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

Enzymatic activity of 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;

Protein crystallography data

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

Zinc Binding Sites:

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 5fbd

Go back to Zinc Binding Sites List in 5fbd
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 5fbd

Go back to Zinc Binding Sites List in 5fbd
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 5fbd

Go back to Zinc Binding Sites List in 5fbd
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

Reference:

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
Page generated: Wed Dec 16 06:13:34 2020

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