Calcium 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:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the APE1 Exonuclease Substrate Complex Wild-Type (pdb code 6w3l). 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 Wild-Type, PDB code: 6w3l:

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


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 Wild-Type within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca101 b:90.4 occ:1.00 OP2 D:DC8 3.2 76.9 1.0 C2' D:DG7 3.4 73.6 1.0 O5' D:DC8 3.5 70.0 1.0 P D:DC8 4.0 78.1 1.0 C6 D:DC8 4.1 54.4 1.0 C3' D:DG7 4.2 78.0 1.0 C2' D:DC8 4.4 61.7 1.0 C3' D:DC8 4.5 69.8 1.0 O3' D:DG7 4.6 78.9 1.0 C5' D:DC8 4.7 68.7 1.0 O4' D:DC8 4.7 60.0 1.0 C1' D:DG7 4.8 69.4 1.0 C5 D:DC8 4.8 57.6 1.0 C4' D:DC8 4.9 62.5 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