Sodium in PDB 6w3l: APE1 Exonuclease Substrate Complex Wild-Type

All present enzymatic activity of APE1 Exonuclease Substrate Complex Wild-Type:
4.2.99.18;

The structure of APE1 Exonuclease Substrate Complex Wild-Type, PDB code: 6w3l 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)	24.77 / 2.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.371, 65.196, 91.258, 90.00, 110.27, 90.00
R / Rfree (%)	21.7 / 27.7

The structure of APE1 Exonuclease Substrate Complex Wild-Type also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the APE1 Exonuclease Substrate Complex Wild-Type (pdb code 6w3l). 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 Substrate Complex Wild-Type, PDB code: 6w3l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the APE1 Exonuclease Substrate Complex Wild-Type


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 Wild-Type within 5.0Å range: probe atom residue distance (Å) B Occ E:Na101 b:65.2 occ:1.00 O5' E:DG1 2.9 82.2 1.0 C5' E:DG1 3.7 72.7 1.0

Sodium binding site 2 out of 2 in the APE1 Exonuclease Substrate Complex Wild-Type


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 Wild-Type within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:55.6 occ:1.00 OD2 A:ASP283 2.3 54.8 1.0 OE1 A:GLN95 2.6 54.3 1.0 CG A:ASP283 3.1 50.7 1.0 OG A:SER66 3.2 54.3 1.0 CB A:ASP283 3.3 44.4 1.0 N A:ASN68 3.4 52.7 1.0 CA A:TRP67 3.5 50.2 1.0 N A:TRP67 3.5 47.3 1.0 CD A:GLN95 3.6 51.9 1.0 C A:TRP67 3.7 51.6 1.0 C A:SER66 3.7 55.2 1.0 O A:SER66 3.8 56.4 1.0 C A:GLY209 3.8 49.6 1.0 NE2 A:GLN95 4.0 52.2 1.0 N A:ASP210 4.1 53.8 1.0 CB A:SER66 4.1 50.4 1.0 O A:GLY209 4.1 55.0 1.0 CA A:GLY209 4.1 49.5 1.0 CG1 A:ILE312 4.2 51.8 1.0 OD1 A:ASP283 4.3 41.0 1.0 CD1 A:ILE312 4.4 48.7 1.0 CA A:ASP283 4.4 45.4 1.0 CA A:ASN68 4.5 46.3 1.0 CB A:ASN68 4.5 47.1 1.0 CA A:SER66 4.5 49.0 1.0 O A:TRP67 4.6 53.7 1.0 CA A:ASP210 4.6 51.2 1.0 N A:GLY209 4.7 57.6 1.0 O A:CYS310 4.9 51.0 1.0 CB A:ASP210 4.9 50.3 1.0 CG A:GLN95 4.9 52.8 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