Sodium in PDB 5wn4: APE1 Exonuclease Substrate Complex with A C/T Mismatch

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

The structure of APE1 Exonuclease Substrate Complex with A C/T Mismatch, PDB code: 5wn4 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)	24.56 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.334, 63.845, 90.924, 90.00, 109.66, 90.00
R / Rfree (%)	20.4 / 24.9

The structure of APE1 Exonuclease Substrate Complex with A C/T Mismatch 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 with A C/T Mismatch (pdb code 5wn4). 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 Exonuclease Substrate Complex with A C/T Mismatch, PDB code: 5wn4:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the APE1 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 Exonuclease Substrate Complex with A C/T Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:77.0 occ:1.00 O3' C:DC11 2.4 96.3 1.0 C3' C:DC11 3.7 0.3 1.0 C4' C:DC11 4.7 0.7 1.0 C2' C:DC11 4.7 99.5 1.0

Sodium binding site 2 out of 3 in the APE1 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 Exonuclease Substrate Complex with A C/T Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ E:Na101 b:80.3 occ:1.00 O5' E:DG1 2.8 67.0 1.0 C5' E:DG1 3.5 53.0 1.0 C4' E:DG1 5.0 62.0 1.0

Sodium binding site 3 out of 3 in the APE1 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 Exonuclease Substrate Complex with A C/T Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:47.0 occ:1.00 OE1 A:GLN95 2.4 39.5 1.0 OD1 A:ASP283 2.8 41.2 1.0 OG A:SER66 2.8 38.7 1.0 O A:HOH535 2.9 41.5 1.0 CD A:GLN95 3.4 37.1 1.0 N A:TRP67 3.4 32.4 1.0 CG A:ASP283 3.5 41.2 1.0 N A:ASN68 3.6 37.9 1.0 C A:GLY209 3.6 36.3 1.0 CA A:TRP67 3.7 31.7 1.0 C A:TRP67 3.7 41.2 1.0 CB A:ASP283 3.7 32.9 1.0 C A:SER66 3.7 37.9 1.0 N A:ASP210 3.7 40.1 1.0 CA A:GLY209 3.7 41.4 1.0 NE2 A:GLN95 3.9 33.8 1.0 CB A:SER66 3.9 37.8 1.0 O A:SER66 4.0 36.4 1.0 O A:GLY209 4.0 39.2 1.0 O A:TRP67 4.4 38.4 1.0 CA A:ASP210 4.4 38.0 1.0 CA A:SER66 4.5 38.4 1.0 CA A:ASN68 4.5 36.6 1.0 CB A:ASN68 4.5 41.6 1.0 OD2 A:ASP283 4.5 33.7 1.0 N A:GLY209 4.6 37.6 1.0 CG A:GLN95 4.6 35.1 1.0 CB A:ASP210 4.6 35.5 1.0 CA A:ASP283 4.7 32.6 1.0 CG1 A:ILE312 4.7 34.4 1.0 CD1 A:ILE312 4.8 36.2 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