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Zinc in PDB 5fb9: S1 Nuclease From Aspergillus Oryzae with Unoccupied Active Site

Enzymatic activity of S1 Nuclease From Aspergillus Oryzae with Unoccupied Active Site

All present enzymatic activity of S1 Nuclease From Aspergillus Oryzae with Unoccupied Active Site:
3.1.30.1;

Protein crystallography data

The structure of S1 Nuclease From Aspergillus Oryzae with Unoccupied Active Site, PDB code: 5fb9 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) 43.05 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 43.184, 48.595, 65.469, 107.37, 90.13, 105.72
R / Rfree (%) 14.9 / 17.7

Other elements in 5fb9:

The structure of S1 Nuclease From Aspergillus Oryzae with Unoccupied Active Site also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the S1 Nuclease From Aspergillus Oryzae with Unoccupied Active Site (pdb code 5fb9). 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 with Unoccupied Active Site, PDB code: 5fb9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5fb9

Go back to Zinc Binding Sites List in 5fb9
Zinc binding site 1 out of 6 in the S1 Nuclease From Aspergillus Oryzae with Unoccupied Active Site


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 with Unoccupied Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:7.4
occ:1.00
 O A:HOH801 1.9 8.1 1.0
NE2 A:HIS26 2.0 6.3 1.0
N A:TRP21 2.1 7.7 1.0
OD1 A:ASP139 2.1 9.0 1.0
O A:TRP21 2.2 8.0 1.0
C A:TRP21 2.9 7.9 1.0
CA A:TRP21 3.0 7.2 1.0
CD2 A:HIS26 3.0 5.9 1.0
CE1 A:HIS26 3.1 6.6 1.0
CG A:ASP139 3.1 7.6 1.0
ZN A:ZN402 3.3 8.3 1.0
O A:HOH802 3.3 11.1 1.0
OD2 A:ASP139 3.5 7.5 1.0
CB A:TRP21 3.7 6.9 1.0
OD2 A:ASP65 3.9 8.8 1.0
NE2 A:HIS135 3.9 7.2 1.0
CE1 A:HIS135 4.0 6.5 1.0
CE1 A:HIS145 4.1 8.3 1.0
ND1 A:HIS26 4.1 6.7 1.0
CG A:HIS26 4.2 6.7 1.0
N A:GLY22 4.2 7.9 1.0
NE2 A:HIS145 4.2 7.6 1.0
CG A:TRP21 4.3 6.9 1.0
CD1 A:TRP21 4.4 6.9 1.0
CB A:ASP139 4.5 7.7 1.0
OD1 A:ASP172 4.6 8.4 1.0
CG A:ASP65 4.7 9.1 1.0
CA A:ASP139 4.7 7.0 1.0
OD1 A:ASP65 4.8 10.1 1.0
ZN A:ZN403 4.8 8.7 1.0
ND1 A:HIS145 4.8 7.9 1.0
O A:GLY22 4.9 7.7 1.0
CA A:GLY22 4.9 8.0 1.0
CD2 A:HIS135 5.0 7.0 1.0
O A:HOH1310 5.0 14.8 1.0

Zinc binding site 2 out of 6 in 5fb9

Go back to Zinc Binding Sites List in 5fb9
Zinc binding site 2 out of 6 in the S1 Nuclease From Aspergillus Oryzae with Unoccupied Active Site


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 with Unoccupied Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:8.3
occ:1.00
 O A:HOH801 1.9 8.1 1.0
ND1 A:HIS80 2.0 7.6 1.0
NE2 A:HIS135 2.1 7.2 1.0
OD2 A:ASP139 2.1 7.5 1.0
OD1 A:ASP65 2.7 10.1 1.0
CE1 A:HIS80 2.8 8.2 1.0
CE1 A:HIS135 3.0 6.5 1.0
CG A:ASP139 3.1 7.6 1.0
CD2 A:HIS135 3.1 7.0 1.0
CG A:HIS80 3.1 8.0 1.0
ZN A:ZN401 3.3 7.4 1.0
OD1 A:ASP139 3.3 9.0 1.0
CG A:ASP65 3.5 9.1 1.0
O A:HOH804 3.5 18.0 1.0
OD2 A:ASP65 3.6 8.8 1.0
CB A:HIS80 3.6 8.1 1.0
NE2 A:HIS26 4.0 6.3 1.0
NE2 A:HIS80 4.0 8.6 1.0
ND1 A:HIS135 4.2 7.5 1.0
CD2 A:HIS80 4.2 8.8 1.0
CG A:HIS135 4.2 7.2 1.0
CE1 A:HIS145 4.2 8.3 1.0
NZ A:LYS68 4.3 14.4 1.0
CE1 A:HIS26 4.4 6.6 1.0
CB A:ASP139 4.4 7.7 1.0
O A:HOH802 4.5 11.1 1.0
CA A:HIS80 4.6 8.5 1.0
O A:TRP21 4.8 8.0 1.0
ND1 A:HIS145 4.8 7.9 1.0
CB A:ASP65 4.9 9.5 1.0
CD2 A:HIS26 4.9 5.9 1.0

