Zinc in PDB 4cxp: Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate

All present enzymatic activity of Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate:
3.1.30.1;

The structure of Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate, PDB code: 4cxp was solved by T.-F.Yu, M.Maestre-Reyna, C.-Y.Ko, T.-P.Ko, Y.-J.Sun, T.-Y.Lin, 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)	24.34 / 1.22
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.140, 66.819, 99.556, 90.00, 90.00, 90.00
R / Rfree (%)	11.868 / 13.444

The binding sites of Zinc atom in the Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate (pdb code 4cxp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate, PDB code: 4cxp:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn931 b:10.0 occ:1.00 OD2 A:ASP124 2.2 8.7 1.0 O4 A:SO4961 2.2 6.0 0.7 NE2 A:HIS120 2.2 8.3 1.0 ND1 A:HIS58 2.2 8.4 1.0 O2 A:SO4961 2.4 9.8 0.7 OD1 A:ASP45 2.4 9.8 1.0 S A:SO4961 2.8 9.3 0.7 CE1 A:HIS58 3.0 8.5 1.0 CG A:ASP124 3.1 7.8 1.0 CE1 A:HIS120 3.2 8.4 1.0 CD2 A:HIS120 3.2 8.5 1.0 CG A:HIS58 3.3 8.6 1.0 CG A:ASP45 3.4 10.1 1.0 OD1 A:ASP124 3.5 8.5 1.0 ZN A:ZN933 3.5 8.1 1.0 O1 A:SO4961 3.7 10.1 0.7 OD2 A:ASP45 3.7 14.8 1.0 CB A:HIS58 3.7 8.7 1.0 O3 A:SO4961 4.1 8.5 0.7 NZ A:LYS48 4.2 13.7 1.0 CE A:LYS48 4.2 11.8 1.0 NE2 A:HIS58 4.2 9.3 1.0 ND1 A:HIS120 4.3 8.5 1.0 CG A:HIS120 4.3 8.1 1.0 CE1 A:HIS130 4.3 8.6 1.0 CD2 A:HIS58 4.4 9.2 1.0 CB A:ASP124 4.5 7.9 1.0 NE2 A:HIS6 4.5 8.2 1.0 O A:HOH2121 4.6 16.7 1.0 CB A:ASP45 4.7 11.1 1.0 CA A:HIS58 4.8 8.7 1.0 CE1 A:HIS6 5.0 8.5 1.0

Zinc binding site 2 out of 3 in the Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn932 b:9.7 occ:1.00 O A:HOH2260 2.1 14.1 1.0 O3 A:SO4961 2.1 8.5 0.7 NE2 A:HIS130 2.1 8.8 1.0 NE2 A:HIS154 2.2 9.4 1.0 OD2 A:ASP158 2.2 9.2 1.0 OD1 A:ASP158 2.5 8.2 1.0 CG A:ASP158 2.7 7.9 1.0 CE1 A:HIS130 3.0 8.6 1.0 CD2 A:HIS154 3.1 9.1 1.0 CD2 A:HIS130 3.2 8.3 1.0 CE1 A:HIS154 3.2 9.3 1.0 S A:SO4961 3.4 9.3 0.7 O2 A:SO4961 4.0 9.8 0.7 O A:HOH2123 4.1 27.1 1.0 O A:HOH2269 4.1 33.2 1.0 CB A:ASP158 4.2 7.8 1.0 N A:TRP1 4.2 7.6 1.0 ND1 A:HIS130 4.2 8.6 1.0 O A:HOH2001 4.2 16.7 1.0 O1 A:SO4961 4.2 10.1 0.7 CG A:HIS130 4.3 8.2 1.0 ND1 A:HIS154 4.3 9.2 1.0 CG A:HIS154 4.3 9.1 1.0 NE2 A:GLN127 4.3 8.0 1.0 O A:HOH2050 4.4 32.0 1.0 O4 A:SO4961 4.5 6.0 0.7 O A:HOH2299 4.5 16.3 1.0 O A:HOH2121 4.6 16.7 1.0 CA A:TRP1 4.9 7.8 1.0 ZN A:ZN933 4.9 8.1 1.0

Zinc binding site 3 out of 3 in the Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn933 b:8.1 occ:1.00 O4 A:SO4961 1.9 6.0 0.7 NE2 A:HIS6 2.0 8.2 1.0 OD1 A:ASP124 2.1 8.5 1.0 N A:TRP1 2.1 7.6 1.0 O A:TRP1 2.3 8.3 1.0 C A:TRP1 3.0 8.0 1.0 CA A:TRP1 3.0 7.8 1.0 CE1 A:HIS6 3.0 8.5 1.0 CD2 A:HIS6 3.0 8.2 1.0 CG A:ASP124 3.1 7.8 1.0 S A:SO4961 3.1 9.3 0.7 O3 A:SO4961 3.2 8.5 0.7 OD2 A:ASP124 3.5 8.7 1.0 ZN A:ZN931 3.5 10.0 1.0 CB A:TRP1 3.6 7.5 1.0 CE1 A:HIS120 3.8 8.4 1.0 NE2 A:HIS120 3.8 8.3 1.0 O1 A:SO4961 4.0 10.1 0.7 ND1 A:HIS6 4.1 9.0 1.0 CG A:HIS6 4.2 8.5 1.0 O2 A:SO4961 4.2 9.8 0.7 N A:GLY2 4.3 8.7 1.0 CG A:TRP1 4.3 7.6 1.0 CD1 A:TRP1 4.4 7.7 1.0 OD2 A:ASP45 4.4 14.8 1.0 CB A:ASP124 4.4 7.9 1.0 CE1 A:HIS130 4.5 8.6 1.0 NE2 A:HIS130 4.6 8.8 1.0 CA A:ASP124 4.7 7.3 1.0 ND1 A:HIS120 4.7 8.5 1.0 OD1 A:ASP158 4.8 8.2 1.0 CD2 A:HIS120 4.8 8.5 1.0 OD1 A:ASP45 4.8 9.8 1.0 ZN A:ZN932 4.9 9.7 1.0 O A:HOH2001 5.0 16.7 1.0 O A:GLY2 5.0 9.0 1.0 N A:ASP124 5.0 7.3 1.0

T.-F.Yu, M.Maestre-Reyna, C.-Y.Ko, T.-P.Ko, Y.-J.Sun, T.-Y.Lin, J.-F.Shaw, A.H.-J.Wang. Structural Insights of the Ssdna Binding Site in the Multifunctional Endonuclease ATBFN2 From Arabidopsis Thaliana To Be Published.