Manganese in PDB 7lpj: APE1 Mn-Bound Phosphorothioate Substrate Complex with Abasic Ribonucleotide Dna

All present enzymatic activity of APE1 Mn-Bound Phosphorothioate Substrate Complex with Abasic Ribonucleotide Dna:
4.2.99.18;

The structure of APE1 Mn-Bound Phosphorothioate Substrate Complex with Abasic Ribonucleotide Dna, PDB code: 7lpj 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)	48.82 / 2.56
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.171, 60.901, 73.32, 82.91, 77.58, 86.25
R / Rfree (%)	18.3 / 24.8

The binding sites of Manganese atom in the APE1 Mn-Bound Phosphorothioate Substrate Complex with Abasic Ribonucleotide Dna (pdb code 7lpj). 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 Mn-Bound Phosphorothioate Substrate Complex with Abasic Ribonucleotide Dna, PDB code: 7lpj:

Manganese binding site 1 out of 1 in the APE1 Mn-Bound Phosphorothioate Substrate Complex with Abasic Ribonucleotide Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of APE1 Mn-Bound Phosphorothioate Substrate Complex with Abasic Ribonucleotide Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:50.9 occ:1.00 OE2 D:GLU96 2.2 44.7 1.0 O D:HOH501 2.3 36.9 1.0 O D:HOH519 2.3 44.0 1.0 O D:HOH502 2.4 41.0 1.0 OD2 D:ASP70 2.4 39.1 1.0 OE1 D:GLU96 2.8 32.6 1.0 CD D:GLU96 2.8 37.3 1.0 CG D:ASP70 3.5 40.1 1.0 OP1 E:YA411 3.9 45.5 0.4 CB D:ASP70 4.0 31.4 1.0 SP3 E:YA411 4.1 41.9 0.6 O C:HOH104 4.1 29.5 1.0 NZ D:LYS98 4.2 43.3 1.0 OD1 D:ASP308 4.3 32.5 1.0 OD2 D:ASP308 4.3 38.2 1.0 CG D:GLU96 4.3 29.9 1.0 CA D:ASP70 4.4 29.4 1.0 OD1 D:ASP70 4.5 42.0 1.0 OD1 D:ASN68 4.6 25.6 1.0 CG D:ASP308 4.7 33.8 1.0 P E:YA411 4.8 60.4 0.4 CE D:LYS98 4.8 47.7 1.0 P E:YA411 4.8 60.4 0.6 O3' E:DC10 4.8 53.4 1.0 C4' E:DC10 4.8 51.9 1.0 OP1 E:YA411 5.0 46.0 0.6 OH D:TYR171 5.0 38.9 1.0

N.M.Hoitsma, T.H.Click, P.K.Agarwal, B.D.Freudenthal. Altered APE1 Activity on Abasic Ribonucleotides Is Mediated By Changes in the Nucleoside Sugar Pucker. Comput Struct Biotechnol J V. 19 3293 2021.
ISSN: ESSN 2001-0370
PubMed: 34188778
DOI: 10.1016/J.CSBJ.2021.05.035