Zinc binding site 3 out of 6 in 5fb9

Go back to Zinc Binding Sites List in 5fb9
Zinc binding site 3 out of 6 in the S1 Nuclease From Aspergillus Oryzae with Unoccupied Active Site


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 with Unoccupied Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:8.7
occ:1.00
 OD2 A:ASP172 2.0 7.4 1.0
O A:HOH802 2.0 11.1 1.0
O A:HOH803 2.1 11.4 1.0
NE2 A:HIS168 2.1 8.8 1.0
NE2 A:HIS145 2.1 7.6 1.0
CG A:ASP172 2.6 7.7 1.0
OD1 A:ASP172 2.7 8.4 1.0
CE1 A:HIS145 3.0 8.3 1.0
CD2 A:HIS168 3.0 7.8 1.0
CE1 A:HIS168 3.1 8.6 1.0
CD2 A:HIS145 3.1 7.6 1.0
O A:HOH1371 4.1 29.0 1.0
CB A:ASP172 4.1 7.2 1.0
O A:HOH1310 4.1 14.8 1.0
ND1 A:HIS145 4.2 7.9 1.0
CG A:HIS168 4.2 8.2 1.0
N A:TRP21 4.2 7.7 1.0
ND1 A:HIS168 4.2 8.7 1.0
CG A:HIS145 4.2 7.6 1.0
O A:HOH1011 4.2 21.9 1.0
O A:HOH804 4.3 18.0 1.0
O A:HOH1168 4.3 13.4 1.0
NE2 A:GLN142 4.5 7.3 1.0
CE1 A:PHE81 4.6 14.5 1.0
O A:HOH801 4.6 8.1 1.0
ZN A:ZN401 4.8 7.4 1.0
CA A:TRP21 5.0 7.2 1.0

Zinc binding site 4 out of 6 in 5fb9

Go back to Zinc Binding Sites List in 5fb9
Zinc binding site 4 out of 6 in the S1 Nuclease From Aspergillus Oryzae with Unoccupied Active Site


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 with Unoccupied Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:8.2
occ:1.00
 NE2 B:HIS26 2.0 7.0 1.0
O B:HOH801 2.1 9.5 1.0
N B:TRP21 2.1 7.2 1.0
OD1 B:ASP139 2.1 7.4 1.0
O B:TRP21 2.2 6.5 1.0
C B:TRP21 2.9 7.2 1.0
CD2 B:HIS26 3.0 7.5 1.0
CA B:TRP21 3.0 7.3 1.0
CE1 B:HIS26 3.1 8.3 1.0
CG B:ASP139 3.1 7.3 1.0
ZN B:ZN402 3.3 8.8 1.0
O B:HOH802 3.3 12.2 1.0
OD2 B:ASP139 3.5 8.9 1.0
CB B:TRP21 3.7 7.3 1.0
OD2 B:ASP65 3.9 9.8 1.0
NE2 B:HIS135 3.9 8.8 1.0
CE1 B:HIS135 4.0 7.8 1.0
CE1 B:HIS145 4.1 8.7 1.0
ND1 B:HIS26 4.1 7.8 1.0
CG B:HIS26 4.1 7.9 1.0
N B:GLY22 4.2 8.0 1.0
NE2 B:HIS145 4.3 8.4 1.0
CG B:TRP21 4.4 7.5 1.0
CD1 B:TRP21 4.4 8.0 1.0
CB B:ASP139 4.5 7.7 1.0
OD1 B:ASP172 4.6 8.3 1.0
CG B:ASP65 4.7 9.5 1.0
CA B:ASP139 4.7 7.7 1.0
ZN B:ZN403 4.8 9.4 1.0
OD1 B:ASP65 4.8 10.8 1.0
ND1 B:HIS145 4.8 8.0 1.0
O B:GLY22 4.9 9.0 1.0
CA B:GLY22 5.0 8.2 1.0
CD2 B:HIS135 5.0 8.1 1.0

