Zinc in PDB 4cxo: Bifunctional Endonuclease in Complex with Ssdna

All present enzymatic activity of Bifunctional Endonuclease in Complex with Ssdna:
3.1.30.1;

The structure of Bifunctional Endonuclease in Complex with Ssdna, PDB code: 4cxo 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)	27.98 / 1.67
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.902, 66.159, 98.148, 90.00, 90.00, 90.00
R / Rfree (%)	14.002 / 19.145

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

Zinc binding site 1 out of 3 in the Bifunctional Endonuclease in Complex with Ssdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bifunctional Endonuclease in Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn451 b:22.7 occ:1.00 O4 A:SO4461 2.1 20.4 1.0 OD2 A:ASP124 2.2 18.2 1.0 ND1 A:HIS58 2.2 18.7 1.0 NE2 A:HIS120 2.2 19.1 1.0 O2 A:SO4461 2.4 25.6 1.0 OD1 A:ASP45 2.5 19.7 1.0 S A:SO4461 2.7 25.3 1.0 CE1 A:HIS58 2.9 21.7 1.0 CG A:ASP124 3.2 19.1 1.0 CE1 A:HIS120 3.2 20.9 1.0 CD2 A:HIS120 3.2 19.2 1.0 CG A:HIS58 3.3 21.0 1.0 CG A:ASP45 3.5 21.8 1.0 OD1 A:ASP124 3.5 19.5 1.0 ZN A:ZN453 3.5 19.5 1.0 O1 A:SO4461 3.7 24.7 1.0 CB A:HIS58 3.7 21.8 1.0 OD2 A:ASP45 3.8 26.4 1.0 O3 A:SO4461 4.0 22.0 1.0 NE2 A:HIS58 4.1 21.4 1.0 CE A:LYS48 4.2 31.0 1.0 CD2 A:HIS58 4.3 20.2 1.0 ND1 A:HIS120 4.3 18.6 1.0 NZ A:LYS48 4.3 35.6 1.0 CG A:HIS120 4.4 17.7 1.0 CE1 A:HIS130 4.4 19.0 1.0 CB A:ASP124 4.5 17.9 1.0 NE2 A:HIS6 4.5 18.8 1.0 CB A:ASP45 4.8 22.6 1.0 CA A:HIS58 4.8 21.7 1.0 CE1 A:HIS6 4.9 19.3 1.0 CA A:ASP45 5.0 21.6 1.0

Zinc binding site 2 out of 3 in the Bifunctional Endonuclease in Complex with Ssdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bifunctional Endonuclease in Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn452 b:22.2 occ:1.00 O3' A:TMP401 2.1 28.4 1.0 O3 A:SO4461 2.1 22.0 1.0 NE2 A:HIS154 2.1 19.5 1.0 NE2 A:HIS130 2.2 18.5 1.0 OD2 A:ASP158 2.2 19.1 1.0 OD1 A:ASP158 2.5 18.5 1.0 CG A:ASP158 2.6 19.4 1.0 CE1 A:HIS130 3.0 19.0 1.0 CE1 A:HIS154 3.1 21.0 1.0 CD2 A:HIS154 3.2 21.9 1.0 CD2 A:HIS130 3.2 18.3 1.0 C3' A:TMP401 3.4 37.9 1.0 S A:SO4461 3.5 25.3 1.0 C4' A:TMP401 3.8 37.5 1.0 O2 A:SO4461 3.9 25.6 1.0 C1' A:TMP401 4.0 38.2 1.0 O4' A:TMP401 4.0 39.7 1.0 C2' A:TMP401 4.1 40.7 1.0 N A:TRP1 4.1 17.2 1.0 CB A:ASP158 4.1 17.4 1.0 O1 A:SO4461 4.2 24.7 1.0 ND1 A:HIS130 4.2 20.0 1.0 ND1 A:HIS154 4.2 20.2 1.0 CG A:HIS154 4.3 21.3 1.0 CG A:HIS130 4.3 19.1 1.0 O A:HOH2001 4.3 29.4 1.0 NE2 A:GLN127 4.4 17.0 1.0 O4 A:SO4461 4.6 20.4 1.0 O A:HOH2183 4.6 28.6 1.0 CA A:TRP1 4.8 19.4 1.0 ZN A:ZN453 4.9 19.5 1.0

Zinc binding site 3 out of 3 in the Bifunctional Endonuclease in Complex with Ssdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Bifunctional Endonuclease in Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn453 b:19.5 occ:1.00 O4 A:SO4461 1.9 20.4 1.0 NE2 A:HIS6 2.0 18.8 1.0 N A:TRP1 2.1 17.2 1.0 OD1 A:ASP124 2.1 19.5 1.0 O A:TRP1 2.3 17.5 1.0 CA A:TRP1 2.9 19.4 1.0 C A:TRP1 2.9 17.9 1.0 CE1 A:HIS6 3.0 19.3 1.0 S A:SO4461 3.0 25.3 1.0 CD2 A:HIS6 3.0 16.9 1.0 CG A:ASP124 3.1 19.1 1.0 O3 A:SO4461 3.1 22.0 1.0 OD2 A:ASP124 3.5 18.2 1.0 CB A:TRP1 3.5 18.2 1.0 ZN A:ZN451 3.5 22.7 1.0 NE2 A:HIS120 3.8 19.1 1.0 CE1 A:HIS120 3.8 20.9 1.0 O1 A:SO4461 3.9 24.7 1.0 ND1 A:HIS6 4.1 17.1 1.0 O2 A:SO4461 4.1 25.6 1.0 CG A:HIS6 4.1 17.4 1.0 N A:GLY2 4.2 16.7 1.0 CG A:TRP1 4.3 17.1 1.0 CD1 A:TRP1 4.3 15.7 1.0 OD2 A:ASP45 4.4 26.4 1.0 CB A:ASP124 4.4 17.9 1.0 CE1 A:HIS130 4.5 19.0 1.0 CA A:ASP124 4.7 16.4 1.0 NE2 A:HIS130 4.7 18.5 1.0 ND1 A:HIS120 4.8 18.6 1.0 CD2 A:HIS120 4.8 19.2 1.0 OD1 A:ASP158 4.8 18.5 1.0 OD1 A:ASP45 4.8 19.7 1.0 ZN A:ZN452 4.9 22.2 1.0 O A:GLY2 5.0 17.9 1.0 N A:ASP124 5.0 16.9 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.