Sodium in PDB 5wn2: APE1 Exonuclease Substrate Complex with Phosphoglycolate

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

The structure of APE1 Exonuclease Substrate Complex with Phosphoglycolate, PDB code: 5wn2 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)	24.68 / 2.29
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.363, 64.310, 91.144, 90.00, 110.14, 90.00
R / Rfree (%)	18.9 / 24

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

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the APE1 Exonuclease Substrate Complex with Phosphoglycolate (pdb code 5wn2). 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 with Phosphoglycolate, PDB code: 5wn2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the APE1 Exonuclease Substrate Complex with Phosphoglycolate


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 Phosphoglycolate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:48.6 occ:1.00 NZ A:LYS125 3.3 56.8 1.0 OH A:TYR128 3.6 33.6 1.0 CZ A:ARG181 3.8 38.2 1.0 NE A:ARG181 3.8 35.4 1.0 OP1 D:DC8 3.8 40.9 1.0 NH1 A:ARG181 3.8 32.5 1.0 CD A:ARG181 4.0 33.7 1.0 O5' D:DC8 4.2 39.2 1.0 NH2 A:ARG181 4.3 40.0 1.0 CZ A:TYR128 4.3 37.1 1.0 O A:HOH508 4.3 33.7 1.0 OP1 D:DG9 4.4 35.8 0.6 P D:DC8 4.5 39.1 1.0 O3' D:DC8 4.6 39.8 1.0 OP1 D:DG9 4.6 35.7 0.4 C5' D:DC8 4.7 34.4 1.0 CE A:LYS125 4.8 53.3 1.0 OP2 D:DG9 4.8 34.6 0.4 CE1 A:TYR128 4.8 36.4 1.0 P D:DG9 4.9 32.3 0.4 P D:DG9 4.9 32.3 0.6 C3' D:DC8 4.9 34.0 1.0 OP2 D:DG9 4.9 34.7 0.6 CE2 A:TYR128 4.9 38.3 1.0 OP2 D:DC8 5.0 41.5 1.0 CG A:ARG181 5.0 37.4 1.0

Sodium binding site 2 out of 2 in the APE1 Exonuclease Substrate Complex with Phosphoglycolate


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 Phosphoglycolate within 5.0Å range: probe atom residue distance (Å) B Occ E:Na103 b:42.6 occ:1.00 N3 E:DG1 2.9 49.0 1.0 N2 E:DG1 3.4 47.9 1.0 C2 E:DG1 3.6 51.5 1.0 O4' E:DG2 3.6 41.6 1.0 O4' E:DG1 3.6 38.6 1.0 C1' E:DG1 3.9 45.6 1.0 C4 E:DG2 3.9 48.9 1.0 C4 E:DG1 3.9 47.7 1.0 N9 E:DG2 3.9 46.8 1.0 N3 E:DG2 4.1 51.0 1.0 C1' E:DG2 4.2 47.1 1.0 C4' E:DG1 4.2 37.6 1.0 N9 E:DG1 4.3 44.0 1.0 C5 E:DG2 4.4 50.5 1.0 C8 E:DG2 4.5 44.7 1.0 C2 E:DG2 4.6 56.6 1.0 N7 E:DG2 4.8 49.3 1.0 C4' E:DG2 4.8 45.9 1.0 N1 E:DG1 4.9 54.6 1.0 O3' E:DG1 5.0 41.9 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