Zinc in PDB 1k3w: Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Dna

The structure of Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Dna, PDB code: 1k3w was solved by G.Golan, D.O.Zharkov, R.Gilboa, A.S.Fernandes, J.H.Kycia, S.E.Gerchman, R.A.Rieger, A.P.Grollman, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.42
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	76.030, 76.030, 164.933, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 20.3

The binding sites of Zinc atom in the Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Dna (pdb code 1k3w). 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 A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Dna, PDB code: 1k3w:

Zinc binding site 1 out of 1 in the Crystal Structure of A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Dna


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 A Trapped Reaction Intermediate of the Dna Repair Enzyme Endonuclease VIII with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:15.7 occ:1.00 SG A:CYS240 2.3 17.0 1.0 SG A:CYS260 2.3 15.6 1.0 SG A:CYS257 2.3 17.1 1.0 SG A:CYS237 2.4 16.0 1.0 CB A:CYS237 3.1 18.9 1.0 CB A:CYS257 3.2 16.0 1.0 CB A:CYS260 3.4 14.9 1.0 CB A:CYS240 3.5 15.9 1.0 N A:CYS260 3.7 15.3 1.0 N A:CYS240 3.8 16.3 1.0 CA A:CYS260 4.1 14.2 1.0 CA A:CYS240 4.2 16.7 1.0 C A:GLY259 4.3 16.4 1.0 NE1 A:TRP176 4.3 14.0 1.0 CA A:GLY259 4.5 18.0 1.0 N A:GLY259 4.6 16.1 1.0 CB A:ARG239 4.6 17.2 1.0 CA A:CYS237 4.6 18.2 1.0 CA A:CYS257 4.6 16.1 1.0 N A:GLY241 4.7 17.8 1.0 C A:CYS240 4.7 17.5 1.0 CB A:SER242 4.7 19.4 1.0 N A:SER242 4.8 18.6 1.0 C A:ARG239 4.8 17.0 1.0 C A:CYS257 4.9 16.7 1.0 O A:CYS257 5.0 16.9 1.0 C A:CYS260 5.0 14.0 1.0

D.O.Zharkov, G.Golan, R.Gilboa, A.S.Fernandes, S.E.Gerchman, J.H.Kycia, R.A.Rieger, A.P.Grollman, G.Shoham. Structural Analysis of An Escherichia Coli Endonuclease VIII Covalent Reaction Intermediate. Embo J. V. 21 789 2002.
ISSN: ISSN 0261-4189
PubMed: 11847126
DOI: 10.1093/EMBOJ/21.4.789