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Calcium 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:

Zinc (Zn) 6 atoms
Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 5 binding sites of Calcium where determined in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and Adenosine 5'-Monophosphate, PDB code: 5fbb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5fbb

Go back to Calcium Binding Sites List in 5fbb
Calcium binding site 1 out of 5 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 Calcium with other atoms in the Ca 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:Ca901

b:15.8
occ:1.00
 O A:HOH1570 2.2 17.3 1.0
O8 A:BTB1001 2.2 17.1 1.0
OD1 A:ASP213 2.4 16.0 1.0
O6 A:BTB1001 2.4 18.0 1.0
O4 A:BTB1001 2.4 24.9 1.0
O A:ASP209 2.5 12.2 1.0
O1 A:BTB1001 2.6 26.0 1.0
N A:BTB1001 2.7 20.8 1.0
C6 A:BTB1001 3.3 20.6 1.0
C2 A:BTB1001 3.4 24.6 1.0
C8 A:BTB1001 3.4 19.2 1.0
C4 A:BTB1001 3.4 22.9 1.0
C7 A:BTB1001 3.5 20.2 1.0
C5 A:BTB1001 3.5 20.6 1.0
C1 A:BTB1001 3.5 25.8 1.0
C A:ASP209 3.5 13.8 1.0
CG A:ASP213 3.6 16.9 1.0
CA A:SER210 4.3 12.8 1.0
N A:SER210 4.3 11.2 1.0
OD2 A:ASP213 4.3 17.5 1.0
O A:HOH1600 4.4 29.2 1.0
CA A:ASP209 4.5 17.1 1.0
N A:ASP213 4.6 13.9 1.0
OG1 A:THR212 4.6 13.9 1.0
CA A:ASP213 4.6 14.9 1.0
CB A:ASP209 4.6 22.4 1.0
CB A:ASP213 4.7 14.7 1.0
C3 A:BTB1001 4.8 24.9 1.0
O A:HOH1554 4.9 31.6 1.0

Calcium binding site 2 out of 5 in 5fbb

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Calcium binding site 2 out of 5 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 Calcium with other atoms in the Ca 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:Ca902

b:21.8
occ:0.50
 O A:HOH1507 2.0 15.4 0.5
O8 A:BTB1002 2.3 20.5 0.5
O4 A:BTB1002 2.3 14.4 0.5
O6 A:BTB1002 2.4 18.8 0.5
N A:BTB1002 2.6 17.9 0.5
O3 A:BTB1002 2.8 18.1 0.5
C6 A:BTB1002 3.2 18.7 0.5
C8 A:BTB1002 3.2 18.7 0.5
C7 A:BTB1002 3.3 19.0 0.5
C2 A:BTB1002 3.3 16.9 0.5
C4 A:BTB1002 3.3 16.3 0.5
C3 A:BTB1002 3.4 17.6 0.5
C5 A:BTB1002 3.5 18.4 0.5
O A:HOH1503 3.8 10.6 0.5
OE2 A:GLU177 4.2 16.8 0.5
CG2 A:THR173 4.3 14.2 1.0
OG1 A:THR173 4.4 13.6 1.0
OE1 A:GLU177 4.4 15.8 0.5
O A:HOH1572 4.4 15.2 0.5
C1 A:BTB1002 4.8 17.9 0.5
O A:HOH1560 4.8 43.1 1.0
N A:ASN23 4.9 11.8 1.0
OE2 A:GLU177 4.9 15.9 0.5
O A:HOH1520 5.0 28.3 1.0

Calcium binding site 3 out of 5 in 5fbb

Go back to Calcium Binding Sites List in 5fbb
Calcium binding site 3 out of 5 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 Calcium with other atoms in the Ca 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:Ca903

b:26.9
occ:1.00
 O A:SER206 2.3 20.9 1.0
O B:HOH1523 2.5 25.4 1.0
O B:HOH1708 2.5 43.8 1.0
O A:HOH1642 2.7 32.2 1.0
O B:HOH1535 2.7 30.7 1.0
O B:HOH1712 2.9 40.6 1.0
C A:SER206 3.6 19.8 1.0
CA A:SER206 4.3 18.0 1.0
CB A:SER206 4.3 17.7 1.0
OE1 B:GLU74 4.4 21.0 1.0
N A:LYS207 4.6 18.4 1.0
OE2 B:GLU74 4.6 22.6 1.0
CA A:LYS207 4.8 19.5 0.5
CA A:LYS207 4.8 20.1 0.5
O A:HOH1506 4.9 23.0 1.0
CD B:GLU74 5.0 21.1 1.0

