Manganese in PDB 5wn5: APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+

All present enzymatic activity of APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+:
4.2.99.18;

The structure of APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+, PDB code: 5wn5 was solved by B.D.Freudenthal, A.M.Whitaker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.74 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.503, 64.444, 91.522, 90.00, 109.93, 90.00
R / Rfree (%)	22.6 / 26.1

The structure of APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+ also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+ (pdb code 5wn5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+, PDB code: 5wn5:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn101 b:0.3 occ:1.00 O6 E:DG7 3.0 0.8 1.0 C6 E:DC6 3.4 0.3 1.0 C6 E:DG7 3.5 0.4 1.0 C5 E:DC6 3.6 0.4 1.0 N7 E:DG7 3.6 0.6 1.0 C5 E:DG7 3.8 0.1 1.0 C2' E:DC6 3.8 0.4 1.0 N1 E:DC6 4.0 0.8 1.0 C4 E:DC6 4.4 0.4 1.0 C1' E:DC6 4.5 0.3 1.0 N1 E:DG7 4.6 0.5 1.0 C8 E:DG7 4.7 0.8 1.0 C2 E:DC6 4.8 0.1 1.0 OP2 E:DC6 4.9 0.2 1.0 N3 E:DC6 4.9 0.2 1.0 C4 E:DG7 5.0 0.2 1.0

Manganese binding site 2 out of 3 in the APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:94.5 occ:1.00 OD1 A:ASP70 1.7 58.6 1.0 OE2 A:GLU96 2.8 58.9 1.0 CG A:ASP70 2.8 52.0 1.0 OE1 A:GLU96 3.1 54.7 1.0 CD A:GLU96 3.3 56.5 1.0 OD2 A:ASP70 3.5 61.7 1.0 OD2 A:ASP308 4.0 35.1 1.0 CB A:ASP70 4.0 48.9 1.0 OD1 A:ASP308 4.3 41.6 1.0 O A:HOH507 4.3 53.4 1.0 CG A:ASP308 4.6 39.0 1.0 CG A:GLU96 4.7 51.0 1.0 CA A:ASP70 4.8 43.6 1.0 NZ A:LYS98 4.9 50.9 1.0

Manganese binding site 3 out of 3 in the APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of APE1 Exonuclease Substrate Complex with A C/T Mismatch and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:89.9 occ:1.00 OD1 B:ASP70 1.9 53.1 1.0 O D:HOH207 2.5 62.9 1.0 OE2 B:GLU96 2.6 57.2 1.0 OE1 B:GLU96 2.8 49.8 1.0 CD B:GLU96 3.0 50.1 1.0 SP2 D:C7R10 3.0 58.9 0.5 CG B:ASP70 3.1 54.6 1.0 OP1 D:C7R10 3.1 60.5 0.5 CB B:ASP70 3.9 45.8 1.0 OD2 B:ASP308 4.0 42.0 1.0 OD2 B:ASP70 4.0 60.1 1.0 OD1 B:ASP308 4.1 44.8 1.0 O3' D:DG9 4.2 59.2 0.2 CG B:GLU96 4.3 45.6 1.0 P D:C7R10 4.4 67.2 0.5 P D:C7R10 4.4 67.6 0.5 CA B:ASP70 4.5 47.7 1.0 CG B:ASP308 4.5 40.6 1.0 NZ B:LYS98 4.5 52.7 1.0 C4' D:DG9 4.5 56.5 0.2 C4' D:DG9 4.6 56.7 0.8 O3' D:DG9 4.7 58.8 0.8 OD1 B:ASN68 4.7 43.4 1.0 O4' D:DG9 4.7 57.4 0.2 O4' D:DG9 4.8 57.5 0.8 CE B:LYS98 4.8 48.3 1.0 OH B:TYR171 4.9 43.9 1.0

A.M.Whitaker, T.S.Flynn, B.D.Freudenthal. Molecular Snapshots of APE1 Proofreading Mismatches and Removing Dna Damage. Nat Commun V. 9 399 2018.
ISSN: ESSN 2041-1723
PubMed: 29374164
DOI: 10.1038/S41467-017-02175-Y