Magnesium in PDB 4qhe: Crystal Structure of MG2+ Bound Human APE1

All present enzymatic activity of Crystal Structure of MG2+ Bound Human APE1:
4.2.99.18;

The structure of Crystal Structure of MG2+ Bound Human APE1, PDB code: 4qhe was solved by H.He, Q.Chen, M.M.Georgiadis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	46.491, 137.545, 45.054, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 19.3

The binding sites of Magnesium atom in the Crystal Structure of MG2+ Bound Human APE1 (pdb code 4qhe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of MG2+ Bound Human APE1, PDB code: 4qhe:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of MG2+ Bound Human APE1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of MG2+ Bound Human APE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:15.5 occ:0.65 MG A:MG401 0.0 15.5 0.7 MG A:MG401 0.7 11.6 0.3 O A:HOH511 1.9 19.2 1.0 OD1 A:ASP70 1.9 15.0 1.0 OE2 A:GLU96 2.0 13.2 0.5 O A:HOH613 2.1 18.1 1.0 O A:HOH520 2.2 12.4 1.0 OE2 A:GLU96 2.5 8.4 0.5 O A:HOH553 2.5 16.7 0.5 CD A:GLU96 2.9 12.3 0.5 O A:HOH553 2.9 15.8 0.5 CG A:ASP70 3.0 13.4 1.0 OE1 A:GLU96 3.1 13.1 0.5 CD A:GLU96 3.3 8.1 0.5 OE1 A:GLU96 3.5 10.1 0.5 O A:HOH624 3.7 27.1 1.0 CB A:ASP70 3.7 11.6 1.0 OD2 A:ASP70 3.9 17.5 1.0 CA A:ASP70 4.0 10.8 1.0 OD2 A:ASP308 4.0 14.9 1.0 OD1 A:ASP308 4.1 11.6 1.0 O A:HOH567 4.3 19.2 1.0 CG A:GLU96 4.3 10.8 0.5 O A:HOH644 4.3 31.3 1.0 CG A:ASP308 4.5 12.0 1.0 OD1 A:ASN68 4.5 9.1 1.0 CG A:GLU96 4.7 8.4 0.5 O A:HOH642 4.8 31.9 1.0 N A:ASP70 4.9 10.0 1.0 C A:ASP70 4.9 11.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of MG2+ Bound Human APE1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of MG2+ Bound Human APE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:11.6 occ:0.35 MG A:MG401 0.0 11.6 0.3 MG A:MG401 0.7 15.5 0.7 OE2 A:GLU96 1.7 13.2 0.5 O A:HOH520 1.9 12.4 1.0 OE2 A:GLU96 2.0 8.4 0.5 O A:HOH553 2.0 16.7 0.5 O A:HOH553 2.2 15.8 0.5 O A:HOH613 2.3 18.1 1.0 O A:HOH511 2.3 19.2 1.0 CD A:GLU96 2.3 12.3 0.5 OE1 A:GLU96 2.4 13.1 0.5 OD1 A:ASP70 2.5 15.0 1.0 CD A:GLU96 2.9 8.1 0.5 OE1 A:GLU96 3.2 10.1 0.5 CG A:ASP70 3.5 13.4 1.0 CG A:GLU96 3.8 10.8 0.5 O A:HOH567 3.9 19.2 1.0 CB A:ASP70 4.0 11.6 1.0 CA A:ASP70 4.0 10.8 1.0 OD1 A:ASN68 4.1 9.1 1.0 O A:HOH624 4.2 27.1 1.0 CG A:GLU96 4.3 8.4 0.5 OD1 A:ASP308 4.3 11.6 1.0 OD2 A:ASP308 4.4 14.9 1.0 ND2 A:ASN68 4.5 9.6 1.0 OD2 A:ASP70 4.5 17.5 1.0 OH A:TYR171 4.5 15.7 1.0 CB A:GLU96 4.6 9.9 0.5 CB A:GLU96 4.6 7.6 0.5 CG A:ASN68 4.7 8.6 1.0 O A:HOH642 4.7 31.9 1.0 N A:ASP70 4.8 10.0 1.0 CG A:ASP308 4.8 12.0 1.0

H.He, Q.Chen, M.M.Georgiadis. High-Resolution Crystal Structures Reveal Plasticity in the Metal Binding Site of Apurinic/Apyrimidinic Endonuclease I. Biochemistry V. 53 6520 2014.
ISSN: ISSN 0006-2960
PubMed: 25251148
DOI: 10.1021/BI500676P