Manganese in PDB 9dp2: APE1 N174A Product Complex with Abasic Dna

The structure of APE1 N174A Product Complex with Abasic Dna, PDB code: 9dp2 was solved by K.D.Dehart, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.03 / 1.99
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.256, 61.831, 72.617, 82.99, 78.28, 87.17
R / Rfree (%)	18.5 / 20.3

The binding sites of Manganese atom in the APE1 N174A Product Complex with Abasic Dna (pdb code 9dp2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the APE1 N174A Product Complex with Abasic Dna, PDB code: 9dp2:

Manganese binding site 1 out of 1 in the APE1 N174A Product Complex with Abasic Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of APE1 N174A Product Complex with Abasic Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:42.0 occ:1.00 O A:HOH506 2.2 20.8 1.0 O A:HOH501 2.2 29.9 1.0 O A:HOH549 2.3 26.1 1.0 OE1 A:GLU96 2.4 21.2 1.0 OP2 D:3DR1 2.4 24.0 1.0 O E:HOH102 2.5 35.4 1.0 OE2 A:GLU96 2.9 26.9 1.0 CD A:GLU96 3.0 24.3 1.0 OD1 A:ASP70 3.6 28.5 1.0 P D:3DR1 3.7 23.5 1.0 OP3 D:3DR1 3.9 23.3 1.0 OD2 A:ASP308 4.1 25.0 1.0 OD1 A:ASP308 4.2 20.0 1.0 OD1 A:ASN68 4.4 17.3 1.0 O3' E:DC10 4.4 51.8 1.0 ND2 A:ASN68 4.4 17.3 1.0 CG A:GLU96 4.4 23.5 1.0 CG A:ASP70 4.4 33.1 1.0 NE2 A:HIS309 4.5 15.1 1.0 O5' D:3DR1 4.5 26.2 1.0 OH A:TYR171 4.5 23.5 1.0 CG A:ASP308 4.6 21.7 1.0 O F:HOH124 4.6 34.5 1.0 O D:HOH110 4.6 31.0 1.0 CD2 A:HIS309 4.7 15.5 1.0 CG A:ASN68 4.8 15.5 1.0 CB A:ASP70 4.8 16.2 1.0 OP1 D:3DR1 4.9 20.7 1.0

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