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Zinc in PDB 5fbb: S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate

Enzymatic activity of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate

All present enzymatic activity of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate:
3.1.30.1;

Protein crystallography data

The structure of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate, PDB code: 5fbb 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) 35.51 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 42.840, 47.640, 62.600, 106.42, 90.09, 106.25
R / Rfree (%) 14.5 / 18.8

Other elements in 5fbb:

The structure of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate also contains other interesting chemical elements:

Calcium (Ca) 5 atoms
Sodium (Na) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate (pdb code 5fbb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate, PDB code: 5fbb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5fbb

Go back to Zinc Binding Sites List in 5fbb
Zinc binding site 1 out of 6 in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate


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 Adenosine 5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:9.8
occ:1.00
OD1 A:ASP139 2.0 9.7 1.0
O3 A:PO4601 2.1 17.0 1.0
NE2 A:HIS26 2.1 8.1 1.0
N A:TRP21 2.1 9.6 1.0
O A:TRP21 2.1 10.4 1.0
O1 A:PO4601 2.8 21.5 1.0
C A:TRP21 2.8 10.5 1.0
P A:PO4601 2.9 23.8 1.0
CA A:TRP21 2.9 9.9 1.0
CE1 A:HIS26 3.0 8.7 1.0
CD2 A:HIS26 3.1 8.1 1.0
CG A:ASP139 3.1 9.3 1.0
ZN A:ZN402 3.4 10.1 1.0
OD2 A:ASP139 3.5 9.0 1.0
CB A:TRP21 3.6 10.5 1.0
O4 A:PO4601 3.8 23.3 1.0
NE2 A:HIS135 4.0 6.5 1.0
OD2 A:ASP65 4.0 12.0 1.0
O2 A:PO4601 4.1 24.8 1.0
CE1 A:HIS135 4.1 6.7 1.0
ND1 A:HIS26 4.1 8.3 1.0
N A:GLY22 4.2 10.1 1.0
CE1 A:HIS145 4.2 11.0 1.0
CG A:HIS26 4.2 8.2 1.0
NE2 A:HIS145 4.3 10.4 1.0
CG A:TRP21 4.4 9.9 1.0
CB A:ASP139 4.5 9.7 1.0
CD1 A:TRP21 4.5 9.9 1.0
OD1 A:ASP172 4.6 9.4 1.0
ZN A:ZN403 4.6 11.8 1.0
CA A:ASP139 4.7 8.9 1.0
OD1 A:ASP65 4.8 10.2 1.0
CG A:ASP65 4.8 11.9 1.0
CA A:GLY22 4.9 10.9 1.0
O A:GLY22 4.9 10.7 1.0
ND1 A:HIS145 5.0 9.9 1.0
CG A:ASP172 5.0 10.6 1.0
CD2 A:HIS135 5.0 6.9 1.0
O A:HOH1584 5.0 20.5 1.0
O A:HOH1571 5.0 17.6 1.0

Zinc binding site 2 out of 6 in 5fbb

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Zinc binding site 2 out of 6 in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate


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 Adenosine 5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:10.1
occ:1.00
O3 A:PO4601 1.9 17.0 1.0
OD2 A:ASP139 2.0 9.0 1.0
NE2 A:HIS135 2.1 6.5 1.0
ND1 A:HIS80 2.1 9.8 1.0
OD1 A:ASP65 2.6 10.2 1.0
CE1 A:HIS80 2.9 9.3 1.0
O2 A:PO4601 3.0 24.8 1.0
CD2 A:HIS135 3.0 6.9 1.0
CG A:ASP139 3.0 9.3 1.0
CE1 A:HIS135 3.1 6.7 1.0
P A:PO4601 3.1 23.8 1.0
CG A:HIS80 3.2 9.9 1.0
OD1 A:ASP139 3.4 9.7 1.0
ZN A:ZN401 3.4 9.8 1.0
CG A:ASP65 3.4 11.9 1.0
CB A:HIS80 3.6 10.5 1.0
OD2 A:ASP65 3.7 12.0 1.0
O4 A:PO4601 4.0 23.3 1.0
NE2 A:HIS26 4.0 8.1 1.0
NE2 A:HIS80 4.1 9.4 1.0
ND1 A:HIS135 4.2 7.0 1.0
CG A:HIS135 4.2 7.1 1.0
NZ A:LYS68 4.2 14.7 1.0
CD2 A:HIS80 4.2 9.7 1.0
O1 A:PO4601 4.3 21.5 1.0
CB A:ASP139 4.4 9.7 1.0
CE1 A:HIS26 4.4 8.7 1.0
CE1 A:HIS145 4.4 11.0 1.0
CA A:HIS80 4.6 10.2 1.0
CB A:ASP65 4.9 10.8 1.0
O A:TRP21 4.9 10.4 1.0
CD2 A:HIS26 5.0 8.1 1.0

