Copper in PDB 1gqh: Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Kojic Acid

All present enzymatic activity of Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Kojic Acid:
1.13.11.24;

The structure of Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Kojic Acid, PDB code: 1gqh was solved by R.A.Steiner, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.39 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.640, 55.396, 124.425, 90.00, 98.26, 90.00
R / Rfree (%)	17.8 / 22.8

The binding sites of Copper atom in the Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Kojic Acid (pdb code 1gqh). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Kojic Acid, PDB code: 1gqh:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Kojic Acid


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1352 b:12.7 occ:1.00 O2 A:KOJ1351 1.8 26.1 1.0 NE2 A:HIS68 1.9 10.6 1.0 NE2 A:HIS112 2.1 9.4 1.0 NE2 A:HIS66 2.2 12.0 1.0 OE1 A:GLU73 2.3 22.3 1.0 O3 A:KOJ1351 2.4 21.0 1.0 C2 A:KOJ1351 2.8 24.2 1.0 CE1 A:HIS68 2.8 8.9 1.0 CE1 A:HIS112 2.9 10.3 1.0 CD2 A:HIS68 3.0 10.1 1.0 C3 A:KOJ1351 3.0 22.7 1.0 CD2 A:HIS66 3.1 9.0 1.0 CD A:GLU73 3.2 21.2 1.0 CE1 A:HIS66 3.2 10.7 1.0 CD2 A:HIS112 3.2 9.2 1.0 OE2 A:GLU73 3.3 23.6 1.0 ND1 A:HIS68 3.9 8.9 1.0 CG A:HIS68 4.0 9.4 1.0 C1 A:KOJ1351 4.1 26.8 1.0 ND1 A:HIS112 4.1 9.4 1.0 O A:HOH2285 4.1 22.1 0.5 CG A:HIS112 4.3 9.4 1.0 ND1 A:HIS66 4.3 10.2 1.0 CG A:HIS66 4.3 9.9 1.0 C4 A:KOJ1351 4.4 23.9 1.0 CG A:GLU73 4.6 16.6 1.0

Copper binding site 2 out of 4 in the Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Kojic Acid


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu1352 b:14.1 occ:1.00 NE2 B:HIS68 2.0 9.9 1.0 NE2 B:HIS112 2.1 10.8 1.0 O2 B:KOJ1351 2.1 30.2 1.0 NE2 B:HIS66 2.1 11.5 1.0 OE1 B:GLU73 2.3 23.2 1.0 O3 B:KOJ1351 2.4 31.0 1.0 CE1 B:HIS68 3.0 10.6 1.0 CD2 B:HIS68 3.0 9.5 1.0 C2 B:KOJ1351 3.0 30.0 1.0 CE1 B:HIS112 3.0 13.1 1.0 CE1 B:HIS66 3.1 12.4 1.0 C3 B:KOJ1351 3.1 29.7 1.0 CD2 B:HIS66 3.1 11.1 1.0 CD2 B:HIS112 3.1 11.9 1.0 CD B:GLU73 3.4 22.4 1.0 OE2 B:GLU73 3.9 26.9 1.0 ND1 B:HIS68 4.1 8.6 1.0 CG B:HIS68 4.1 10.5 1.0 ND1 B:HIS112 4.1 12.4 1.0 ND1 B:HIS66 4.2 12.6 1.0 CG B:HIS112 4.2 12.5 1.0 CG B:HIS66 4.2 10.8 1.0 C1 B:KOJ1351 4.3 30.4 1.0 C4 B:KOJ1351 4.4 31.0 1.0 CG B:GLU73 4.7 18.1 1.0 CZ B:PHE75 4.8 15.0 1.0 CB B:GLU73 4.9 13.2 1.0

Copper binding site 3 out of 4 in the Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Kojic Acid


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu1352 b:13.6 occ:1.00 NE2 C:HIS68 1.8 12.0 1.0 O2 C:KOJ1351 1.8 31.3 1.0 OE1 C:GLU73 2.0 22.1 1.0 NE2 C:HIS66 2.1 11.4 1.0 NE2 C:HIS112 2.1 8.9 1.0 CE1 C:HIS68 2.6 13.3 1.0 O3 C:KOJ1351 3.0 32.3 1.0 CD2 C:HIS68 3.0 12.1 1.0 CE1 C:HIS66 3.0 11.4 1.0 CE1 C:HIS112 3.0 9.2 1.0 C2 C:KOJ1351 3.0 30.7 1.0 CD C:GLU73 3.1 20.5 1.0 CD2 C:HIS66 3.1 11.7 1.0 CD2 C:HIS112 3.1 8.5 1.0 C3 C:KOJ1351 3.5 31.1 1.0 OE2 C:GLU73 3.5 22.3 1.0 ND1 C:HIS68 3.8 11.9 1.0 O C:HOH2247 3.8 35.8 0.5 CG C:HIS68 4.0 10.8 1.0 ND1 C:HIS66 4.1 9.0 1.0 ND1 C:HIS112 4.1 9.1 1.0 CG C:HIS66 4.2 10.5 1.0 C1 C:KOJ1351 4.2 31.0 1.0 CG C:HIS112 4.2 9.7 1.0 CG C:GLU73 4.4 17.4 1.0 CZ C:PHE75 4.8 15.3 1.0 C4 C:KOJ1351 4.8 30.2 1.0 CB C:GLU73 5.0 12.9 1.0

Copper binding site 4 out of 4 in the Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Kojic Acid


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu1352 b:12.1 occ:1.00 O2 D:KOJ1351 1.8 26.1 1.0 NE2 D:HIS68 2.0 11.8 1.0 NE2 D:HIS112 2.0 10.3 1.0 NE2 D:HIS66 2.1 9.1 1.0 OE1 D:GLU73 2.3 20.9 1.0 O3 D:KOJ1351 2.4 25.6 1.0 C2 D:KOJ1351 2.7 27.1 1.0 CE1 D:HIS68 2.8 10.9 1.0 CE1 D:HIS66 2.9 8.9 1.0 CE1 D:HIS112 2.9 11.4 1.0 C3 D:KOJ1351 3.0 27.8 1.0 CD2 D:HIS68 3.0 12.2 1.0 CD2 D:HIS112 3.0 11.4 1.0 CD2 D:HIS66 3.1 10.3 1.0 CD D:GLU73 3.3 20.9 1.0 OE2 D:GLU73 3.5 22.4 1.0 ND1 D:HIS68 3.9 12.0 1.0 C1 D:KOJ1351 4.0 28.1 1.0 ND1 D:HIS66 4.0 8.3 1.0 ND1 D:HIS112 4.1 11.5 1.0 CG D:HIS68 4.1 11.2 1.0 CG D:HIS112 4.1 11.4 1.0 CG D:HIS66 4.2 9.8 1.0 C4 D:KOJ1351 4.4 29.1 1.0 CG D:GLU73 4.7 16.9 1.0 CZ D:PHE75 5.0 15.0 1.0

R.A.Steiner, I.M.Kooter, B.W.Dijkstra. Functional Analysis of the Copper-Dependent Quercetin 2,3-Dioxygenase.1.Ligand-Induced Coordination Changes Probed By X-Ray Crystallography: Inhibition, Ordering Effect and Mechanistic Insights Biochemistry V. 41 7955 2002.
ISSN: ISSN 0006-2960
PubMed: 12069585
DOI: 10.1021/BI0159736