Zinc in PDB 3w52: Zinc-Dependent Bifunctional Nuclease

All present enzymatic activity of Zinc-Dependent Bifunctional Nuclease:
3.1.30.1;

The structure of Zinc-Dependent Bifunctional Nuclease, PDB code: 3w52 was solved by T.L.Chou, T.P.Ko, C.Y.Ko, J.F.Shaw, A.H.J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.254, 66.727, 99.487, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19.6

The binding sites of Zinc atom in the Zinc-Dependent Bifunctional Nuclease (pdb code 3w52). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Zinc-Dependent Bifunctional Nuclease, PDB code: 3w52:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Zinc-Dependent Bifunctional Nuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc-Dependent Bifunctional Nuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn309 b:12.0 occ:1.00 OD2 A:ASP124 2.1 7.4 1.0 O1 A:SO4312 2.1 9.1 1.0 NE2 A:HIS120 2.1 7.1 1.0 ND1 A:HIS58 2.2 7.8 1.0 O2 A:SO4312 2.5 12.5 1.0 OD1 A:ASP45 2.5 10.5 1.0 S A:SO4312 2.9 15.0 1.0 CE1 A:HIS58 3.0 10.0 1.0 CG A:ASP124 3.1 6.7 1.0 CD2 A:HIS120 3.1 7.8 1.0 CE1 A:HIS120 3.1 7.5 1.0 CG A:HIS58 3.3 7.6 1.0 OD1 A:ASP124 3.5 7.3 1.0 CG A:ASP45 3.5 13.8 1.0 ZN A:ZN311 3.5 9.7 1.0 O4 A:SO4312 3.7 12.7 1.0 CB A:HIS58 3.7 8.3 1.0 OD2 A:ASP45 3.9 15.9 1.0 O3 A:SO4312 4.0 11.8 1.0 NE2 A:HIS58 4.2 10.3 1.0 ND1 A:HIS120 4.2 6.5 1.0 CG A:HIS120 4.3 8.2 1.0 NZ A:LYS48 4.3 16.1 1.0 CE A:LYS48 4.3 14.2 1.0 CD2 A:HIS58 4.3 8.6 1.0 CE1 A:HIS130 4.4 9.4 1.0 CB A:ASP124 4.4 7.8 1.0 NE2 A:HIS6 4.5 7.0 1.0 O A:HOH507 4.7 19.4 1.0 CA A:HIS58 4.8 9.1 1.0 CB A:ASP45 4.9 12.3 1.0 CE1 A:HIS6 5.0 8.6 1.0

Zinc binding site 2 out of 3 in the Zinc-Dependent Bifunctional Nuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc-Dependent Bifunctional Nuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn310 b:11.5 occ:1.00 O3 A:SO4312 2.1 11.8 1.0 OD2 A:ASP158 2.1 8.1 1.0 NE2 A:HIS130 2.1 8.2 1.0 NE2 A:HIS154 2.1 8.4 1.0 O A:HOH501 2.2 14.4 1.0 OD1 A:ASP158 2.5 8.4 1.0 CG A:ASP158 2.7 7.0 1.0 CE1 A:HIS130 2.9 9.4 1.0 CD2 A:HIS154 3.1 10.5 1.0 CE1 A:HIS154 3.2 9.0 1.0 CD2 A:HIS130 3.2 8.0 1.0 S A:SO4312 3.4 15.0 1.0 O2 A:SO4312 3.9 12.5 1.0 ND1 A:HIS130 4.1 9.7 1.0 CB A:ASP158 4.2 7.6 1.0 O A:HOH729 4.2 30.1 1.0 N A:TRP1 4.2 8.3 1.0 O A:HOH772 4.2 34.3 1.0 N9 A:ADE308 4.2 34.6 1.0 CG A:HIS154 4.2 7.5 1.0 O4 A:SO4312 4.3 12.7 1.0 ND1 A:HIS154 4.3 7.2 1.0 O A:HOH506 4.3 15.9 1.0 CG A:HIS130 4.3 7.2 1.0 NE2 A:GLN127 4.4 7.2 1.0 O A:HOH507 4.4 19.4 1.0 O1 A:SO4312 4.5 9.1 1.0 O A:HOH505 4.5 18.3 1.0 CA A:TRP1 4.9 7.4 1.0 ZN A:ZN311 5.0 9.7 1.0

Zinc binding site 3 out of 3 in the Zinc-Dependent Bifunctional Nuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc-Dependent Bifunctional Nuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn311 b:9.7 occ:1.00 NE2 A:HIS6 2.0 7.0 1.0 O1 A:SO4312 2.0 9.1 1.0 N A:TRP1 2.0 8.3 1.0 OD1 A:ASP124 2.1 7.3 1.0 O A:TRP1 2.3 6.6 1.0 CA A:TRP1 2.9 7.4 1.0 C A:TRP1 3.0 6.1 1.0 CD2 A:HIS6 3.0 7.3 1.0 CE1 A:HIS6 3.0 8.6 1.0 CG A:ASP124 3.1 6.7 1.0 S A:SO4312 3.2 15.0 1.0 O3 A:SO4312 3.3 11.8 1.0 OD2 A:ASP124 3.5 7.4 1.0 ZN A:ZN309 3.5 12.0 1.0 CB A:TRP1 3.6 6.4 1.0 NE2 A:HIS120 3.8 7.1 1.0 CE1 A:HIS120 3.8 7.5 1.0 O4 A:SO4312 4.0 12.7 1.0 ND1 A:HIS6 4.1 8.5 1.0 CG A:HIS6 4.1 7.4 1.0 O2 A:SO4312 4.2 12.5 1.0 N A:GLY2 4.3 8.9 1.0 CG A:TRP1 4.3 6.7 1.0 CD1 A:TRP1 4.4 7.7 1.0 OD2 A:ASP45 4.4 15.9 1.0 CE1 A:HIS130 4.4 9.4 1.0 CB A:ASP124 4.4 7.8 1.0 CA A:ASP124 4.7 5.9 1.0 NE2 A:HIS130 4.7 8.2 1.0 ND1 A:HIS120 4.8 6.5 1.0 CD2 A:HIS120 4.8 7.8 1.0 OD1 A:ASP158 4.8 8.4 1.0 OD1 A:ASP45 4.9 10.5 1.0 ZN A:ZN310 5.0 11.5 1.0 N A:ASP124 5.0 6.5 1.0 O A:GLY2 5.0 8.8 1.0

T.L.Chou, T.P.Ko, C.Y.Ko, T.Y.Lin, R.T.Guo, T.F.Yu, H.C.Chan, J.F.Shaw, A.H.J.Wang. Mechanistic Insights to Catalysis By A Zinc-Dependent Bi-Functional Nuclease From Arabidopsis Thaliana Biocatal Agric Biotechnol 2013.
ISSN: ISSN 1878-8181
DOI: 10.1016/J.BCAB.2013.03.006