Atomistry » Calcium » PDB 5eym-5fk0 » 5fbb
Atomistry »
  Calcium »
    PDB 5eym-5fk0 »
      5fbb »

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

Go back to Calcium Binding Sites List in 5fbb
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: Sun Jul 14 19:09:28 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy