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Zinc in PDB 2opf: Crystal Structure of the Dna Repair Enzyme Endonuclease-VIII (Nei) From E. Coli (R252A) in Complex with Ap-Site Containing Dna Substrate

Enzymatic activity of Crystal Structure of the Dna Repair Enzyme Endonuclease-VIII (Nei) From E. Coli (R252A) 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 (R252A) 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 (R252A) in Complex with Ap-Site Containing Dna Substrate, PDB code: 2opf was solved by G.Golan, D.O.Zharov, A.P.Grollman, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.41 / 1.85
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 73.556, 73.556, 170.113, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 26.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Dna Repair Enzyme Endonuclease-VIII (Nei) From E. Coli (R252A) in Complex with Ap-Site Containing Dna Substrate (pdb code 2opf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of the Dna Repair Enzyme Endonuclease-VIII (Nei) From E. Coli (R252A) in Complex with Ap-Site Containing Dna Substrate, PDB code: 2opf:

Zinc binding site 1 out of 1 in 2opf

Go back to Zinc Binding Sites List in 2opf
Zinc binding site 1 out of 1 in the Crystal Structure of the Dna Repair Enzyme Endonuclease-VIII (Nei) From E. Coli (R252A) 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 (R252A) in Complex with Ap-Site Containing Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:32.4
occ:1.00
 SG A:CYS257 2.2 32.1 1.0
SG A:CYS260 2.3 31.8 1.0
SG A:CYS237 2.3 32.7 1.0
SG A:CYS240 2.4 32.6 1.0
CB A:CYS237 3.0 35.4 1.0
CB A:CYS257 3.2 31.4 1.0
CB A:CYS260 3.3 31.7 1.0
CB A:CYS240 3.5 37.5 1.0
N A:CYS260 3.6 33.9 1.0
N A:CYS240 3.8 35.8 1.0
CA A:CYS260 4.0 32.0 1.0
CA A:CYS240 4.1 36.7 1.0
C A:GLY259 4.2 35.9 1.0
NE1 A:TRP176 4.3 28.9 1.0
CA A:GLY259 4.5 36.0 1.0
CA A:CYS237 4.6 37.4 1.0
CB A:ARG239 4.6 36.4 1.0
CA A:CYS257 4.6 31.7 1.0
CD A:ARG239 4.6 39.1 1.0
CB A:SER242 4.6 40.0 1.0
N A:GLY259 4.6 37.0 1.0
C A:CYS240 4.7 39.0 1.0
N A:GLY241 4.7 39.1 1.0
N A:SER242 4.7 38.9 1.0
C A:ARG239 4.8 36.0 1.0
CG A:ARG239 4.8 36.6 1.0
C A:CYS257 4.9 32.7 1.0
O A:CYS257 4.9 33.0 1.0
C A:CYS260 5.0 31.7 1.0
O A:GLY259 5.0 37.8 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 02:42:59 2024

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