Atomistry » Zinc » PDB 2omg-2ovx » 2oq4
Atomistry »
  Zinc »
    PDB 2omg-2ovx »
      2oq4 »

Zinc in PDB 2oq4: Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate

Enzymatic activity of Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate

All present enzymatic activity of Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate:
4.2.99.18;

Protein crystallography data

The structure of Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate, PDB code: 2oq4 was solved by G.Golan, D.O.Zharkov, A.P.Grollman, G.Shoahm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.00 / 2.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.130, 107.130, 164.860, 90.00, 90.00, 90.00
R / Rfree (%) 37.4 / 43.2

Other elements in 2oq4:

The structure of Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate (pdb code 2oq4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate, PDB code: 2oq4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2oq4

Go back to Zinc Binding Sites List in 2oq4
Zinc binding site 1 out of 2 in the Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:52.9
occ:1.00
 SG A:CYS257 2.1 44.6 1.0
SG A:CYS237 2.1 31.4 1.0
CB A:CYS260 2.5 42.4 1.0
SG A:CYS240 2.5 38.3 1.0
SG A:CYS260 2.8 46.2 1.0
CB A:CYS257 3.1 47.4 1.0
CB A:CYS237 3.2 37.5 1.0
CB A:CYS240 3.6 39.5 1.0
CA A:CYS260 3.7 31.8 1.0
N A:CYS260 3.8 34.0 1.0
N A:CYS240 3.9 44.0 1.0
CA A:CYS240 4.2 44.5 1.0
N A:GLY241 4.3 44.7 1.0
C A:GLY259 4.3 37.0 1.0
NE1 A:TRP176 4.4 37.3 1.0
N A:SER242 4.4 33.5 1.0
CA A:CYS257 4.5 38.3 1.0
CA A:CYS237 4.6 43.7 1.0
CB A:SER242 4.7 54.9 1.0
O A:GLY259 4.7 37.7 1.0
CB A:ARG239 4.7 38.9 1.0
C A:CYS240 4.7 45.4 1.0
C A:ARG239 4.9 42.4 1.0
C A:CYS260 4.9 30.0 1.0
C A:CYS257 5.0 39.5 1.0

Zinc binding site 2 out of 2 in 2oq4

Go back to Zinc Binding Sites List in 2oq4
Zinc binding site 2 out of 2 in the Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Dna Repair Enzyme Endonuclease- VIII (Nei) From E. Coli (E2Q) in Complex with Ap-Site Containing Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:66.7
occ:1.00
 SG B:CYS260 2.0 42.9 1.0
SG B:CYS237 2.3 41.3 1.0
SG B:CYS257 2.4 60.4 1.0
SG B:CYS240 2.8 40.0 1.0
CB B:CYS260 3.2 41.9 1.0
CB B:CYS237 3.2 42.9 1.0
CB B:CYS257 3.3 62.2 1.0
N B:CYS260 3.3 50.9 1.0
N B:CYS240 3.7 62.6 1.0
CB B:CYS240 3.7 38.8 1.0
CA B:CYS260 3.9 47.6 1.0
CB B:ARG239 4.1 40.1 1.0
CA B:CYS240 4.2 63.5 1.0
O B:CYS257 4.3 63.8 1.0
NE1 B:TRP176 4.3 48.3 1.0
CB B:SER242 4.6 42.7 1.0
C B:ARG239 4.7 41.1 1.0
CA B:CYS257 4.7 63.7 1.0
CA B:CYS237 4.7 62.1 1.0
C B:CYS260 4.7 46.7 1.0
CA B:ARG239 4.8 41.7 1.0
N B:SER242 4.8 57.2 1.0
CD1 B:TRP176 4.8 47.8 1.0
C B:CYS240 4.8 64.3 1.0
CD B:ARG239 4.9 36.0 1.0
N B:GLY241 4.9 40.4 1.0
N B:ARG239 4.9 43.1 1.0
CG B:ARG239 4.9 38.4 1.0
C B:CYS257 5.0 63.6 1.0

Reference:

G.Golan, D.O.Zharkov, A.P.Grollman, G.Shoham. Active Site Plasticity of Endonuclease VIII: Conformational Changes Compensating For Different Substrates and Mutations of Critical Residues To Be Published.
Page generated: Thu Oct 17 02:43:24 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy