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

Enzymatic activity of 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;

Protein crystallography data

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

Zinc Binding Sites:

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 4zvl

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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 4zvl

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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 4zvl

Go back to Zinc Binding Sites List in 4zvl
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

Reference:

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
Page generated: Wed Dec 16 06:00:08 2020

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