Zinc in PDB 5fbd: S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine

All present enzymatic activity of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine:
3.1.30.1;

The structure of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine, PDB code: 5fbd was solved by T.Koval, L.H.Oestergaard, J.Dohnalek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.08 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.040, 62.426, 84.118, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 21.2

The binding sites of Zinc atom in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine (pdb code 5fbd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine, PDB code: 5fbd:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:6.3 occ:1.00 O1 A:PO4601 2.0 10.9 1.0 N A:TRP21 2.1 7.0 1.0 NE2 A:HIS26 2.1 5.2 1.0 OD1 A:ASP139 2.1 5.2 1.0 O A:TRP21 2.2 6.6 1.0 C A:TRP21 2.9 6.7 1.0 CA A:TRP21 3.0 6.8 1.0 CE1 A:HIS26 3.0 5.6 1.0 CD2 A:HIS26 3.1 5.6 1.0 CG A:ASP139 3.2 4.8 1.0 P A:PO4601 3.3 10.4 1.0 OD2 A:ASP139 3.5 4.9 1.0 O A:HOH1002 3.6 4.2 0.5 ZN A:ZN402 3.7 5.7 1.0 O2 A:PO4601 3.7 8.7 1.0 CB A:TRP21 3.8 6.7 1.0 OD2 A:ASP65 3.9 6.1 1.0 NE2 A:HIS135 4.1 4.5 1.0 ND1 A:HIS26 4.1 5.8 1.0 O4 A:PO4601 4.2 10.1 1.0 NE2 A:HIS145 4.2 6.7 1.0 CG A:HIS26 4.2 5.8 1.0 O3 A:PO4601 4.2 9.6 1.0 N A:GLY22 4.2 6.7 1.0 CE1 A:HIS145 4.2 6.5 1.0 CE1 A:HIS135 4.3 4.5 1.0 ZN A:ZN403 4.3 8.8 1.0 OD2 A:ASP172 4.4 9.4 1.0 OD1 A:ASP172 4.4 9.0 1.0 CB A:ASP139 4.5 4.9 1.0 CG A:TRP21 4.5 6.8 1.0 CD1 A:TRP21 4.6 6.4 1.0 CG A:ASP172 4.6 8.8 1.0 CA A:ASP139 4.6 4.9 1.0 O A:HOH1134 4.8 18.6 1.0 CG A:ASP65 4.8 6.3 1.0 OD1 A:ASP65 4.9 5.8 1.0 O A:GLY22 4.9 6.2 1.0 O A:HOH1122 5.0 17.5 1.0 CA A:GLY22 5.0 6.5 1.0

Zinc binding site 2 out of 3 in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:5.7 occ:1.00 ND1 A:HIS80 2.0 3.9 1.0 O2 A:PO4601 2.0 8.7 1.0 OD2 A:ASP139 2.0 4.9 1.0 NE2 A:HIS135 2.2 4.5 1.0 OD1 A:ASP65 2.3 5.8 1.0 CE1 A:HIS80 2.8 3.9 1.0 CD2 A:HIS135 3.1 4.7 1.0 CG A:ASP139 3.1 4.8 1.0 CG A:HIS80 3.1 4.1 1.0 P A:PO4601 3.2 10.4 1.0 CE1 A:HIS135 3.2 4.5 1.0 CG A:ASP65 3.2 6.3 1.0 OD2 A:ASP65 3.4 6.1 1.0 OD1 A:ASP139 3.5 5.2 1.0 O1 A:PO4601 3.5 10.9 1.0 CB A:HIS80 3.6 4.5 1.0 ZN A:ZN401 3.7 6.3 1.0 O4 A:PO4601 3.8 10.1 1.0 NZ A:LYS68 3.8 6.4 1.0 NE2 A:HIS80 4.0 3.8 1.0 CD2 A:HIS80 4.2 3.9 1.0 CG A:HIS135 4.2 4.5 1.0 NE2 A:HIS26 4.2 5.2 1.0 ND1 A:HIS135 4.3 4.7 1.0 O3 A:PO4601 4.4 9.6 1.0 CE1 A:HIS145 4.4 6.5 1.0 CB A:ASP139 4.4 4.9 1.0 CE1 A:HIS26 4.5 5.6 1.0 CB A:ASP65 4.6 6.3 1.0 CA A:HIS80 4.6 4.7 1.0 O A:HOH1002 4.8 4.2 0.5 CA A:ASP65 5.0 6.3 1.0

Zinc binding site 3 out of 3 in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:8.8 occ:1.00 O3 A:PO4601 1.9 9.6 1.0 OD2 A:ASP172 2.0 9.4 1.0 NE2 A:HIS145 2.1 6.7 1.0 NE2 A:HIS168 2.1 9.0 1.0 CG A:ASP172 2.7 8.8 1.0 OD1 A:ASP172 2.8 9.0 1.0 O1 A:PO4601 2.9 10.9 1.0 CE1 A:HIS145 2.9 6.5 1.0 CE1 A:HIS168 3.0 9.2 1.0 P A:PO4601 3.0 10.4 1.0 CD2 A:HIS168 3.1 9.5 1.0 CD2 A:HIS145 3.1 6.5 1.0 C1' A:DCZ701 3.9 14.3 1.0 O4' A:DCZ701 3.9 14.6 1.0 O4 A:PO4601 4.1 10.1 1.0 ND1 A:HIS145 4.1 6.4 1.0 O2 A:PO4601 4.1 8.7 1.0 N A:TRP21 4.1 7.0 1.0 CB A:ASP172 4.1 9.3 1.0 ND1 A:HIS168 4.1 9.0 1.0 CG A:HIS145 4.2 6.2 1.0 CG A:HIS168 4.2 8.8 1.0 C4' A:DCZ701 4.2 15.8 1.0 O A:HOH1134 4.3 18.6 1.0 ZN A:ZN401 4.3 6.3 1.0 C2' A:DCZ701 4.5 13.7 1.0 O2 A:DCZ701 4.5 12.9 1.0 NE2 A:GLN142 4.6 6.7 1.0 O A:HOH1274 4.6 24.9 1.0 O A:HOH1307 4.7 21.5 1.0 OD1 A:ASP139 4.8 5.2 1.0 O A:TRP21 4.8 6.6 1.0 C3' A:DCZ701 5.0 14.6 1.0 CA A:TRP21 5.0 6.8 1.0

T.Koval, L.H.Stergaard, J.Lehmbeck, A.Nrgaard, P.Lipovova, J.Duskova, T.Skalova, M.Trundova, P.Kolenko, K.Fejfarova, J.Stransky, L.Svecova, J.Hasek, J.Dohnalek. Structural and Catalytic Properties of S1 Nuclease From Aspergillus Oryzae Responsible For Substrate Recognition, Cleavage, Non-Specificity, and Inhibition. Plos One V. 11 68832 2016.
ISSN: ESSN 1932-6203
PubMed: 28036383
DOI: 10.1371/JOURNAL.PONE.0168832