Manganese in PDB 6w4i: APE1 Y269A Product Complex with Abasic Dna

All present enzymatic activity of APE1 Y269A Product Complex with Abasic Dna:
4.2.99.18;

The structure of APE1 Y269A Product Complex with Abasic Dna, PDB code: 6w4i 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)	43.58 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.381, 150.233, 156.450, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22.7

The binding sites of Manganese atom in the APE1 Y269A Product Complex with Abasic Dna (pdb code 6w4i). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the APE1 Y269A Product Complex with Abasic Dna, PDB code: 6w4i:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the APE1 Y269A 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 Y269A Product Complex with Abasic Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:26.3 occ:1.00 OP1 D:3DR1 2.1 22.7 1.0 O A:HOH555 2.1 21.5 1.0 O3' P:DC10 2.2 28.5 1.0 OE2 A:GLU96 2.2 23.7 1.0 O A:HOH513 2.3 23.2 1.0 O A:HOH520 2.4 25.9 1.0 CD A:GLU96 3.1 26.0 1.0 OE1 A:GLU96 3.3 25.8 1.0 P D:3DR1 3.4 24.0 1.0 C3' P:DC10 3.4 34.0 1.0 OP3 D:3DR1 3.8 23.1 1.0 O P:HOH105 4.0 34.2 1.0 ND2 A:ASN68 4.1 19.2 1.0 O5' D:3DR1 4.1 26.6 1.0 OD1 A:ASP308 4.1 22.6 1.0 C2' P:DC10 4.1 32.7 1.0 NE2 A:HIS309 4.2 21.1 1.0 OD2 A:ASP308 4.3 26.7 1.0 OD1 A:ASN68 4.3 17.2 1.0 OD2 A:ASP70 4.3 29.5 1.0 OH A:TYR171 4.4 23.8 1.0 CG A:GLU96 4.5 26.2 1.0 OP2 D:3DR1 4.5 19.4 1.0 CD2 A:HIS309 4.6 21.7 1.0 C4' P:DC10 4.6 30.3 1.0 CG A:ASN68 4.6 18.8 1.0 CG A:ASP308 4.6 26.1 1.0 O A:HOH586 4.7 31.4 1.0 C1' P:DC10 4.9 35.0 1.0 C5' D:3DR1 4.9 23.7 1.0 CG A:ASP70 4.9 29.2 1.0 CB A:GLU96 5.0 20.3 1.0

Manganese binding site 2 out of 2 in the APE1 Y269A 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 2 of APE1 Y269A Product Complex with Abasic Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:27.1 occ:1.00 O B:HOH526 2.1 27.4 1.0 O3' E:DC10 2.1 28.5 1.0 OP1 C:3DR1 2.2 22.1 1.0 O B:HOH533 2.2 17.6 1.0 OE1 B:GLU96 2.2 26.3 1.0 O B:HOH527 2.3 23.1 1.0 CD B:GLU96 3.1 30.4 1.0 C3' E:DC10 3.3 31.3 1.0 P C:3DR1 3.4 25.9 1.0 OE2 B:GLU96 3.4 30.1 1.0 OP3 C:3DR1 3.7 25.1 1.0 O E:HOH102 4.0 27.4 1.0 ND2 B:ASN68 4.0 18.7 1.0 C2' E:DC10 4.0 31.7 1.0 OD1 B:ASP308 4.1 26.3 1.0 O5' C:3DR1 4.1 27.7 1.0 OD2 B:ASP308 4.3 27.7 1.0 OH B:TYR171 4.3 24.8 1.0 NE2 B:HIS309 4.3 23.4 1.0 OD1 B:ASN68 4.3 24.5 1.0 C4' E:DC10 4.5 33.6 1.0 CG B:GLU96 4.5 31.8 1.0 OD1 B:ASP70 4.5 29.9 1.0 CG B:ASN68 4.6 22.9 1.0 OP2 C:3DR1 4.6 25.0 1.0 CG B:ASP308 4.6 29.1 1.0 CD2 B:HIS309 4.7 23.7 1.0 C1' E:DC10 4.8 33.6 1.0 C5' C:3DR1 5.0 25.0 1.0 CB B:GLU96 5.0 25.0 1.0

N.M.Hoitsma, A.M.Whitaker, E.C.Beckwitt, S.Jang, P.K.Agarwal, B.Van Houten, B.D.Freudenthal. Characterizing the APE1 Dna Intercalating Loop During Dna Sculpting To Be Published.