Magnesium in PDB 9dp4: APE1 N174Q Product Complex with Abasic Dna

All present enzymatic activity of APE1 N174Q Product Complex with Abasic Dna:
3.1.11.2;

The structure of APE1 N174Q Product Complex with Abasic Dna, PDB code: 9dp4 was solved by K.D.Dehart, N.M.Hoitsma, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.52 / 2.25
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	153.423, 153.423, 45.373, 90, 90, 90
R / Rfree (%)	21.5 / 24.9

The binding sites of Magnesium atom in the APE1 N174Q Product Complex with Abasic Dna (pdb code 9dp4). 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 N174Q Product Complex with Abasic Dna, PDB code: 9dp4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the APE1 N174Q Product Complex with Abasic Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of APE1 N174Q Product Complex with Abasic Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:38.6 occ:1.00 OE2 B:GLU96 2.6 30.7 1.0 OD1 B:ASP70 2.8 30.5 1.0 OE1 B:GLU96 3.0 27.9 1.0 CD B:GLU96 3.1 25.9 1.0 OP2 G:3DR1 3.3 32.1 1.0 O3' H:DC10 3.3 44.4 1.0 CG B:ASP70 3.5 30.4 1.0 O H:HOH107 3.5 43.2 1.0 OD2 B:ASP308 3.8 34.9 1.0 OD2 B:ASP70 3.9 28.4 1.0 OD1 B:ASP308 4.2 33.6 1.0 CB B:ASP70 4.4 27.7 1.0 CG B:ASP308 4.4 30.7 1.0 P G:3DR1 4.5 35.2 1.0 CG B:GLU96 4.6 21.9 1.0 C3' H:DC10 4.7 47.8 1.0 OD1 B:ASN68 4.7 23.4 1.0 OP3 G:3DR1 4.8 36.9 1.0 OH B:TYR171 4.8 36.1 1.0 O2 H:DC10 5.0 57.9 1.0 O5' G:3DR1 5.0 32.8 1.0 C1' H:DC10 5.0 60.2 1.0

Magnesium binding site 2 out of 2 in the APE1 N174Q Product Complex with Abasic Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of APE1 N174Q Product Complex with Abasic Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:35.8 occ:1.00 O A:HOH539 2.2 22.0 1.0 O D:HOH201 2.4 26.4 1.0 OP2 D:3DR1 2.4 26.6 1.0 O A:HOH581 2.7 26.7 1.0 OE2 A:GLU96 3.1 42.6 1.0 O3' E:DC10 3.2 44.7 1.0 P D:3DR1 3.4 25.5 1.0 OE1 A:GLU96 3.4 36.5 1.0 OP3 D:3DR1 3.4 32.4 1.0 CD A:GLU96 3.5 32.1 1.0 O5' D:3DR1 3.7 25.8 1.0 OD2 A:ASP308 3.9 32.3 1.0 OH A:TYR171 3.9 33.4 1.0 C3' E:DC10 4.3 49.2 1.0 C4' E:DC10 4.4 44.7 1.0 NE2 A:GLN174 4.5 35.6 1.0 OP1 D:3DR1 4.7 25.0 1.0 OD1 A:ASP70 4.7 35.5 1.0 NE2 A:HIS309 4.7 22.4 1.0 CG A:ASP308 4.8 28.6 1.0 OD1 A:ASN68 4.8 21.7 1.0 OD1 A:ASP308 4.8 28.8 1.0 C5' E:DC10 4.8 50.0 1.0 CG A:GLU96 4.9 26.9 1.0 CZ A:TYR171 4.9 33.2 1.0 C5' D:3DR1 4.9 19.6 1.0

K.D.Dehart, N.M.Hoitsma, S.H.Thompson, B.D.Freudenthal. N174 Physically and Chemically Stabilizes the APE1 Endonuclease Reaction To Be Published.