Magnesium in PDB 6p93: Human APE1 K98A Ap-Endonuclease Product Complex

All present enzymatic activity of Human APE1 K98A Ap-Endonuclease Product Complex:
4.2.99.18;

The structure of Human APE1 K98A Ap-Endonuclease Product Complex, PDB code: 6p93 was solved by A.W.Whitaker, W.J.Stark, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.97 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.351, 60.493, 72.620, 83.72, 79.66, 88.46
R / Rfree (%)	17.2 / 22.6

The structure of Human APE1 K98A Ap-Endonuclease Product Complex also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Human APE1 K98A Ap-Endonuclease Product Complex (pdb code 6p93). 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 Human APE1 K98A Ap-Endonuclease Product Complex, PDB code: 6p93:

Magnesium binding site 1 out of 1 in the Human APE1 K98A Ap-Endonuclease Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human APE1 K98A Ap-Endonuclease Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:26.2 occ:1.00 O A:HOH501 2.0 29.8 1.0 O A:HOH539 2.1 18.3 1.0 O A:HOH530 2.1 15.4 1.0 OE1 A:GLU96 2.2 21.6 1.0 OP2 D:3DR1 2.2 20.1 1.0 O3' P:DC10 2.2 25.7 1.0 OE2 A:GLU96 2.7 29.7 1.0 CD A:GLU96 2.8 22.0 1.0 P D:3DR1 3.4 23.6 1.0 C3' P:DC10 3.6 28.0 1.0 OP3 D:3DR1 3.7 22.1 1.0 O5' D:3DR1 4.1 24.4 1.0 ND2 A:ASN68 4.1 14.6 1.0 C4' P:DC10 4.2 30.4 1.0 C2' P:DC10 4.2 27.4 1.0 CG A:GLU96 4.3 17.5 1.0 NE2 A:HIS309 4.3 11.8 1.0 OD1 A:ASP308 4.3 16.7 1.0 OD2 A:ASP308 4.3 18.0 1.0 OH A:TYR171 4.3 24.1 1.0 C1' P:DC10 4.4 29.1 1.0 OD1 A:ASN68 4.4 13.4 1.0 OD1 A:ASP70 4.4 23.4 1.0 CD2 A:HIS309 4.6 13.3 1.0 OP1 D:3DR1 4.6 14.1 1.0 CG A:ASN68 4.7 11.8 1.0 CG A:ASP308 4.7 18.7 1.0 O4' P:DC10 4.7 29.4 1.0 C5' D:3DR1 5.0 23.3 1.0

D.R.Mcneill, A.M.Whitaker, W.J.Stark, J.L.Illuzzi, P.J.Mckinnon, B.D.Freudenthal, D.M.Wilson. Functions of the Major Abasic Endonuclease (APE1) in Cell Viability and Genotoxin Resistance. Mutagenesis 2019.
ISSN: ISSN 1464-3804
PubMed: 31816044
DOI: 10.1093/MUTAGE/GEZ046