Sodium in PDB 5wn3: APE1 F266A Exonuclease Substrate Complex with A C/T Mismatch

All present enzymatic activity of APE1 F266A Exonuclease Substrate Complex with A C/T Mismatch:
4.2.99.18;

The structure of APE1 F266A Exonuclease Substrate Complex with A C/T Mismatch, PDB code: 5wn3 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)	24.76 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.144, 65.545, 91.441, 90.00, 110.08, 90.00
R / Rfree (%)	21 / 25.8

The structure of APE1 F266A Exonuclease Substrate Complex with A C/T Mismatch also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the APE1 F266A Exonuclease Substrate Complex with A C/T Mismatch (pdb code 5wn3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the APE1 F266A Exonuclease Substrate Complex with A C/T Mismatch, PDB code: 5wn3:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the APE1 F266A Exonuclease Substrate Complex with A C/T Mismatch


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of APE1 F266A Exonuclease Substrate Complex with A C/T Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:37.5 occ:1.00 OE1 A:GLN95 2.5 29.4 1.0 OD1 A:ASP283 2.8 29.2 1.0 OG A:SER66 2.9 30.1 1.0 O A:HOH560 2.9 30.0 1.0 CG A:ASP283 3.5 30.8 1.0 N A:TRP67 3.5 28.9 1.0 CD A:GLN95 3.5 28.5 1.0 C A:GLY209 3.6 30.2 1.0 CA A:GLY209 3.6 32.7 1.0 CB A:ASP283 3.6 22.7 1.0 N A:ASN68 3.6 30.4 1.0 C A:SER66 3.6 30.2 1.0 CA A:TRP67 3.8 28.1 1.0 CB A:SER66 3.8 32.2 1.0 C A:TRP67 3.8 32.4 1.0 N A:ASP210 3.8 32.1 1.0 O A:SER66 3.8 28.3 1.0 O A:GLY209 4.0 30.6 1.0 NE2 A:GLN95 4.0 26.8 1.0 CA A:SER66 4.4 25.9 1.0 N A:GLY209 4.4 31.4 1.0 CA A:ASP210 4.5 30.8 1.0 CG1 A:ILE312 4.6 26.4 1.0 OD2 A:ASP283 4.6 26.1 1.0 CA A:ASN68 4.6 27.2 1.0 CB A:ASN68 4.6 25.6 1.0 CA A:ASP283 4.6 27.9 1.0 CD1 A:ILE312 4.6 26.7 1.0 O A:TRP67 4.7 27.6 1.0 CB A:ASP210 4.7 26.6 1.0 CG A:GLN95 4.7 24.4 1.0

Sodium binding site 2 out of 3 in the APE1 F266A Exonuclease Substrate Complex with A C/T Mismatch


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of APE1 F266A Exonuclease Substrate Complex with A C/T Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:61.5 occ:1.00 OE2 B:GLU217 2.4 49.0 1.0 NH1 B:ARG237 3.2 34.8 1.0 NH2 B:ARG237 3.3 35.5 1.0 CD B:GLU217 3.4 51.2 1.0 CG B:GLU217 3.6 37.8 1.0 CZ B:ARG237 3.7 33.8 1.0 CE B:LYS227 3.7 46.6 1.0 NZ B:LYS227 3.7 53.4 1.0 O B:HOH514 4.5 33.7 1.0 OE1 B:GLU217 4.5 44.1 1.0

Sodium binding site 3 out of 3 in the APE1 F266A Exonuclease Substrate Complex with A C/T Mismatch


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of APE1 F266A Exonuclease Substrate Complex with A C/T Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:61.7 occ:1.00 O B:HIS289 3.9 35.2 1.0 O A:GLN245 4.0 47.0 1.0 C B:HIS289 4.0 31.5 1.0 CB B:HIS289 4.1 39.0 1.0 N B:SER290 4.2 32.7 1.0 CA B:SER290 4.3 38.9 1.0 C A:GLN245 4.5 44.8 1.0 CB A:GLN245 4.5 44.9 1.0 CA B:HIS289 4.7 35.1 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