Zinc in PDB 2nq9: High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) Y72A Mutant Bound to Damaged Dna

All present enzymatic activity of High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) Y72A Mutant Bound to Damaged Dna:
3.1.21.2;

The structure of High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) Y72A Mutant Bound to Damaged Dna, PDB code: 2nq9 was solved by E.D.Garcin-Hosfield, D.J.Hosfield, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.500, 59.100, 51.200, 90.00, 94.00, 90.00
R / Rfree (%)	22 / 23.4

The binding sites of Zinc atom in the High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) Y72A Mutant Bound to Damaged Dna (pdb code 2nq9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) Y72A Mutant Bound to Damaged Dna, PDB code: 2nq9:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) Y72A Mutant Bound to Damaged Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) Y72A Mutant Bound to Damaged Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:13.7 occ:1.00 OP2 C:3DR307 1.9 15.2 1.0 NE2 A:HIS109 2.1 14.1 1.0 OE1 A:GLU145 2.1 11.1 1.0 NE2 A:HIS69 2.1 12.4 1.0 CD A:GLU145 2.9 9.7 1.0 P C:3DR307 2.9 15.7 1.0 CD2 A:HIS109 2.9 13.5 1.0 OP1 C:3DR307 3.0 15.2 1.0 OE2 A:GLU145 3.0 11.0 1.0 CD2 A:HIS69 3.1 11.4 1.0 CE1 A:HIS69 3.1 12.0 1.0 CE1 A:HIS109 3.1 13.8 1.0 ZN A:ZN402 3.5 16.2 1.0 OP3 C:3DR307 3.8 14.9 1.0 CE1 A:HIS216 3.9 8.2 1.0 OD1 A:ASN107 4.0 11.7 1.0 O5' C:3DR307 4.1 12.8 1.0 CG A:HIS109 4.1 13.0 1.0 ND1 A:HIS109 4.2 13.6 1.0 ND1 A:HIS69 4.2 11.4 1.0 CG A:HIS69 4.2 10.5 1.0 ND1 A:HIS216 4.3 10.4 1.0 CG A:GLU145 4.3 9.3 1.0 C5' C:3DR307 4.4 12.7 1.0 O C:HOH331 4.4 18.7 1.0 OE2 A:GLU261 4.4 11.2 1.0 CE1 A:HIS182 4.6 8.1 1.0 CB A:GLU145 4.7 8.7 1.0 O A:HOH567 4.9 17.6 1.0 OE1 A:GLU261 5.0 10.8 1.0

Zinc binding site 2 out of 3 in the High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) Y72A Mutant Bound to Damaged Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) Y72A Mutant Bound to Damaged Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:16.2 occ:1.00 ND1 A:HIS216 2.1 10.4 1.0 OD1 A:ASP179 2.2 10.4 1.0 OE1 A:GLU261 2.2 10.8 1.0 OE2 A:GLU145 2.2 11.0 1.0 OP2 C:3DR307 2.4 15.2 1.0 OP3 C:3DR307 2.7 14.9 1.0 CE1 A:HIS216 3.0 8.2 1.0 P C:3DR307 3.1 15.7 1.0 CD A:GLU261 3.1 9.1 1.0 CG A:HIS216 3.2 8.3 1.0 CD A:GLU145 3.2 9.7 1.0 OE2 A:GLU261 3.3 11.2 1.0 CG A:ASP179 3.3 8.5 1.0 ZN A:ZN401 3.5 13.7 1.0 OE1 A:GLU145 3.6 11.1 1.0 CB A:HIS216 3.6 8.8 1.0 CE1 A:HIS182 3.7 8.1 1.0 CB A:ASP179 3.8 8.3 1.0 O5' C:3DR307 3.9 12.8 1.0 OD1 A:ASN218 4.1 12.3 1.0 NE2 A:HIS182 4.1 10.4 1.0 NE2 A:HIS216 4.1 10.9 1.0 CD2 A:HIS216 4.2 8.2 1.0 CG A:GLU145 4.4 9.3 1.0 OD2 A:ASP179 4.4 9.6 1.0 OP1 C:3DR307 4.4 15.2 1.0 ND1 A:HIS182 4.4 10.3 1.0 CG A:GLU261 4.4 9.5 1.0 ZN A:ZN403 4.5 15.2 1.0 CE1 A:HIS231 4.5 10.4 1.0 NE2 A:HIS231 4.9 11.0 1.0 CD2 A:HIS182 4.9 7.8 1.0 NE2 A:HIS109 5.0 14.1 1.0 CA A:ASP179 5.0 7.8 1.0 C5' C:3DR307 5.0 12.7 1.0

Zinc binding site 3 out of 3 in the High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) Y72A Mutant Bound to Damaged Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) Y72A Mutant Bound to Damaged Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:15.2 occ:1.00 OP3 C:3DR307 2.1 14.9 1.0 NE2 A:HIS231 2.2 11.0 1.0 O3' B:DT306 2.2 13.7 1.0 NE2 A:HIS182 2.3 10.4 1.0 OD1 A:ASP229 2.3 12.1 1.0 OD2 A:ASP229 2.5 13.1 1.0 CG A:ASP229 2.7 10.6 1.0 CE1 A:HIS231 3.1 10.4 1.0 CD2 A:HIS182 3.2 7.8 1.0 C3' B:DT306 3.2 13.2 1.0 CD2 A:HIS231 3.2 10.3 1.0 CE1 A:HIS182 3.3 8.1 1.0 P C:3DR307 3.3 15.7 1.0 OP1 C:3DR307 3.7 15.2 1.0 C4' B:DT306 3.9 13.5 1.0 O5' C:3DR307 3.9 12.8 1.0 ND1 A:HIS231 4.2 10.1 1.0 OD1 A:ASP179 4.2 10.4 1.0 CB A:ASP229 4.3 11.1 1.0 CG A:HIS231 4.3 10.1 1.0 CG A:HIS182 4.4 9.2 1.0 ND1 A:HIS182 4.4 10.3 1.0 C5' B:DT306 4.4 14.1 1.0 ZN A:ZN402 4.5 16.2 1.0 OP2 C:3DR307 4.5 15.2 1.0 C2' B:DT306 4.5 13.9 1.0 O A:HOH564 4.6 13.0 1.0 O A:HOH424 4.9 18.5 1.0 CG A:ASP179 5.0 8.5 1.0 OE1 A:GLU261 5.0 10.8 1.0

E.D.Garcin, D.J.Hosfield, S.A.Desai, B.J.Haas, M.Bjoras, R.P.Cunningham, J.A.Tainer. Dna Apurinic-Apyrimidinic Site Binding and Excision By Endonuclease IV. Nat.Struct.Mol.Biol. V. 15 515 2008.
ISSN: ISSN 1545-9993
PubMed: 18408731
DOI: 10.1038/NSMB.1414