Chlorine 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
Sodium	(Na)	3 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the APE1 F266A Exonuclease Substrate Complex with A C/T Mismatch, PDB code: 5wn3:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the APE1 F266A Exonuclease Substrate Complex with A C/T Mismatch


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl404 b:66.8 occ:1.00 N A:ASP163 3.3 44.6 1.0 OD2 A:ASP163 3.3 53.4 1.0 CG A:ASP163 3.5 56.5 1.0 CB A:PHE162 3.8 42.7 1.0 CD2 A:PHE162 3.8 41.8 1.0 CB A:ASP163 3.9 42.5 1.0 OD1 A:ASP163 3.9 50.5 1.0 CA A:PHE162 4.0 39.1 1.0 C A:PHE162 4.2 41.2 1.0 CA A:ASP163 4.2 42.8 1.0 CG A:PHE162 4.3 41.7 1.0 O A:ALA138 4.7 48.7 1.0 CG A:LEU140 4.9 40.1 1.0 CD2 A:LEU140 4.9 44.3 1.0 CE2 A:PHE162 4.9 43.6 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 A:Cl405 b:38.4 occ:1.00 O A:HOH563 2.9 31.1 1.0 OG1 A:THR260 3.0 30.8 1.0 N A:ASN259 3.1 26.4 1.0 C A:TYR257 3.3 27.8 1.0 CA A:TYR257 3.4 27.3 1.0 N A:PRO258 3.6 28.5 1.0 N A:THR260 3.7 29.6 1.0 CA A:ASN259 3.7 32.1 1.0 C A:ASN259 3.8 29.6 1.0 O A:TYR257 3.8 26.1 1.0 CB A:TYR257 3.8 26.9 1.0 CB A:ASN259 3.9 32.4 1.0 CD A:PRO258 3.9 23.0 1.0 CB A:THR260 4.1 30.8 1.0 C A:PRO258 4.2 29.5 1.0 CA A:THR260 4.4 27.8 1.0 CG A:PRO258 4.4 25.7 1.0 CA A:PRO258 4.4 29.8 1.0 O A:ASN259 4.5 32.9 1.0 ND2 A:ASN259 4.5 26.2 1.0 CD1 A:TYR257 4.7 27.3 1.0 N A:TYR257 4.7 26.8 1.0 O A:LEU256 4.7 25.2 1.0 CG A:ASN259 4.7 34.9 1.0 CG A:TYR257 4.8 28.6 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