Calcium binding site 4 out of 5 in 5fbb

Go back to Calcium Binding Sites List in 5fbb
Calcium binding site 4 out of 5 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 Calcium with other atoms in the Ca 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:Ca901

b:17.1
occ:1.00
 O B:HOH1550 2.2 19.9 1.0
O8 B:BTB1001 2.2 20.9 1.0
OD1 B:ASP213 2.3 15.6 1.0
O3 B:BTB1001 2.4 21.2 1.0
O4 B:BTB1001 2.4 21.1 1.0
O B:ASP209 2.4 14.4 1.0
O6 B:BTB1001 2.5 20.3 1.0
N B:BTB1001 2.6 18.2 1.0
C6 B:BTB1001 3.2 19.8 1.0
C8 B:BTB1001 3.2 21.1 1.0
C2 B:BTB1001 3.3 20.4 1.0
C3 B:BTB1001 3.4 19.9 1.0
C7 B:BTB1001 3.4 19.2 1.0
C5 B:BTB1001 3.4 19.0 1.0
C4 B:BTB1001 3.5 22.4 1.0
C B:ASP209 3.5 16.9 1.0
CG B:ASP213 3.6 16.5 1.0
CA B:SER210 4.2 14.5 1.0
N B:SER210 4.2 14.3 1.0
OD2 B:ASP213 4.3 19.4 1.0
O B:HOH1576 4.3 32.9 1.0
OG1 B:THR212 4.6 14.7 1.0
CA B:ASP209 4.6 18.8 1.0
N B:ASP213 4.6 10.9 1.0
CA B:ASP213 4.6 13.1 1.0
CB B:ASP213 4.7 13.9 1.0
CB B:ASP209 4.7 22.1 1.0
C1 B:BTB1001 4.8 21.1 1.0
C B:SER210 4.9 12.8 1.0

Calcium binding site 5 out of 5 in 5fbb

Go back to Calcium Binding Sites List in 5fbb
Calcium binding site 5 out of 5 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 Calcium with other atoms in the Ca 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:Ca902

b:23.0
occ:1.00
 O B:HOH1595 2.3 16.2 1.0
O B:HOH1585 2.3 27.1 1.0
O3 B:BTB1002 2.4 21.1 1.0
O8 B:BTB1002 2.4 28.7 1.0
O1 B:BTB1002 2.4 23.8 1.0
O6 B:BTB1002 2.4 20.3 1.0
O B:HOH1543 2.5 27.4 1.0
N B:BTB1002 2.6 22.8 1.0
C6 B:BTB1002 3.2 23.7 1.0
C2 B:BTB1002 3.3 24.6 1.0
C3 B:BTB1002 3.4 24.7 1.0
C5 B:BTB1002 3.4 22.9 1.0
C1 B:BTB1002 3.4 22.8 1.0
C8 B:BTB1002 3.4 27.6 1.0
C7 B:BTB1002 3.5 24.9 1.0
OE2 B:GLU177 4.1 20.1 0.5
O B:HOH1536 4.4 23.7 1.0
CG2 B:THR173 4.4 11.5 1.0
O B:HOH1505 4.4 39.2 1.0
OE2 B:GLU177 4.4 10.1 0.5
OG1 B:THR173 4.6 12.4 1.0
OE1 B:GLU177 4.7 10.9 0.5
OD2 A:ASP219 4.7 17.5 1.0
C4 B:BTB1002 4.8 27.2 1.0
CB A:SER222 4.8 15.8 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 Jul 9 05:53:35 2025

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