Zinc in PDB 4zvl: Oxidized Quinone Reductase 2 in Complex with Acridine Orange

All present enzymatic activity of Oxidized Quinone Reductase 2 in Complex with Acridine Orange:
1.10.99.2;

The structure of Oxidized Quinone Reductase 2 in Complex with Acridine Orange, PDB code: 4zvl was solved by K.K.Leung, B.H.Shilton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.370, 83.060, 106.270, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 19

The binding sites of Zinc atom in the Oxidized Quinone Reductase 2 in Complex with Acridine Orange (pdb code 4zvl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Oxidized Quinone Reductase 2 in Complex with Acridine Orange, PDB code: 4zvl:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Oxidized Quinone Reductase 2 in Complex with Acridine Orange


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Oxidized Quinone Reductase 2 in Complex with Acridine Orange within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:21.1 occ:1.00 ND1 A:HIS173 2.0 16.8 1.0 ND1 A:HIS177 2.0 20.1 1.0 O A:CYS222 2.1 20.3 1.0 SG A:CYS222 2.2 18.0 1.0 HB3 A:CYS222 2.6 23.1 1.0 CB A:CYS222 2.8 19.3 1.0 HA A:HIS173 2.9 18.7 1.0 CE1 A:HIS173 2.9 20.5 1.0 C A:CYS222 3.0 16.4 1.0 CG A:HIS177 3.0 23.9 1.0 CE1 A:HIS177 3.0 27.3 1.0 HB2 A:HIS177 3.0 17.9 1.0 CG A:HIS173 3.0 18.8 1.0 HE1 A:HIS173 3.1 24.6 1.0 HB3 A:HIS177 3.1 17.9 1.0 HB2 A:HIS173 3.2 15.8 1.0 HE1 A:HIS177 3.2 32.7 1.0 CB A:HIS177 3.3 14.9 1.0 CB A:HIS173 3.4 13.2 1.0 CA A:CYS222 3.5 17.2 1.0 CA A:HIS173 3.6 15.6 1.0 HB2 A:CYS222 3.7 23.1 1.0 HA A:CYS222 4.0 20.6 1.0 N A:THR223 4.1 23.5 1.0 NE2 A:HIS173 4.1 16.9 1.0 HA A:THR223 4.1 35.5 1.0 NE2 A:HIS177 4.1 20.9 1.0 CD2 A:HIS177 4.1 23.8 1.0 CD2 A:HIS173 4.1 21.0 1.0 HE1 A:HIS227 4.2 29.4 1.0 HB3 A:HIS173 4.4 15.8 1.0 H A:CYS222 4.6 26.9 1.0 N A:CYS222 4.6 22.4 1.0 N A:HIS173 4.6 17.3 1.0 CA A:THR223 4.6 29.6 1.0 C A:HIS173 4.6 15.9 1.0 O A:GLN172 4.7 16.9 1.0 HE1 A:TYR132 4.7 22.4 1.0 H A:THR223 4.7 28.2 1.0 O A:HIS173 4.7 12.5 1.0 HD1 A:TYR132 4.7 29.1 1.0 HZ3 A:TRP169 4.7 23.8 1.0 CA A:HIS177 4.8 14.8 1.0 HE2 A:HIS173 4.9 20.2 1.0 HE2 A:HIS177 4.9 25.0 1.0 C A:GLN172 4.9 14.3 1.0 O A:HOH535 5.0 34.4 1.0 HD2 A:HIS177 5.0 28.5 1.0

Zinc binding site 2 out of 3 in the Oxidized Quinone Reductase 2 in Complex with Acridine Orange


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Oxidized Quinone Reductase 2 in Complex with Acridine Orange within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:24.1 occ:1.00 O A:HOH516 2.0 22.4 1.0 NE2 A:HIS72 2.1 19.8 1.0 OD2 A:ASP127 2.1 20.7 1.0 OD1 A:ASP127 2.4 32.6 1.0 CG A:ASP127 2.6 26.1 1.0 CE1 A:HIS72 2.9 28.6 1.0 HE1 A:HIS72 3.0 34.3 1.0 CD2 A:HIS72 3.2 20.1 1.0 HD2 A:LYS76 3.3 40.1 1.0 HD2 A:HIS72 3.5 24.1 1.0 HA2 A:GLY123 3.5 23.8 1.0 ND1 A:HIS72 4.1 20.8 1.0 CB A:ASP127 4.1 23.6 1.0 HG2 A:GLN122 4.2 22.8 1.0 HA3 A:GLY123 4.2 23.8 1.0 CG A:HIS72 4.2 20.6 1.0 CA A:GLY123 4.2 19.8 1.0 HE22 A:GLN122 4.2 26.9 1.0 CD A:LYS76 4.3 33.4 1.0 O A:HOH496 4.3 34.2 1.0 HB2 A:ASP127 4.4 28.4 1.0 HB3 A:ASP127 4.4 28.4 1.0 HZ2 A:LYS76 4.4 58.4 1.0 HE3 A:LYS76 4.6 39.4 1.0 HG3 A:LYS76 4.7 28.8 1.0 N A:GLY123 4.7 19.8 1.0 HG2 A:LYS76 4.7 28.8 1.0 HA A:ASP127 4.7 30.4 1.0 H A:GLY123 4.8 23.8 1.0 HD1 A:HIS72 4.8 25.0 1.0 CG A:LYS76 4.8 24.0 1.0 HD3 A:LYS76 4.9 40.1 1.0 CE A:LYS76 4.9 32.8 1.0 H A:ILE128 4.9 38.5 1.0 NE2 A:GLN122 5.0 22.4 1.0

Zinc binding site 3 out of 3 in the Oxidized Quinone Reductase 2 in Complex with Acridine Orange


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Oxidized Quinone Reductase 2 in Complex with Acridine Orange within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:17.6 occ:1.00 ND1 B:HIS173 2.0 15.4 1.0 ND1 B:HIS177 2.1 22.1 1.0 O B:CYS222 2.1 18.7 1.0 SG B:CYS222 2.3 15.2 1.0 HB3 B:CYS222 2.7 17.4 1.0 CB B:CYS222 2.9 14.5 1.0 HA B:HIS173 2.9 16.9 1.0 CE1 B:HIS173 3.0 19.1 1.0 C B:CYS222 3.0 15.9 1.0 CG B:HIS177 3.0 18.0 1.0 HB2 B:HIS177 3.0 15.9 1.0 CG B:HIS173 3.1 14.8 1.0 HB3 B:HIS177 3.1 15.9 1.0 CE1 B:HIS177 3.1 14.8 1.0 HE1 B:HIS173 3.1 22.9 1.0 HB2 B:HIS173 3.1 16.0 1.0 CB B:HIS177 3.2 13.3 1.0 HE1 B:HIS177 3.3 17.7 1.0 CB B:HIS173 3.4 13.3 1.0 CA B:CYS222 3.5 12.5 1.0 CA B:HIS173 3.6 14.1 1.0 HB2 B:CYS222 3.8 17.4 1.0 HA B:CYS222 4.0 15.0 1.0 HA B:THR223 4.1 19.5 1.0 N B:THR223 4.1 16.2 1.0 NE2 B:HIS173 4.1 14.3 1.0 CD2 B:HIS177 4.2 18.2 1.0 CD2 B:HIS173 4.2 14.0 1.0 NE2 B:HIS177 4.2 16.6 1.0 HE1 B:HIS227 4.3 18.7 1.0 HB3 B:HIS173 4.4 16.0 1.0 HE1 B:TYR132 4.5 15.3 1.0 N B:HIS173 4.6 12.0 1.0 N B:CYS222 4.6 14.7 1.0 CA B:THR223 4.6 16.2 1.0 C B:HIS173 4.6 10.4 1.0 HD1 B:TYR132 4.6 16.6 1.0 H B:CYS222 4.6 17.7 1.0 O B:GLN172 4.6 14.6 1.0 O B:HIS173 4.6 12.2 1.0 HZ3 B:TRP169 4.7 16.3 1.0 H B:THR223 4.8 19.4 1.0 CA B:HIS177 4.8 10.0 1.0 HE2 B:HIS173 4.9 17.2 1.0 C B:GLN172 4.9 10.8 1.0 HE2 B:HIS177 5.0 19.9 1.0 HD2 B:HIS177 5.0 21.9 1.0

K.K.Leung, B.H.Shilton. Binding of Dna-Intercalating Agents to Oxidized and Reduced Quinone Reductase 2. Biochemistry V. 54 7438 2015.
ISSN: ISSN 0006-2960
PubMed: 26636353
DOI: 10.1021/ACS.BIOCHEM.5B00884