Sodium in PDB 6w3u: APE1 Exonuclease Substrate Complex R237C

All present enzymatic activity of APE1 Exonuclease Substrate Complex R237C:
4.2.99.18;

The structure of APE1 Exonuclease Substrate Complex R237C, PDB code: 6w3u 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)	46.76 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.177, 65.622, 91.717, 90.00, 110.52, 90.00
R / Rfree (%)	18.4 / 25

The structure of APE1 Exonuclease Substrate Complex R237C also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the APE1 Exonuclease Substrate Complex R237C (pdb code 6w3u). 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 R237C, PDB code: 6w3u:

Sodium binding site 1 out of 1 in the APE1 Exonuclease Substrate Complex R237C


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 R237C within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:45.0 occ:1.00 OE1 A:GLN95 2.6 41.5 1.0 OG A:SER66 2.9 40.2 1.0 OD1 A:ASP283 2.9 35.3 1.0 O A:HOH511 3.1 40.6 1.0 CB A:ASP283 3.5 37.5 1.0 CG A:ASP283 3.5 36.0 1.0 C A:GLY209 3.5 39.0 1.0 CA A:GLY209 3.5 38.5 1.0 CD A:GLN95 3.6 38.6 1.0 N A:TRP67 3.6 37.9 1.0 N A:ASN68 3.6 43.9 1.0 CB A:SER66 3.7 41.6 1.0 C A:SER66 3.7 37.9 1.0 N A:ASP210 3.8 43.7 1.0 O A:SER66 3.8 42.3 1.0 O A:GLY209 3.9 40.2 1.0 CA A:TRP67 3.9 40.0 1.0 C A:TRP67 3.9 43.1 1.0 NE2 A:GLN95 4.0 38.0 1.0 CA A:SER66 4.3 39.9 1.0 N A:GLY209 4.3 41.2 1.0 CD1 A:ILE312 4.5 35.7 1.0 CA A:ASP283 4.5 36.9 1.0 CA A:ASP210 4.5 41.9 1.0 CG1 A:ILE312 4.5 36.4 1.0 OD2 A:ASP283 4.6 35.0 1.0 CA A:ASN68 4.6 42.4 1.0 CB A:ASN68 4.6 39.2 1.0 O A:TRP67 4.8 43.6 1.0 CG A:GLN95 4.8 40.8 1.0 CB A:ASP210 4.8 42.2 1.0

A.M.Whitaker, W.J.Stark, T.S.Flynn, B.D.Freudenthal. Molecular and Structural Characterization of Disease-Associated APE1 Polymorphisms. Dna Repair (Amst.) V.1-92 02867 2020.
ISSN: ISSN 1568-7856
PubMed: 32454397
DOI: 10.1016/J.DNAREP.2020.102867