Manganese in PDB 1de9: Human APE1 Endonuclease with Bound Abasic Dna and MN2+ Ion

All present enzymatic activity of Human APE1 Endonuclease with Bound Abasic Dna and MN2+ Ion:
4.2.99.18;

The structure of Human APE1 Endonuclease with Bound Abasic Dna and MN2+ Ion, PDB code: 1de9 was solved by C.D.Mol, T.Izumi, S.Mitra, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.060, 98.350, 101.050, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 27.4

The binding sites of Manganese atom in the Human APE1 Endonuclease with Bound Abasic Dna and MN2+ Ion (pdb code 1de9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Human APE1 Endonuclease with Bound Abasic Dna and MN2+ Ion, PDB code: 1de9:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human APE1 Endonuclease with Bound Abasic Dna and MN2+ Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human APE1 Endonuclease with Bound Abasic Dna and MN2+ Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1000 b:19.7 occ:1.00 OP1 Y:3DR6 2.1 26.5 1.0 OE2 A:GLU96 2.6 33.1 1.0 O3' X:DC5 2.6 60.8 1.0 OE1 A:GLU96 2.7 31.9 1.0 CD A:GLU96 3.0 33.7 1.0 OD2 A:ASP308 3.2 32.1 1.0 P Y:3DR6 3.3 24.2 1.0 C3' X:DC5 3.7 61.7 1.0 OP2 Y:3DR6 3.9 27.9 1.0 OD1 A:ASP308 3.9 31.9 1.0 CG A:ASP308 4.0 29.3 1.0 OP3 Y:3DR6 4.0 26.3 1.0 OD1 A:ASP70 4.1 25.5 1.0 NE2 A:HIS309 4.2 34.5 1.0 OD1 A:ASN68 4.2 18.6 1.0 CB A:ASP70 4.3 29.3 1.0 CD2 A:HIS309 4.3 29.1 1.0 ND2 A:ASN68 4.3 23.5 1.0 O5' Y:3DR6 4.4 24.8 1.0 CG A:ASP70 4.4 30.1 1.0 C2' X:DC5 4.4 61.9 1.0 CG A:GLU96 4.5 30.6 1.0 CG A:ASN68 4.6 27.1 1.0 C5' Y:3DR6 4.8 27.7 1.0 C4' X:DC5 4.9 60.5 1.0 CA A:ASP70 4.9 29.4 1.0

Manganese binding site 2 out of 2 in the Human APE1 Endonuclease with Bound Abasic Dna and MN2+ Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human APE1 Endonuclease with Bound Abasic Dna and MN2+ Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1001 b:33.1 occ:1.00 OP1 V:3DR6 2.2 40.1 1.0 O3' U:DC5 2.3 71.8 1.0 OE2 B:GLU96 2.4 19.9 1.0 OE1 B:GLU96 2.6 25.6 1.0 CD B:GLU96 2.9 20.7 1.0 C2' U:DC5 3.0 76.0 1.0 C3' U:DC5 3.1 75.2 1.0 P V:3DR6 3.4 39.7 1.0 OD2 B:ASP308 3.5 36.5 1.0 OP2 V:3DR6 3.6 40.5 1.0 OD1 B:ASN68 3.9 37.2 1.0 OD1 B:ASP308 4.1 35.8 1.0 CG B:ASP308 4.2 36.2 1.0 O5' V:3DR6 4.3 43.3 1.0 OD1 B:ASP70 4.3 26.7 1.0 CG B:GLU96 4.4 19.6 1.0 C4' U:DC5 4.4 77.3 1.0 OP3 V:3DR6 4.5 38.4 1.0 NE2 B:HIS309 4.5 28.2 1.0 C1' U:DC5 4.5 76.3 1.0 CD2 B:HIS309 4.6 26.1 1.0 OH B:TYR171 4.7 38.3 1.0 CG B:ASN68 4.7 37.7 1.0 C5' V:3DR6 4.7 43.2 1.0 ND2 B:ASN68 4.8 41.0 1.0

C.D.Mol, T.Izumi, S.Mitra, J.A.Tainer. Dna-Bound Structures and Mutants Reveal Abasic Dna Binding By APE1 and Dna Repair Coordination Nature V. 403 451 2000.
ISSN: ISSN 0028-0836
PubMed: 10667800
DOI: 10.1038/35000249