Zinc binding site 3 out of 6 in 5fbb

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Zinc binding site 3 out of 6 in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate


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 Adenosine 5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:11.8
occ:1.00
OD2 A:ASP172 2.1 12.1 1.0
O A:HOH1203 2.1 16.2 1.0
O1 A:PO4601 2.1 21.5 1.0
NE2 A:HIS145 2.1 10.4 1.0
NE2 A:HIS168 2.2 12.5 1.0
CG A:ASP172 2.7 10.6 1.0
OD1 A:ASP172 2.7 9.4 1.0
CE1 A:HIS145 3.0 11.0 1.0
CD2 A:HIS168 3.1 11.8 1.0
CE1 A:HIS168 3.1 13.6 1.0
CD2 A:HIS145 3.2 10.6 1.0
P A:PO4601 3.2 23.8 1.0
O2 A:PO4601 3.6 24.8 1.0
O4 A:PO4601 4.0 23.3 1.0
N A:TRP21 4.1 9.6 1.0
ND1 A:HIS145 4.1 9.9 1.0
O A:HOH1584 4.2 20.5 1.0
CB A:ASP172 4.2 9.4 1.0
ND1 A:HIS168 4.2 13.2 1.0
CG A:HIS168 4.2 12.0 1.0
CG A:HIS145 4.3 9.9 1.0
O A:HOH1632 4.4 32.0 1.0
NE2 A:GLN142 4.5 9.7 1.0
O3 A:PO4601 4.5 17.0 1.0
ZN A:ZN401 4.6 9.8 1.0
C2 A:AMP701 4.7 17.4 1.0
O A:TRP21 4.8 10.4 1.0
CA A:TRP21 4.9 9.9 1.0
C A:TRP21 4.9 10.5 1.0

Zinc binding site 4 out of 6 in 5fbb

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Zinc binding site 4 out of 6 in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:10.0
occ:1.00
O1 B:PO4601 1.9 15.2 1.0
NE2 B:HIS26 2.0 7.2 1.0
OD1 B:ASP139 2.1 7.2 1.0
N B:TRP21 2.1 8.6 1.0
O B:TRP21 2.2 8.1 1.0
O3 B:PO4601 2.8 21.6 1.0
P B:PO4601 2.8 23.8 1.0
C B:TRP21 2.9 8.7 1.0
CA B:TRP21 2.9 8.5 1.0
CE1 B:HIS26 3.0 7.6 1.0
CD2 B:HIS26 3.0 8.0 1.0
CG B:ASP139 3.1 7.6 1.0
ZN B:ZN402 3.4 9.5 1.0
OD2 B:ASP139 3.5 6.9 1.0
CB B:TRP21 3.7 8.6 1.0
O4 B:PO4601 3.7 24.2 1.0
NE2 B:HIS135 3.9 7.7 1.0
OD2 B:ASP65 4.0 14.8 1.0
O2 B:PO4601 4.1 27.5 1.0
CE1 B:HIS135 4.1 7.9 1.0
ND1 B:HIS26 4.1 7.7 1.0
CG B:HIS26 4.1 7.6 1.0
CE1 B:HIS145 4.2 8.1 1.0
N B:GLY22 4.2 8.6 1.0
NE2 B:HIS145 4.3 8.2 1.0
CB B:ASP139 4.5 7.8 1.0
CG B:TRP21 4.5 8.9 1.0
OD1 B:ASP172 4.6 10.1 1.0
ZN B:ZN403 4.6 11.4 1.0
CD1 B:TRP21 4.6 8.5 1.0
CA B:ASP139 4.7 8.0 1.0
OD1 B:ASP65 4.7 13.2 1.0
CG B:ASP65 4.8 14.3 1.0
O B:HOH1591 4.9 20.2 1.0
CG B:ASP172 4.9 11.1 1.0
CA B:GLY22 5.0 9.7 1.0
CD2 B:HIS135 5.0 7.9 1.0
O B:GLY22 5.0 9.2 1.0
ND1 B:HIS145 5.0 8.1 1.0

