Atomistry » Calcium » PDB 5w7a-5wn3 » 5wn2
Atomistry »
  Calcium »
    PDB 5w7a-5wn3 »
      5wn2 »

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

Enzymatic activity of APE1 Exonuclease Substrate Complex with Phosphoglycolate

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

Protein crystallography data

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

Other elements in 5wn2:

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

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the APE1 Exonuclease Substrate Complex with Phosphoglycolate (pdb code 5wn2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the APE1 Exonuclease Substrate Complex with Phosphoglycolate, PDB code: 5wn2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5wn2

Go back to Calcium Binding Sites List in 5wn2
Calcium binding site 1 out of 2 in the APE1 Exonuclease Substrate Complex with Phosphoglycolate


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 Phosphoglycolate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca101

b:59.0
occ:1.00
O3' E:DC21 2.2 58.9 1.0
O E:HOH209 2.3 58.3 1.0
C3' E:DC21 3.2 45.2 1.0
C4' E:DC21 3.6 40.2 1.0
C2' E:DC21 4.5 45.8 1.0
C5' E:DC21 4.6 43.2 1.0
O4' E:DC21 4.7 38.6 1.0

Calcium binding site 2 out of 2 in 5wn2

Go back to Calcium Binding Sites List in 5wn2
Calcium binding site 2 out of 2 in the APE1 Exonuclease Substrate Complex with Phosphoglycolate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of APE1 Exonuclease Substrate Complex with Phosphoglycolate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca102

b:30.0
occ:1.00
O5' E:DG1 4.0 45.9 1.0
C5' E:DG1 4.4 37.5 1.0

Reference:

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
Page generated: Mon Jul 15 13:17:30 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy