Sodium in PDB 5wn5: APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+

All present enzymatic activity of APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+:
4.2.99.18;

The structure of APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+, PDB code: 5wn5 was solved by B.D.Freudenthal, A.M.Whitaker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.74 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.503, 64.444, 91.522, 90.00, 109.93, 90.00
R / Rfree (%)	22.6 / 26.1

The structure of APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+ also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Sodium atom in the APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+ (pdb code 5wn5). 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 APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+, PDB code: 5wn5:

Sodium binding site 1 out of 1 in the APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:44.1 occ:1.00 O A:ASP283 2.9 32.6 1.0 NH1 A:ARG281 3.0 33.5 1.0 O A:HOH526 3.0 41.2 1.0 CB A:PHE253 3.6 40.4 1.0 CD A:ARG281 3.6 33.7 1.0 CA A:TYR284 3.9 38.8 1.0 CG A:ARG281 4.0 39.6 1.0 C A:ASP283 4.0 38.4 1.0 CZ A:ARG281 4.0 39.3 1.0 CG A:PHE253 4.1 33.1 1.0 NE A:ARG281 4.3 36.3 1.0 N A:TYR284 4.4 35.9 1.0 CD2 A:TYR284 4.4 32.7 1.0 CD1 A:ILE300 4.6 38.0 1.0 CD1 A:PHE253 4.6 32.6 1.0 CB A:TYR284 4.6 31.5 1.0 N A:PHE285 4.6 43.7 1.0 OD1 A:ASP251 4.7 39.0 1.0 CG2 A:ILE312 4.7 32.8 1.0 CG1 A:ILE300 4.7 35.2 1.0 CG A:TYR284 4.7 35.7 1.0 CD2 A:PHE253 4.7 36.2 1.0 C A:TYR284 4.7 37.2 1.0 CA A:PHE253 4.9 37.0 1.0 OG A:SER298 4.9 41.6 1.0 CD1 A:ILE312 4.9 41.1 1.0 CG2 A:THR265 4.9 30.5 1.0

A.M.Whitaker, T.S.Flynn, B.D.Freudenthal. Molecular Snapshots of APE1 Proofreading Mismatches and Removing Dna Damage. Nat Commun V. 9 399 2018.
ISSN: ESSN 2041-1723
PubMed: 29374164
DOI: 10.1038/S41467-017-02175-Y