Atomistry » Zinc » PDB 5f8h-5fi3 » 5fbb
Atomistry »
  Zinc »
    PDB 5f8h-5fi3 »
      5fbb »

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

Go back to Zinc Binding Sites List in 5fbb
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

Go back to Zinc Binding Sites List in 5fbb
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

Go back to Zinc Binding Sites List in 5fbb
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: Sun Oct 27 15:56:51 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy