Calcium in PDB 9r0q: Paraoxonase-1 in Complex with Terbium(III) and 2-Hydroxyquinoline

All present enzymatic activity of Paraoxonase-1 in Complex with Terbium(III) and 2-Hydroxyquinoline:
3.1.1.2; 3.1.1.81; 3.1.8.1;

The structure of Paraoxonase-1 in Complex with Terbium(III) and 2-Hydroxyquinoline, PDB code: 9r0q was solved by J.Smerkolj, M.Pavsic, M.Golicnik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.82 / 2.35
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.064, 98.064, 138.877, 90, 90, 90
R / Rfree (%)	19 / 22.9

The structure of Paraoxonase-1 in Complex with Terbium(III) and 2-Hydroxyquinoline also contains other interesting chemical elements:

Terbium	(Tb)	2 atoms
Bromine	(Br)	2 atoms

The binding sites of Calcium atom in the Paraoxonase-1 in Complex with Terbium(III) and 2-Hydroxyquinoline (pdb code 9r0q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Paraoxonase-1 in Complex with Terbium(III) and 2-Hydroxyquinoline, PDB code: 9r0q:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Paraoxonase-1 in Complex with Terbium(III) and 2-Hydroxyquinoline


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Paraoxonase-1 in Complex with Terbium(III) and 2-Hydroxyquinoline within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:38.9 occ:0.53 TB A:TB401 0.0 38.7 0.5 OD1 A:ASN224 2.3 43.8 1.0 O1 A:OCH405 2.3 41.8 0.9 OD1 A:ASP269 2.3 42.8 1.0 OE2 A:GLU53 2.3 40.5 1.0 OD1 A:ASN270 2.5 37.6 1.0 OD1 A:ASN168 2.6 35.7 1.0 O A:HOH533 2.7 33.7 1.0 CG A:ASN224 3.3 43.3 1.0 CG A:ASN270 3.4 34.0 1.0 C1 A:OCH405 3.4 50.5 0.9 CD A:GLU53 3.4 43.0 1.0 CG A:ASP269 3.4 39.9 1.0 ND2 A:ASN224 3.6 39.7 1.0 CG A:ASN168 3.7 35.0 1.0 ND2 A:ASN270 3.8 38.5 1.0 OD2 A:ASP269 3.9 47.7 1.0 OE1 A:GLU53 3.9 36.7 1.0 N2 A:OCH405 4.0 54.1 0.9 ND2 A:ASN168 4.0 35.1 1.0 NE2 A:HIS115 4.1 40.3 1.0 C10 A:OCH405 4.6 59.5 0.9 N A:ASN270 4.6 35.0 1.0 C A:ASP269 4.6 36.9 1.0 CB A:ASN224 4.6 36.3 1.0 CG A:GLU53 4.7 35.6 1.0 CB A:ASP269 4.7 37.3 1.0 CB A:ASN270 4.7 31.1 1.0 CD2 A:HIS115 4.7 37.6 1.0 C A:ASN224 4.8 36.2 1.0 N A:GLY225 4.9 36.3 1.0 CA A:ASP269 4.9 35.0 1.0 CA A:ASN270 4.9 33.3 1.0 O A:ASN168 4.9 30.3 1.0 O A:ASP269 5.0 36.7 1.0 CA A:ASN224 5.0 33.2 1.0 CB A:ASN168 5.0 33.7 1.0

Calcium binding site 2 out of 2 in the Paraoxonase-1 in Complex with Terbium(III) and 2-Hydroxyquinoline


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Paraoxonase-1 in Complex with Terbium(III) and 2-Hydroxyquinoline within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:35.2 occ:0.95 TB A:TB402 0.0 35.4 0.1 OD2 A:ASP54 2.3 32.4 1.0 O A:HOH519 2.3 35.6 1.0 O A:HOH508 2.4 29.3 1.0 OD2 A:ASP169 2.4 35.1 1.0 O A:HOH525 2.4 30.6 1.0 O A:ILE117 2.4 32.4 1.0 OD1 A:ASP169 2.5 29.6 1.0 CG A:ASP169 2.8 34.5 1.0 CG A:ASP54 3.3 37.7 1.0 C A:ILE117 3.6 30.9 1.0 OD1 A:ASP54 3.6 37.2 1.0 O A:ILE170 3.8 30.0 1.0 N A:ILE117 3.8 27.9 1.0 O A:HOH510 3.9 31.9 1.0 O A:HOH516 4.3 32.1 1.0 CA A:ILE117 4.3 29.6 1.0 CB A:ASP169 4.3 32.3 1.0 OE1 A:GLU56 4.6 44.5 1.0 N A:SER118 4.7 32.6 1.0 O A:ILE226 4.7 34.0 1.0 CB A:ASP54 4.7 29.9 1.0 O A:HOH530 4.8 44.3 1.0 C A:GLY116 4.8 32.8 1.0 CG1 A:ILE117 4.8 29.3 1.0 CA A:GLY116 4.9 30.2 1.0 N A:ILE170 4.9 25.9 1.0 CA A:SER118 4.9 34.7 1.0 C A:ILE170 4.9 32.4 1.0

J.Smerkolj, M.Bahun, N.Poklar Ulrih, A.Bavec, M.Pavsic, M.Golicnik. Intramolecular Sensitization and Structure of A TB3+/2-Hydroxyquinoline Conjugate in the Paraoxonase 1 Active Site Dalton Trans 2025.
ISSN: ESSN 1477-9234
DOI: 10.1039/D5DT01484K