Magnesium in PDB 6w2p: APE1 Endonuclease Product Complex L104R

All present enzymatic activity of APE1 Endonuclease Product Complex L104R:
4.2.99.18;

The structure of APE1 Endonuclease Product Complex L104R, PDB code: 6w2p 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)	24.45 / 1.94
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.387, 61.780, 72.278, 83.71, 78.56, 88.02
R / Rfree (%)	20.1 / 23.8

The binding sites of Magnesium atom in the APE1 Endonuclease Product Complex L104R (pdb code 6w2p). 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 L104R, PDB code: 6w2p:

Magnesium binding site 1 out of 1 in the APE1 Endonuclease Product Complex L104R


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 L104R within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:40.8 occ:1.00 O A:HOH509 2.0 27.6 1.0 OP2 D:3DR1 2.1 23.2 1.0 O A:HOH578 2.2 28.8 1.0 OE1 A:GLU96 2.3 22.3 1.0 O3' P:DC10 2.6 36.2 1.0 P D:3DR1 3.1 23.7 1.0 CD A:GLU96 3.1 27.1 1.0 OP3 D:3DR1 3.2 26.8 1.0 OE2 A:GLU96 3.3 37.1 1.0 O5' D:3DR1 3.8 24.1 1.0 C3' P:DC10 4.1 50.7 1.0 ND2 A:ASN68 4.1 17.5 1.0 NE2 A:HIS309 4.1 15.9 1.0 OH A:TYR171 4.2 26.1 1.0 OD2 A:ASP308 4.2 23.2 1.0 OD1 A:ASP308 4.2 21.2 1.0 OD1 A:ASP70 4.4 29.4 1.0 OP1 D:3DR1 4.4 19.2 1.0 OD1 A:ASN68 4.4 19.5 1.0 O D:HOH106 4.5 41.8 1.0 CD2 A:HIS309 4.5 15.2 1.0 CG A:GLU96 4.6 28.2 1.0 CG A:ASP308 4.6 25.6 1.0 C5' D:3DR1 4.6 20.2 1.0 CG A:ASN68 4.6 16.7 1.0 C4' P:DC10 4.7 54.9 1.0 CG A:ASP70 5.0 36.1 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