Zinc binding site 5 out of 6 in 5fb9

Go back to Zinc Binding Sites List in 5fb9
Zinc binding site 5 out of 6 in the S1 Nuclease From Aspergillus Oryzae with Unoccupied Active Site


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 with Unoccupied Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:8.8
occ:1.00
 O B:HOH801 2.0 9.5 1.0
ND1 B:HIS80 2.0 7.2 1.0
OD2 B:ASP139 2.1 8.9 1.0
NE2 B:HIS135 2.1 8.8 1.0
OD1 B:ASP65 2.7 10.8 1.0
CE1 B:HIS80 2.8 8.1 1.0
CG B:ASP139 3.0 7.3 1.0
CE1 B:HIS135 3.0 7.8 1.0
CD2 B:HIS135 3.1 8.1 1.0
CG B:HIS80 3.1 8.2 1.0
ZN B:ZN401 3.3 8.2 1.0
OD1 B:ASP139 3.3 7.4 1.0
O B:HOH804 3.5 17.8 1.0
CG B:ASP65 3.5 9.5 1.0
OD2 B:ASP65 3.6 9.8 1.0
CB B:HIS80 3.6 8.5 1.0
NE2 B:HIS26 3.9 7.0 1.0
NE2 B:HIS80 4.0 8.1 1.0
CD2 B:HIS80 4.2 8.3 1.0
ND1 B:HIS135 4.2 8.2 1.0
CG B:HIS135 4.2 7.9 1.0
CE1 B:HIS145 4.2 8.7 1.0
CE1 B:HIS26 4.4 8.3 1.0
CB B:ASP139 4.4 7.7 1.0
O B:HOH802 4.4 12.2 1.0
NZ B:LYS68 4.4 17.2 1.0
CA B:HIS80 4.6 8.1 1.0
O B:TRP21 4.8 6.5 1.0
ND1 B:HIS145 4.8 8.0 1.0
CB B:ASP65 4.9 9.9 1.0
CD2 B:HIS26 4.9 7.5 1.0

Zinc binding site 6 out of 6 in 5fb9

Go back to Zinc Binding Sites List in 5fb9
Zinc binding site 6 out of 6 in the S1 Nuclease From Aspergillus Oryzae with Unoccupied Active Site


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 with Unoccupied Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:9.4
occ:1.00
 O B:HOH802 2.0 12.2 1.0
OD2 B:ASP172 2.1 8.0 1.0
NE2 B:HIS145 2.1 8.4 1.0
O B:HOH803 2.1 12.4 1.0
NE2 B:HIS168 2.1 9.2 1.0
OD1 B:ASP172 2.6 8.3 1.0
CG B:ASP172 2.7 8.4 1.0
CE1 B:HIS145 3.0 8.7 1.0
CD2 B:HIS168 3.1 8.7 1.0
CD2 B:HIS145 3.1 8.5 1.0
CE1 B:HIS168 3.2 8.4 1.0
ND1 B:HIS145 4.1 8.0 1.0
O B:HOH1304 4.1 14.1 1.0
CB B:ASP172 4.1 8.1 1.0
CG B:HIS145 4.2 7.9 1.0
N B:TRP21 4.2 7.2 1.0
O B:HOH1352 4.2 32.8 1.0
CG B:HIS168 4.2 8.7 1.0
ND1 B:HIS168 4.3 9.6 1.0
O B:HOH1014 4.3 24.6 1.0
O B:HOH1129 4.3 13.9 1.0
O B:HOH804 4.4 17.8 1.0
NE2 B:GLN142 4.4 9.2 1.0
O B:HOH801 4.5 9.5 1.0
CE1 B:PHE81 4.6 16.6 1.0
ZN B:ZN401 4.8 8.2 1.0
CA B:TRP21 4.9 7.3 1.0
O B:TRP21 5.0 6.5 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: Sun Oct 27 15:56:51 2024

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