Zinc in PDB 2nqh: High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant

All present enzymatic activity of High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant:
3.1.21.2;

The structure of High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant, PDB code: 2nqh 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 / 1.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.800, 59.200, 50.900, 90.00, 111.00, 90.00
R / Rfree (%)	15.5 / 19.2

The binding sites of Zinc atom in the High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant (pdb code 2nqh). 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) E261Q Mutant, PDB code: 2nqh:
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) E261Q Mutant


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) E261Q Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.2 occ:1.00 O2 A:PO4999 2.0 10.7 1.0 NE2 A:HIS109 2.0 10.3 1.0 OE2 A:GLU145 2.0 8.0 1.0 NE2 A:HIS69 2.0 9.6 1.0 O1 A:PO4999 2.6 14.8 1.0 P A:PO4999 2.9 13.1 1.0 CD2 A:HIS109 2.9 10.5 1.0 CD A:GLU145 2.9 7.3 1.0 CE1 A:HIS69 3.0 9.2 1.0 CE1 A:HIS109 3.0 12.2 1.0 CD2 A:HIS69 3.1 7.8 1.0 OE1 A:GLU145 3.1 7.7 1.0 ZN A:ZN302 3.5 8.8 1.0 O3 A:PO4999 3.8 11.7 1.0 O4 A:PO4999 4.0 14.1 1.0 OD1 A:ASN107 4.0 10.2 1.0 CG A:HIS109 4.1 9.8 1.0 ND1 A:HIS109 4.1 11.6 1.0 ND1 A:HIS69 4.2 9.7 1.0 CE1 A:HIS216 4.2 6.5 1.0 NE2 A:GLN261 4.2 7.2 1.0 CG A:HIS69 4.2 7.7 1.0 CG A:GLU145 4.3 8.2 1.0 ND1 A:HIS216 4.3 6.6 1.0 CE1 A:HIS182 4.4 7.2 1.0 CB A:GLU145 4.7 7.8 1.0 OE1 A:GLN261 4.9 6.7 1.0 CD A:GLN261 5.0 7.1 1.0

Zinc binding site 2 out of 3 in the High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant


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) E261Q Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:8.8 occ:1.00 O2 A:PO4999 2.1 10.7 1.0 OD1 A:ASP179 2.1 7.3 1.0 OE1 A:GLU145 2.2 7.7 1.0 OE1 A:GLN261 2.2 6.7 1.0 ND1 A:HIS216 2.2 6.6 1.0 CD A:GLN261 3.0 7.1 1.0 CD A:GLU145 3.1 7.3 1.0 NE2 A:GLN261 3.1 7.2 1.0 CE1 A:HIS216 3.1 6.5 1.0 CG A:ASP179 3.2 7.0 1.0 CG A:HIS216 3.2 6.3 1.0 P A:PO4999 3.4 13.1 1.0 OE2 A:GLU145 3.4 8.0 1.0 ZN A:ZN301 3.5 9.2 1.0 CB A:HIS216 3.5 6.4 1.0 CB A:ASP179 3.7 6.9 1.0 CE1 A:HIS182 3.7 7.2 1.0 O4 A:PO4999 3.9 14.1 1.0 O3 A:PO4999 3.9 11.7 1.0 ND2 A:ASN218 4.1 7.7 1.0 NE2 A:HIS182 4.1 7.3 1.0 OD2 A:ASP179 4.3 7.3 1.0 NE2 A:HIS216 4.3 7.2 1.0 ND1 A:HIS182 4.3 6.8 1.0 CG A:GLU145 4.3 8.2 1.0 CD2 A:HIS216 4.3 6.6 1.0 CG A:GLN261 4.4 8.0 1.0 O1 A:PO4999 4.5 14.8 1.0 ZN A:ZN303 4.6 8.9 1.0 CE1 A:HIS231 4.6 9.4 1.0 NE2 A:HIS109 4.8 10.3 1.0 NE2 A:HIS231 4.8 8.3 1.0 CA A:ASP179 4.9 7.2 1.0 NE2 A:HIS69 4.9 9.6 1.0 CD2 A:HIS182 5.0 7.4 1.0

Zinc binding site 3 out of 3 in the High Resolution Crystal Structure of Escherichia Coli Endonuclease IV (Endo IV) E261Q Mutant


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) E261Q Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:8.9 occ:1.00 OD1 A:ASP229 2.0 21.3 1.0 NE2 A:HIS182 2.0 7.3 1.0 O3 A:PO4999 2.0 11.7 1.0 NE2 A:HIS231 2.0 8.3 1.0 OD2 A:ASP229 2.6 16.2 1.0 CG A:ASP229 2.6 13.9 1.0 CE1 A:HIS182 3.0 7.2 1.0 CE1 A:HIS231 3.0 9.4 1.0 CD2 A:HIS231 3.1 8.4 1.0 CD2 A:HIS182 3.1 7.4 1.0 P A:PO4999 3.3 13.1 1.0 O4 A:PO4999 3.9 14.1 1.0 O2 A:PO4999 4.0 10.7 1.0 CB A:ASP229 4.1 12.9 1.0 ND1 A:HIS231 4.1 8.4 1.0 OD1 A:ASP179 4.1 7.3 1.0 ND1 A:HIS182 4.2 6.8 1.0 CG A:HIS231 4.2 7.8 1.0 CG A:HIS182 4.2 7.1 1.0 O A:HOH1247 4.4 50.0 1.0 O1 A:PO4999 4.4 14.8 1.0 O A:HOH1121 4.5 34.1 1.0 ZN A:ZN302 4.6 8.8 1.0 O A:HOH1033 4.7 13.8 1.0 CG A:ASP179 4.9 7.0 1.0 OE1 A:GLN261 4.9 6.7 1.0 CA A:ASP229 5.0 11.0 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