Manganese in PDB 5t4i: A Novel Domain in Human Exog Converts Apoptotic Endonuclease to Dna- Repair Enzyme

The structure of A Novel Domain in Human Exog Converts Apoptotic Endonuclease to Dna- Repair Enzyme, PDB code: 5t4i was solved by M.R.Szymanski, W.Y.Yin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.03 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.508, 79.723, 138.870, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 22.9

The binding sites of Manganese atom in the A Novel Domain in Human Exog Converts Apoptotic Endonuclease to Dna- Repair Enzyme (pdb code 5t4i). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the A Novel Domain in Human Exog Converts Apoptotic Endonuclease to Dna- Repair Enzyme, PDB code: 5t4i:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the A Novel Domain in Human Exog Converts Apoptotic Endonuclease to Dna- Repair Enzyme


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of A Novel Domain in Human Exog Converts Apoptotic Endonuclease to Dna- Repair Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:60.0 occ:1.00 OD1 A:ASN171 2.1 36.3 1.0 OP1 E:DG3 2.3 36.7 1.0 O A:HOH509 2.4 35.1 1.0 O3' E:DT2 2.5 37.3 1.0 P E:DG3 3.0 36.8 1.0 H A:ALA140 3.2 43.3 1.0 CG A:ASN171 3.2 35.4 1.0 HD21 A:ASN171 3.4 50.3 1.0 HD1 A:TRP175 3.5 42.8 1.0 HA2 A:GLY139 3.5 48.3 1.0 ND2 A:ASN171 3.7 41.9 1.0 H4' E:DT2 3.7 47.8 1.0 N A:ALA140 3.7 36.1 1.0 O5' E:DG3 3.8 35.8 1.0 O A:ALA140 3.8 40.5 1.0 C3' E:DT2 3.8 37.1 1.0 HB3 A:ALA140 3.9 40.8 1.0 OE1 A:GLU179 3.9 47.0 1.0 OE1 A:GLN166 4.0 43.4 1.0 H2'' E:DT2 4.1 43.0 1.0 HA A:ASN171 4.1 44.8 1.0 O A:ASN171 4.1 40.6 1.0 OE2 A:GLU179 4.1 44.8 1.0 C4' E:DT2 4.2 39.8 1.0 CA A:GLY139 4.2 40.2 1.0 H5'' E:DT2 4.2 44.9 1.0 OP2 E:DG3 4.3 49.1 1.0 CD1 A:TRP175 4.3 35.6 1.0 C A:GLY139 4.4 38.5 1.0 HA3 A:GLY139 4.4 48.3 1.0 CD A:GLU179 4.4 44.9 1.0 HE22 A:GLN166 4.4 52.2 1.0 CB A:ASN171 4.5 37.0 1.0 C2' E:DT2 4.5 35.8 1.0 H3' E:DT2 4.5 44.5 1.0 CA A:ALA140 4.5 34.8 1.0 HD22 A:ASN171 4.6 50.3 1.0 C A:ALA140 4.6 37.4 1.0 CB A:ALA140 4.6 34.0 1.0 CA A:ASN171 4.6 37.4 1.0 HE1 A:TRP175 4.7 42.8 1.0 C A:ASN171 4.7 42.0 1.0 CD A:GLN166 4.7 42.9 1.0 C5' E:DT2 4.8 37.4 1.0 NE2 A:GLN166 4.9 43.5 1.0 HB3 A:PRO143 4.9 49.3 1.0 NE1 A:TRP175 4.9 35.6 1.0 HB2 A:ALA140 5.0 40.8 1.0

Manganese binding site 2 out of 2 in the A Novel Domain in Human Exog Converts Apoptotic Endonuclease to Dna- Repair Enzyme


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of A Novel Domain in Human Exog Converts Apoptotic Endonuclease to Dna- Repair Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:54.6 occ:1.00 OD1 B:ASN171 2.2 45.0 1.0 O B:HOH501 2.3 33.2 1.0 O B:HOH507 2.3 28.7 1.0 O B:HOH502 2.3 40.2 1.0 OP1 C:DG3 2.4 35.7 1.0 O3' C:DT2 2.5 39.9 1.0 P C:DG3 3.0 34.7 1.0 CG B:ASN171 3.3 41.9 1.0 H B:ALA140 3.3 38.6 1.0 HD1 B:TRP175 3.4 44.8 1.0 HD21 B:ASN171 3.4 51.0 1.0 HA2 B:GLY139 3.5 39.9 1.0 H4' C:DT2 3.6 45.3 1.0 ND2 B:ASN171 3.7 42.5 1.0 C3' C:DT2 3.8 37.2 1.0 O B:ALA140 3.8 32.3 1.0 N B:ALA140 3.8 32.1 1.0 O5' C:DG3 3.8 39.1 1.0 OE1 B:GLU179 3.9 46.8 1.0 HB3 B:ALA140 3.9 40.2 1.0 H5'' C:DT2 4.0 44.1 1.0 OE2 B:GLU179 4.1 44.6 1.0 OE1 B:GLN166 4.1 37.4 1.0 C4' C:DT2 4.1 37.8 1.0 H2'' C:DT2 4.1 43.8 1.0 O B:ASN171 4.2 39.5 1.0 CD1 B:TRP175 4.2 37.3 1.0 CA B:GLY139 4.2 33.2 1.0 HA B:ASN171 4.3 49.4 1.0 OP2 C:DG3 4.3 39.7 1.0 C B:GLY139 4.3 32.7 1.0 HA3 B:GLY139 4.4 39.9 1.0 CD B:GLU179 4.4 44.6 1.0 H3' C:DT2 4.4 44.7 1.0 HE1 B:TRP175 4.5 46.8 1.0 HE22 B:GLN166 4.5 47.0 1.0 C2' C:DT2 4.5 36.5 1.0 CB B:ASN171 4.6 42.7 1.0 CA B:ALA140 4.6 32.4 1.0 HD22 B:ASN171 4.6 51.0 1.0 C5' C:DT2 4.6 36.7 1.0 C B:ALA140 4.6 33.8 1.0 CB B:ALA140 4.7 33.5 1.0 NE1 B:TRP175 4.7 39.0 1.0 CA B:ASN171 4.8 41.1 1.0 C B:ASN171 4.8 40.5 1.0 CD B:GLN166 4.8 39.1 1.0 HB3 B:PRO143 4.8 42.0 1.0 NE2 B:GLN166 5.0 39.1 1.0

M.R.Szymanski, W.Yu, A.M.Gmyrek, M.A.White, I.J.Molineux, J.C.Lee, Y.W.Yin. A Domain in Human Exog Converts Apoptotic Endonuclease to Dna-Repair Exonuclease. Nat Commun V. 8 14959 2017.
ISSN: ESSN 2041-1723
PubMed: 28466855
DOI: 10.1038/NCOMMS14959