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Sodium in PDB 5fbf: S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-5'-Monophosphate

Enzymatic activity of S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-5'-Monophosphate

All present enzymatic activity of S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-5'-Monophosphate:
3.1.30.1;

Protein crystallography data

The structure of S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-5'-Monophosphate, PDB code: 5fbf 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) 44.25 / 1.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.742, 62.388, 62.762, 90.00, 90.00, 90.00
R / Rfree (%) 11.1 / 13.5

Other elements in 5fbf:

The structure of S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-5'-Monophosphate also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-5'-Monophosphate (pdb code 5fbf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-5'-Monophosphate, PDB code: 5fbf:

Sodium binding site 1 out of 1 in 5fbf

Go back to Sodium Binding Sites List in 5fbf
Sodium binding site 1 out of 1 in the S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-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 Two Molecules of 2'-Deoxycytidine-5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na701

b:10.3
occ:1.00
 O A:HOH1079 2.3 10.6 1.0
O A:HOH1340 2.3 12.4 1.0
O A:SER206 2.4 10.7 1.0
O A:HOH1393 2.5 21.2 1.0
OD1 A:ASP209 2.7 7.2 0.6
CG A:ASP209 3.5 7.6 0.6
C A:SER206 3.6 7.8 1.0
OD2 A:ASP209 3.6 7.8 0.6
OG A:SER210 4.0 9.2 1.0
O A:HOH1173 4.2 11.8 1.0
CA A:LYS207 4.2 9.3 1.0
N A:LYS207 4.3 8.8 1.0
O A:HOH1317 4.4 16.0 1.0
CA A:SER206 4.6 7.4 1.0
C A:LYS207 4.8 9.1 1.0
CB A:SER206 4.9 8.2 0.8
CD A:LYS207 4.9 14.0 1.0
CB A:SER206 4.9 9.1 0.2
O A:LYS207 5.0 9.4 1.0
N A:SER210 5.0 7.0 1.0
CB A:ASP209 5.0 8.6 0.6

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 Aug 17 23:48:16 2025

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