Sodium in PDB 7qta: S1 Nuclease From Aspergillus Oryzae in Complex with Uridine

All present enzymatic activity of S1 Nuclease From Aspergillus Oryzae in Complex with Uridine:
3.1.30.1;

The structure of S1 Nuclease From Aspergillus Oryzae in Complex with Uridine, PDB code: 7qta was solved by K.Adamkova, T.Koval, P.Kolenko, L.H.Oestergaard, J.Dohnalek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.20 / 1.06
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.04, 48.186, 65.232, 107.18, 90.11, 105.62
R / Rfree (%)	11.8 / 14.7

The structure of S1 Nuclease From Aspergillus Oryzae in Complex with Uridine also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Sodium atom in the S1 Nuclease From Aspergillus Oryzae in Complex with Uridine (pdb code 7qta). 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 Uridine, PDB code: 7qta:

Sodium binding site 1 out of 1 in the S1 Nuclease From Aspergillus Oryzae in Complex with Uridine


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 Uridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:18.5 occ:1.00 O A:HOH537 2.2 18.1 0.5 O A:HOH767 2.3 26.0 1.0 O A:HOH866 2.4 27.6 1.0 O A:HOH805 2.5 20.0 0.5 O A:HOH732 2.5 37.2 1.0 O A:SER249 2.6 18.1 1.0 O A:HOH510 3.1 14.5 0.5 C A:SER249 3.6 14.8 1.0 O A:HOH794 4.1 26.8 0.5 CA A:SER249 4.1 16.1 1.0 O A:HOH852 4.2 35.6 1.0 O A:HOH592 4.3 20.8 1.0 CB A:SER249 4.6 19.2 1.0 O A:HOH821 4.6 47.3 1.0 N A:THR250 4.7 12.9 1.0

K.Adamkova, T.Koval', L.H.Ostergaard, J.Duskova, M.Maly, L.Svecova, T.Skalova, P.Kolenko, J.Dohnalek. Atomic Resolution Studies of S1 Nuclease Complexes Reveal Details of Rna Interaction with the Enzyme Despite Multiple Lattice-Translocation Defects. Acta Crystallogr D Struct V. 78 1194 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 36189740
DOI: 10.1107/S2059798322008397