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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: Wed Dec 16 03:46:34 2020

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