Magnesium in PDB 6w0q: APE1 Endonuclease Product Complex D148E

All present enzymatic activity of APE1 Endonuclease Product Complex D148E:
4.2.99.18;

The structure of APE1 Endonuclease Product Complex D148E, PDB code: 6w0q 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)	24.81 / 1.89
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.435, 60.496, 72.982, 83.51, 79.62, 88.62
R / Rfree (%)	18.6 / 22.3

The binding sites of Magnesium atom in the APE1 Endonuclease Product Complex D148E (pdb code 6w0q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the APE1 Endonuclease Product Complex D148E, PDB code: 6w0q:

Magnesium binding site 1 out of 1 in the APE1 Endonuclease Product Complex D148E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of APE1 Endonuclease Product Complex D148E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:20.7 occ:1.00 O A:HOH504 2.0 24.4 1.0 O A:HOH535 2.0 20.9 1.0 OP2 D:3DR1 2.0 16.4 1.0 O A:HOH530 2.1 18.1 1.0 OE1 A:GLU96 2.1 18.7 1.0 O3' P:DC10 2.2 21.5 1.0 P D:3DR1 3.0 20.4 1.0 CD A:GLU96 3.0 19.4 1.0 OP3 D:3DR1 3.1 26.1 1.0 OE2 A:GLU96 3.3 30.6 1.0 C3' P:DC10 3.5 23.4 1.0 O5' D:3DR1 3.8 15.5 1.0 NE2 A:HIS309 4.1 13.6 1.0 ND2 A:ASN68 4.1 16.5 1.0 C4' P:DC10 4.2 27.6 1.0 C2' P:DC10 4.2 26.9 1.0 OH A:TYR171 4.2 24.2 1.0 OD2 A:ASP308 4.2 18.5 1.0 C1' P:DC10 4.3 29.9 1.0 OD1 A:ASP308 4.3 17.8 1.0 OP1 D:3DR1 4.3 15.9 1.0 CG A:GLU96 4.4 22.1 1.0 O P:HOH126 4.4 28.6 1.0 OD1 A:ASN68 4.5 15.5 1.0 CD2 A:HIS309 4.6 14.9 1.0 OD1 A:ASP70 4.6 21.7 1.0 C5' D:3DR1 4.6 20.8 1.0 O4' P:DC10 4.6 27.3 1.0 CG A:ASN68 4.6 14.3 1.0 CG A:ASP308 4.7 21.3 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