Zinc binding site 5 out of 6 in 5fbb

Go back to Zinc Binding Sites List in 5fbb
Zinc binding site 5 out of 6 in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:9.5
occ:1.00
O1 B:PO4601 1.9 15.2 1.0
OD2 B:ASP139 2.0 6.9 1.0
ND1 B:HIS80 2.1 10.4 1.0
NE2 B:HIS135 2.1 7.7 1.0
OD1 B:ASP65 2.6 13.2 1.0
O2 B:PO4601 2.9 27.5 1.0
CE1 B:HIS80 2.9 9.6 1.0
P B:PO4601 3.0 23.8 1.0
CD2 B:HIS135 3.0 7.9 1.0
CG B:ASP139 3.1 7.6 1.0
CE1 B:HIS135 3.1 7.9 1.0
CG B:HIS80 3.1 9.5 1.0
OD1 B:ASP139 3.4 7.2 1.0
ZN B:ZN401 3.4 10.0 1.0
CG B:ASP65 3.5 14.3 1.0
CB B:HIS80 3.6 9.4 1.0
OD2 B:ASP65 3.7 14.8 1.0
O4 B:PO4601 3.9 24.2 1.0
NE2 B:HIS26 4.0 7.2 1.0
NE2 B:HIS80 4.1 10.6 1.0
NZ B:LYS68 4.2 14.0 1.0
O3 B:PO4601 4.2 21.6 1.0
ND1 B:HIS135 4.2 7.8 1.0
CG B:HIS135 4.2 7.3 1.0
CD2 B:HIS80 4.2 10.1 1.0
CE1 B:HIS26 4.4 7.6 1.0
CE1 B:HIS145 4.4 8.1 1.0
CB B:ASP139 4.4 7.8 1.0
CA B:HIS80 4.6 9.3 1.0
CB B:ASP65 4.9 12.5 1.0
O B:TRP21 4.9 8.1 1.0
CD2 B:HIS26 5.0 8.0 1.0

Zinc binding site 6 out of 6 in 5fbb

Go back to Zinc Binding Sites List in 5fbb
Zinc binding site 6 out of 6 in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:11.4
occ:1.00
OD2 B:ASP172 2.1 11.2 1.0
O3 B:PO4601 2.1 21.6 1.0
O B:HOH1203 2.1 12.3 1.0
NE2 B:HIS145 2.1 8.2 1.0
NE2 B:HIS168 2.1 11.6 1.0
OD1 B:ASP172 2.7 10.1 1.0
CG B:ASP172 2.7 11.1 1.0
CE1 B:HIS145 3.0 8.1 1.0
CD2 B:HIS168 3.1 12.6 1.0
CE1 B:HIS168 3.2 12.0 1.0
CD2 B:HIS145 3.2 8.4 1.0
P B:PO4601 3.3 23.8 1.0
O2 B:PO4601 3.6 27.5 1.0
O B:HOH1592 4.1 39.5 1.0
O4 B:PO4601 4.1 24.2 1.0
N B:TRP21 4.1 8.6 1.0
ND1 B:HIS145 4.1 8.1 1.0
CB B:ASP172 4.2 10.3 1.0
O B:HOH1591 4.3 20.2 1.0
CG B:HIS168 4.3 11.3 1.0
CG B:HIS145 4.3 8.0 1.0
ND1 B:HIS168 4.3 11.5 1.0
NE2 B:GLN142 4.4 10.1 1.0
O1 B:PO4601 4.5 15.2 1.0
ZN B:ZN401 4.6 10.0 1.0
O B:HOH1651 4.6 30.4 1.0
C2 B:AMP701 4.7 17.9 1.0
O B:TRP21 4.9 8.1 1.0
CA B:TRP21 4.9 8.5 1.0
C B:TRP21 5.0 8.7 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 06:13:32 2020

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