Calcium 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:

Chlorine	(Cl)	1 atom
Sodium	(Na)	3 atoms

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was determined in the APE1 Exonuclease Substrate Complex with A C/T Mismatch, PDB code: 5wn4:

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 D:Ca101 b:79.8 occ:1.00 OP2 D:DC8 3.1 54.6 1.0 C2' D:DG7 3.4 60.4 1.0 O5' D:DC8 3.5 51.9 1.0 P D:DC8 3.9 61.6 1.0 C6 D:DC8 4.1 44.7 1.0 C3' D:DG7 4.2 62.0 1.0 O3' D:DG7 4.5 62.4 1.0 C3' D:DC8 4.6 54.9 1.0 C2' D:DC8 4.6 53.6 1.0 O4' D:DC8 4.7 50.2 1.0 C5 D:DC8 4.7 47.3 1.0 C1' D:DG7 4.7 52.6 1.0 C5' D:DC8 4.7 45.4 1.0 C4' D:DC8 4.9 52.2 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