Magnesium in PDB 5dff: Human APE1 Product Complex

All present enzymatic activity of Human APE1 Product Complex:
4.2.99.18;

The structure of Human APE1 Product Complex, PDB code: 5dff was solved by B.D.Freudenthal, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.38 / 1.57
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.514, 61.716, 72.053, 83.89, 78.81, 88.00
R / Rfree (%)	18.7 / 21.1

The structure of Human APE1 Product Complex also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Human APE1 Product Complex (pdb code 5dff). 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 Product Complex, PDB code: 5dff:

Magnesium binding site 1 out of 1 in the Human APE1 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 Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:19.5 occ:1.00 OP2 D:3DR1 2.0 15.1 1.0 O A:HOH527 2.1 20.0 1.0 O A:HOH504 2.1 25.5 1.0 O A:HOH550 2.1 19.2 1.0 O3' P:DC10 2.1 22.1 1.0 OE1 A:GLU96 2.2 15.5 1.0 CD A:GLU96 3.1 17.3 1.0 P D:3DR1 3.2 16.3 1.0 OE2 A:GLU96 3.4 23.3 1.0 OP3 D:3DR1 3.5 18.6 1.0 C3' P:DC10 3.5 26.7 1.0 O5' D:3DR1 3.8 15.1 1.0 NE2 A:HIS309 4.1 13.7 1.0 C2' P:DC10 4.1 23.8 1.0 ND2 A:ASN68 4.1 13.2 1.0 C4' P:DC10 4.1 26.5 1.0 C1' P:DC10 4.2 25.1 1.0 OD1 A:ASP308 4.2 15.3 1.0 OD2 A:ASP308 4.2 16.9 1.0 OH A:TYR171 4.3 19.6 1.0 OD1 A:ASP70 4.3 22.6 1.0 O D:HOH106 4.3 28.8 1.0 OP1 D:3DR1 4.4 13.8 1.0 CG A:GLU96 4.5 21.9 1.0 OD1 A:ASN68 4.5 13.5 1.0 CD2 A:HIS309 4.5 12.3 1.0 O4' P:DC10 4.5 25.2 1.0 C5' D:3DR1 4.7 14.6 1.0 CG A:ASP308 4.7 15.5 1.0 CG A:ASN68 4.7 13.9 1.0 O P:HOH127 4.7 29.9 1.0 CG A:ASP70 4.9 26.6 1.0

B.D.Freudenthal, W.A.Beard, M.J.Cuneo, N.S.Dyrkheeva, S.H.Wilson. Capturing Snapshots of APE1 Processing Dna Damage. Nat.Struct.Mol.Biol. V. 22 924 2015.
ISSN: ESSN 1545-9985
PubMed: 26458045
DOI: 10.1038/NSMB.3105