Sodium in PDB 5wn1: APE1 Exonuclease Product Complex

All present enzymatic activity of APE1 Exonuclease Product Complex:
4.2.99.18;

The structure of APE1 Exonuclease Product Complex, PDB code: 5wn1 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)	24.52 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.869, 63.528, 90.548, 90.00, 109.43, 90.00
R / Rfree (%)	21.3 / 27

The structure of APE1 Exonuclease Product Complex also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the APE1 Exonuclease Product Complex (pdb code 5wn1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the APE1 Exonuclease Product Complex, PDB code: 5wn1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the APE1 Exonuclease Product Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of APE1 Exonuclease Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:63.2 occ:1.00 NE2 B:GLN235 3.5 60.6 1.0 OE1 B:GLN235 4.0 57.2 1.0 CD B:GLN235 4.1 51.0 1.0 CD2 B:LEU182 4.2 46.5 1.0 CD1 B:LEU179 4.3 49.1 1.0 CD B:PRO234 4.7 42.7 1.0 CB B:THR233 4.8 41.6 1.0 CG2 B:THR233 4.9 43.5 1.0 CE B:LYS228 5.0 68.6 1.0

Sodium binding site 2 out of 2 in the APE1 Exonuclease Product Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of APE1 Exonuclease Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Na102 b:57.8 occ:1.00 O2 D:DT6 3.3 52.1 1.0 O4' E:DC18 3.3 46.8 1.0 O2 E:DT17 3.4 48.3 1.0 C4' E:DC18 3.5 52.7 1.0 C5' E:DC18 3.6 49.6 1.0 C1' E:DT17 4.1 44.6 1.0 C2 E:DT17 4.4 42.0 1.0 C2 D:DT6 4.5 51.8 1.0 C1' E:DC18 4.6 48.2 1.0 O5' E:DC18 4.8 44.3 1.0 O4' D:DG7 4.8 48.4 1.0 O4' E:DT17 4.8 43.8 1.0 N1 E:DT17 4.8 40.2 1.0 C2' E:DT17 4.8 48.7 1.0 C1' D:DT6 4.9 53.2 1.0 O3' E:DT17 4.9 46.0 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