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Sodium 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
Calcium (Ca) 5 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 3 in 5fbb

Go back to Sodium Binding Sites List in 5fbb
Sodium binding site 1 out of 3 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 Sodium with other atoms in the Na 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:Na801

b:21.4
occ:1.00
 O A:HOH1542 2.2 40.3 1.0
O1P A:AMP701 2.4 41.1 1.0
O A:HOH1547 2.5 28.4 1.0
OD2 A:ASP83 2.7 16.2 1.0
O A:HOH1721 2.7 34.7 1.0
P A:AMP701 3.6 44.3 1.0
CG A:ASP83 3.8 15.1 1.0
O2P A:AMP701 3.8 44.6 1.0
O A:HOH1656 3.9 31.1 1.0
CB A:ASP83 4.3 14.3 1.0
OD1 A:ASN148 4.5 15.5 1.0
O A:HOH1624 4.6 17.7 0.5
O5' A:AMP701 4.6 38.7 1.0
O3P A:AMP701 4.7 42.5 1.0
CE1 A:PHE81 4.8 17.6 1.0
OD1 A:ASP83 4.9 15.0 1.0
O A:HOH1585 4.9 18.1 1.0

Sodium binding site 2 out of 3 in 5fbb

Go back to Sodium Binding Sites List in 5fbb
Sodium binding site 2 out of 3 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 Sodium with other atoms in the Na 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:Na802

b:19.4
occ:1.00
 O A:HOH1559 2.2 19.0 1.0
O A:HOH1596 2.3 15.7 1.0
O A:LEU118 2.4 21.5 1.0
OH6 A:ETE1101 2.5 23.3 1.0
OH5 A:ETE1101 2.8 20.3 1.0
C25 A:ETE1101 3.3 21.8 1.0
C15 A:ETE1101 3.4 20.5 1.0
C A:LEU118 3.5 19.7 1.0
C14 A:ETE1101 3.5 24.4 1.0
C26 A:ETE1101 3.6 25.2 1.0
CA A:LEU118 3.8 16.9 1.0
C24 A:ETE1101 4.1 25.1 1.0
O A:LEU117 4.2 14.1 1.0
O A:ILE282 4.2 16.8 1.0
O A:GLN285 4.4 29.3 1.0
N A:GLU119 4.6 19.4 1.0
CB A:LEU118 4.7 18.2 1.0
CD2 A:LEU118 4.7 17.3 1.0
CG A:PRO121 4.7 21.4 1.0
CD A:PRO121 4.9 20.2 1.0
N A:LEU118 4.9 14.3 1.0
OH4 A:ETE1101 5.0 25.4 1.0

Sodium binding site 3 out of 3 in 5fbb

Go back to Sodium Binding Sites List in 5fbb
Sodium binding site 3 out of 3 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 Sodium with other atoms in the Na 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
B:Na801

b:23.1
occ:1.00
 O B:HOH1574 2.1 37.1 1.0
O1P B:AMP701 2.6 45.3 1.0
OD2 B:ASP83 2.6 15.8 1.0
O B:HOH1713 3.2 46.5 1.0
O B:HOH1681 3.7 45.1 1.0
CG B:ASP83 3.8 14.9 1.0
P B:AMP701 3.8 48.1 1.0
O2P B:AMP701 3.9 50.3 1.0
O B:HOH1532 4.2 31.7 1.0
CB B:ASP83 4.3 12.9 1.0
OD1 B:ASN148 4.4 14.7 1.0
O5' B:AMP701 4.8 45.9 1.0
OD1 B:ASP83 4.8 15.2 1.0
CE1 B:PHE81 4.8 16.2 1.0
O3P B:AMP701 4.9 44.3 1.0
C8 B:AMP701 4.9 17.6 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: Mon Oct 7 20:59:13 2024

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