Zinc in PDB 1qum: Crystal Structure of Escherichia Coli Endonuclease IV in Complex with Damaged Dna

All present enzymatic activity of Crystal Structure of Escherichia Coli Endonuclease IV in Complex with Damaged Dna:
3.1.21.2;

The structure of Crystal Structure of Escherichia Coli Endonuclease IV in Complex with Damaged Dna, PDB code: 1qum was solved by D.J.Hosfield, Y.Guan, B.J.Haas, R.P.Cunningham, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.120, 58.727, 51.146, 90.00, 94.97, 90.00
R / Rfree (%)	20.3 / 25.4

The binding sites of Zinc atom in the Crystal Structure of Escherichia Coli Endonuclease IV in Complex with Damaged Dna (pdb code 1qum). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Escherichia Coli Endonuclease IV in Complex with Damaged Dna, PDB code: 1qum:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Escherichia Coli Endonuclease IV in Complex with Damaged 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 Escherichia Coli Endonuclease IV in Complex with Damaged Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:25.4 occ:1.00 NE2 A:HIS109 1.9 29.0 1.0 OE1 A:GLU145 2.0 25.2 1.0 OP2 C:3DR907 2.0 30.1 1.0 NE2 A:HIS69 2.1 25.9 1.0 CD A:GLU145 2.8 22.6 1.0 P C:3DR907 2.9 26.2 1.0 OP1 C:3DR907 2.9 25.0 1.0 CD2 A:HIS109 2.9 29.1 1.0 CE1 A:HIS109 3.0 42.0 1.0 CE1 A:HIS69 3.0 27.7 1.0 CD2 A:HIS69 3.1 23.0 1.0 OE2 A:GLU145 3.1 24.0 1.0 ZN A:ZN303 3.8 34.2 1.0 OP3 C:3DR907 3.8 24.0 1.0 ND1 A:HIS109 4.1 42.8 1.0 CE1 A:HIS216 4.1 22.9 1.0 CG A:HIS109 4.1 35.7 1.0 ND1 A:HIS69 4.2 26.5 1.0 O5' C:3DR907 4.2 26.2 1.0 CG A:HIS69 4.2 25.5 1.0 CG A:GLU145 4.2 26.1 1.0 ND2 A:ASN107 4.3 31.6 1.0 O C:HOH1301 4.4 44.2 1.0 C5' C:3DR907 4.5 24.9 1.0 ND1 A:HIS216 4.5 24.1 1.0 CB A:GLU145 4.6 26.1 1.0 OD1 A:ASN107 4.6 36.0 1.0 OE2 A:GLU261 4.6 27.7 1.0 O C:HOH1168 4.9 52.5 1.0 CG A:ASN107 4.9 31.7 1.0 CE1 A:HIS182 4.9 21.6 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Escherichia Coli Endonuclease IV in Complex with Damaged Dna


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 Escherichia Coli Endonuclease IV in Complex with Damaged Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:26.2 occ:1.00 O3' B:DC906 2.0 27.4 1.0 NE2 A:HIS182 2.1 22.4 1.0 NE2 A:HIS231 2.2 26.0 1.0 OP3 C:3DR907 2.2 24.0 1.0 OD1 A:ASP229 2.2 25.2 1.0 OD2 A:ASP229 2.7 27.4 1.0 CG A:ASP229 2.8 23.8 1.0 CE1 A:HIS182 3.0 21.6 1.0 CD2 A:HIS182 3.1 23.1 1.0 CE1 A:HIS231 3.1 22.3 1.0 C3' B:DC906 3.1 25.9 1.0 CD2 A:HIS231 3.2 26.8 1.0 P C:3DR907 3.5 26.2 1.0 C4' B:DC906 3.8 24.8 1.0 OP1 C:3DR907 3.8 25.0 1.0 O5' C:3DR907 4.0 26.2 1.0 OD2 A:ASP179 4.0 22.8 1.0 O C:HOH1301 4.1 44.2 1.0 ZN A:ZN303 4.1 34.2 1.0 ND1 A:HIS182 4.1 22.6 1.0 CG A:HIS182 4.2 22.4 1.0 ND1 A:HIS231 4.2 21.8 1.0 CB A:ASP229 4.3 26.3 1.0 C5' B:DC906 4.3 26.1 1.0 CG A:HIS231 4.3 20.8 1.0 C2' B:DC906 4.4 31.1 1.0 O A:HOH1012 4.6 27.3 1.0 OP2 C:3DR907 4.7 30.1 1.0 OE1 A:GLU261 4.8 21.9 1.0 O A:HOH1059 4.8 38.6 1.0 CG A:ASP179 4.8 24.3 1.0 OE2 A:GLU145 5.0 24.0 1.0 O C:HOH1168 5.0 52.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Escherichia Coli Endonuclease IV in Complex with Damaged Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Escherichia Coli Endonuclease IV in Complex with Damaged Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:34.2 occ:1.00 OD2 A:ASP179 2.1 22.8 1.0 OE2 A:GLU145 2.2 24.0 1.0 OE1 A:GLU261 2.3 21.9 1.0 ND1 A:HIS216 2.3 24.1 1.0 OP3 C:3DR907 2.3 24.0 1.0 OP2 C:3DR907 2.5 30.1 1.0 P C:3DR907 2.9 26.2 1.0 CE1 A:HIS216 3.2 22.9 1.0 CD A:GLU261 3.2 22.7 1.0 CD A:GLU145 3.2 22.6 1.0 CG A:ASP179 3.2 24.3 1.0 CG A:HIS216 3.4 24.7 1.0 CE1 A:HIS182 3.5 21.6 1.0 OE2 A:GLU261 3.5 27.7 1.0 OE1 A:GLU145 3.7 25.2 1.0 CB A:HIS216 3.7 23.5 1.0 O5' C:3DR907 3.7 26.2 1.0 CB A:ASP179 3.7 22.8 1.0 ZN A:ZN301 3.8 25.4 1.0 NE2 A:HIS182 3.9 22.4 1.0 OD1 A:ASN218 4.0 26.1 1.0 ZN A:ZN302 4.1 26.2 1.0 ND1 A:HIS182 4.2 22.6 1.0 OP1 C:3DR907 4.2 25.0 1.0 OD1 A:ASP179 4.3 24.5 1.0 NE2 A:HIS216 4.3 27.5 1.0 CG A:GLU145 4.3 26.1 1.0 CD2 A:HIS216 4.4 23.1 1.0 CE1 A:HIS231 4.5 22.3 1.0 CG A:GLU261 4.5 23.2 1.0 NE2 A:HIS231 4.7 26.0 1.0 CD2 A:HIS182 4.8 23.1 1.0 C5' C:3DR907 4.9 24.9 1.0 CG A:HIS182 4.9 22.4 1.0 CA A:ASP179 5.0 21.4 1.0

D.J.Hosfield, Y.Guan, B.J.Haas, R.P.Cunningham, J.A.Tainer. Structure of the Dna Repair Enzyme Endonuclease IV and Its Dna Complex: Double-Nucleotide Flipping at Abasic Sites and Three-Metal-Ion Catalysis. Cell(Cambridge,Mass.) V. 98 397 1999.
ISSN: ISSN 0092-8674
PubMed: 10458614
DOI: 10.1016/S0092-8674(00)81968-6