.77 / 2.19
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.544, 93.544, 144.621, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 22.7

Other elements in 3srg:

The structure of Serum Paraoxonase-1 By Directed Evolution at pH 6.5 in Complex with 2- Hydroxyquinoline also contains other interesting chemical elements:

Bromine (Br) 1 atom
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Serum Paraoxonase-1 By Directed Evolution at pH 6.5 in Complex with 2- Hydroxyquinoline (pdb code 3srg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Serum Paraoxonase-1 By Directed Evolution at pH 6.5 in Complex with 2- Hydroxyquinoline, PDB code: 3srg:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3srg

Go back to Calcium Binding Sites List in 3srg
Calcium binding site 1 out of 3 in the Serum Paraoxonase-1 By Directed Evolution at pH 6.5 in Complex with 2- Hydroxyquinoline


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 in Complex with 2- Hydroxyquinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1356

b:19.6
occ:1.00
 OD2 A:ASP54 2.3 20.6 1.0
O A:HOH378 2.3 20.6 1.0
OD1 A:ASP169 2.3 15.2 1.0
O A:ILE117 2.4 20.0 1.0
OD2 A:ASP169 2.5 22.6 1.0
O A:HOH361 2.5 21.0 1.0
O A:HOH360 2.6 16.4 1.0
CG A:ASP169 2.8 20.9 1.0
CG A:ASP54 3.3 22.2 1.0
C A:ILE117 3.6 20.5 1.0
OD1 A:ASP54 3.6 19.0 1.0
O A:ILE170 3.7 21.0 1.0
N A:ILE117 3.7 17.6 1.0
O A:HOH377 4.0 16.9 1.0
CA A:ILE117 4.3 19.0 1.0
O A:HOH369 4.3 19.4 1.0
CB A:ASP169 4.3 17.2 1.0
C A:GLY116 4.6 19.9 1.0
CB A:ASP54 4.6 18.2 1.0
N A:SER118 4.7 19.6 1.0
CA A:GLY116 4.7 15.5 1.0
OE2 A:GLU56 4.7 33.0 1.0
N A:ILE170 4.7 19.3 1.0
O A:ILE226 4.7 19.5 1.0
CG1 A:ILE117 4.7 17.6 1.0
C A:ILE170 4.8 19.7 1.0
CA A:SER118 4.8 20.6 1.0
CB A:SER118 5.0 21.9 1.0

Calcium binding site 2 out of 3 in 3srg

Go back to Calcium Binding Sites List in 3srg
Calcium binding site 2 out of 3 in the Serum Paraoxonase-1 By Directed Evolution at pH 6.5 in Complex with 2- Hydroxyquinoline


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 in Complex with 2- Hydroxyquinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1357

b:21.6
occ:1.00
 OD1 A:ASN224 2.1 33.6 1.0
OD1 A:ASN270 2.2 18.9 1.0
OD2 A:ASP269 2.4 20.2 1.0
O1 A:OCH1358 2.4 27.3 1.0
OE2 A:GLU53 2.4 25.0 1.0
O A:HOH359 2.5 20.6 1.0
OD1 A:ASN168 2.6 21.7 1.0
CG A:ASN270 3.2 20.7 1.0
CG A:ASN224 3.2 28.0 1.0
ND2 A:ASN270 3.5 18.6 1.0
CD A:GLU53 3.5 23.6 1.0
CG A:ASN168 3.6 19.2 1.0
CG A:ASP269 3.6 23.6 1.0
C1 A:OCH1358 3.6 30.1 1.0
ND2 A:ASN224 3.7 29.6 1.0
ND2 A:ASN168 3.9 13.9 1.0
OE1 A:GLU53 4.0 26.1 1.0
N2 A:OCH1358 4.0 33.2 1.0
NE2 A:HIS115 4.1 23.3 1.0
OD1 A:ASP269 4.1 26.3 1.0
CB A:ASN224 4.5 21.0 1.0
C A:ASP269 4.6 20.6 1.0
CB A:ASN270 4.6 17.3 1.0
N A:ASN270 4.6 18.7 1.0
CD2 A:HIS115 4.6 24.4 1.0
C A:ASN224 4.7 20.6 1.0
CG A:GLU53 4.7 22.4 1.0
N A:GLY225 4.7 18.5 1.0
C10 A:OCH1358 4.8 32.8 1.0
CB A:ASP269 4.8 18.5 1.0
O A:ASN168 4.8 15.7 1.0
CA A:ASN224 4.8 20.2 1.0
O A:ASP269 4.9 19.2 1.0
CA A:ASN270 4.9 18.6 1.0
CB A:ASN168 4.9 16.0 1.0
CA A:ASP269 5.0 19.3 1.0
CB A:ASP169 5.0 17.2 1.0

Calcium binding site 3 out of 3 in 3srg

Go back to Calcium Binding Sites List in 3srg
Calcium binding site 3 out of 3 in the Serum Paraoxonase-1 By Directed Evolution at pH 6.5 in Complex with 2- Hydroxyquinoline


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Serum Paraoxonase-1 By Directed Evolution at pH 6.5 in Complex with 2- Hydroxyquinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1363

b:74.0
occ:1.00
 O A:GLU218 3.6 27.0 1.0
O A:GLY219 4.1 26.9 1.0
CE1 A:HIS246 4.2 29.0 1.0
CE1 A:PHE220 4.3 26.1 1.0
C A:GLY219 4.4 26.7 1.0
CZ A:PHE220 4.4 20.8 1.0
O A:HOH387 4.5 28.9 1.0
OH A:TYR248 4.5 36.2 1.0
ND1 A:HIS246 4.6 25.5 1.0
CD1 A:PHE220 4.6 25.0 1.0
C A:GLU218 4.7 25.2 1.0
CE2 A:PHE220 4.7 23.9 1.0
O A:HOH389 4.7 33.0 1.0
O A:HOH429 4.7 34.0 1.0
CG A:PHE220 4.9 24.1 1.0
CD2 A:PHE220 4.9 23.4 1.0
N A:PHE220 4.9 25.7 1.0
CA A:GLY219 4.9 25.6 1.0

Reference:

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
Page generated: Sat Dec 12 04:30:31 2020

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