Magnesium in PDB 7tr7: APE1 Product Complex with Abasic Ssdna

All present enzymatic activity of APE1 Product Complex with Abasic Ssdna:
4.2.99.18;

The structure of APE1 Product Complex with Abasic Ssdna, PDB code: 7tr7 was solved by B.D.Freudenthal, N.M.Hoitsma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.81 / 2.00
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	83.717, 83.717, 204.179, 90, 90, 120
R / Rfree (%)	18.2 / 21.5

The binding sites of Magnesium atom in the APE1 Product Complex with Abasic Ssdna (pdb code 7tr7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the APE1 Product Complex with Abasic Ssdna, PDB code: 7tr7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the APE1 Product Complex with Abasic Ssdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of APE1 Product Complex with Abasic Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:19.5 occ:1.00 OP1 D:3DR1 2.0 14.7 1.0 O A:HOH559 2.1 15.5 1.0 OE1 A:GLU96 2.1 21.2 1.0 O A:HOH507 2.2 19.8 1.0 O D:HOH113 2.2 24.6 1.0 O A:HOH533 2.2 18.6 1.0 CD A:GLU96 3.0 27.4 1.0 P D:3DR1 3.3 17.1 1.0 OE2 A:GLU96 3.3 22.9 1.0 OP3 D:3DR1 3.6 20.3 1.0 O5' D:3DR1 3.9 19.6 1.0 O A:HOH644 4.0 27.1 1.0 ND2 A:ASN68 4.1 13.9 1.0 NE2 A:HIS309 4.1 12.4 1.0 OD2 A:ASP308 4.2 20.6 1.0 O D:HOH106 4.2 25.6 1.0 OD1 A:ASP308 4.2 19.6 1.0 OH A:TYR171 4.2 26.3 1.0 OD1 A:ASP70 4.3 20.5 1.0 OD1 A:ASN68 4.3 15.4 1.0 CG A:GLU96 4.4 20.9 1.0 OP2 D:3DR1 4.5 19.2 1.0 CD2 A:HIS309 4.6 13.2 1.0 CG A:ASN68 4.6 13.9 1.0 O D:HOH107 4.6 30.9 1.0 CG A:ASP308 4.7 23.4 1.0 O A:HOH579 4.7 29.6 1.0 C5' D:3DR1 4.8 20.4 1.0 CG A:ASP70 4.9 23.1 1.0

Magnesium binding site 2 out of 2 in the APE1 Product Complex with Abasic Ssdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of APE1 Product Complex with Abasic Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:21.4 occ:1.00 O C:HOH216 2.0 25.1 1.0 OP1 C:3DR1 2.2 15.6 1.0 P C:3DR1 3.4 17.6 1.0 OP3 C:3DR1 3.6 20.1 1.0 O5' C:3DR1 4.0 18.8 1.0 O C:HOH214 4.2 24.6 1.0 OP2 C:3DR1 4.7 17.3 1.0 O C:HOH210 4.7 33.4 1.0 C5' C:3DR1 4.9 22.8 1.0

N.M.Hoitsma, T.H.Khoang, B.D.Freudenthal. Mechanistic Insight Into Ap-Endonuclease 1 Cleavage of Abasic Sites at Stalled Replication Forks To Be Published.