Magnesium in PDB 5t5c: 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: 5t5c 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)	39.23 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.499, 80.267, 139.177, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.6

The binding sites of Magnesium atom in the A Novel Domain in Human Exog Converts Apoptotic Endonuclease to Dna- Repair Enzyme (pdb code 5t5c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the A Novel Domain in Human Exog Converts Apoptotic Endonuclease to Dna- Repair Enzyme, PDB code: 5t5c:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg401 b:33.3 occ:0.97 OD1 A:ASN171 2.0 34.6 1.0 O A:HOH509 2.0 27.8 1.0 O A:HOH534 2.1 34.3 1.0 O A:HOH536 2.3 35.8 1.0 OP1 C:DG3 2.4 34.2 1.0 O3' C:DT2 2.4 35.8 1.0 P C:DG3 3.0 36.9 1.0 CG A:ASN171 3.1 33.5 1.0 H A:ALA140 3.2 33.7 1.0 HD21 A:ASN171 3.4 39.3 1.0 HA2 A:GLY139 3.5 34.9 1.0 HD1 A:TRP175 3.5 38.0 1.0 H4' C:DT2 3.6 43.7 1.0 ND2 A:ASN171 3.7 32.8 1.0 C3' C:DT2 3.7 36.6 1.0 O5' C:DG3 3.8 37.4 1.0 N A:ALA140 3.9 28.1 1.0 OE1 A:GLU179 3.9 34.5 1.0 O A:ALA140 4.0 32.3 1.0 H5'' C:DT2 4.0 41.2 1.0 H2'' C:DT2 4.0 42.7 1.0 C4' C:DT2 4.0 36.4 1.0 O A:ASN171 4.1 37.3 1.0 HA A:ASN171 4.1 40.1 1.0 HB3 A:ALA140 4.2 36.3 1.0 O C:HOH202 4.2 38.4 1.0 OP2 C:DG3 4.2 33.7 1.0 OE2 A:GLU179 4.2 36.7 1.0 OE1 A:GLN166 4.3 32.4 1.0 CA A:GLY139 4.3 29.1 1.0 H3' C:DT2 4.4 43.9 1.0 CB A:ASN171 4.4 33.7 1.0 CD1 A:TRP175 4.4 31.6 1.0 HA3 A:GLY139 4.4 34.9 1.0 C2' C:DT2 4.4 35.6 1.0 CD A:GLU179 4.5 34.2 1.0 C A:GLY139 4.5 28.5 1.0 HD22 A:ASN171 4.5 39.3 1.0 HE22 A:GLN166 4.5 39.6 1.0 CA A:ASN171 4.6 33.4 1.0 C5' C:DT2 4.6 34.3 1.0 C A:ASN171 4.7 37.0 1.0 CA A:ALA140 4.7 29.3 1.0 C A:ALA140 4.8 31.3 1.0 CD A:GLN166 4.9 33.2 1.0 CB A:ALA140 4.9 30.2 1.0 NE2 A:GLN166 4.9 33.0 1.0 H2' C:DT2 5.0 42.7 1.0 HB3 A:ASN171 5.0 40.4 1.0 HB3 A:TRP175 5.0 38.3 1.0 HE1 A:TRP175 5.0 37.9 1.0 HB2 A:ASN171 5.0 40.4 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg401 b:30.7 occ:1.00 OD1 B:ASN171 2.0 28.9 1.0 O B:HOH536 2.1 24.8 1.0 O B:HOH541 2.1 26.8 1.0 OP1 E:DG3 2.2 27.7 1.0 O B:HOH531 2.2 27.2 1.0 O3' E:DT2 2.5 31.2 1.0 P E:DG3 3.0 30.5 1.0 CG B:ASN171 3.2 29.5 1.0 H B:ALA140 3.3 29.4 1.0 HD1 B:TRP175 3.4 30.6 1.0 HD21 B:ASN171 3.5 36.9 1.0 HA2 B:GLY139 3.6 31.6 1.0 H4' E:DT2 3.6 36.9 1.0 ND2 B:ASN171 3.7 30.7 1.0 C3' E:DT2 3.7 30.7 1.0 O5' E:DG3 3.8 32.2 1.0 OE2 B:GLU179 3.9 29.9 1.0 N B:ALA140 3.9 24.5 1.0 HA B:ASN171 4.0 32.8 1.0 O B:ALA140 4.0 28.4 1.0 H2'' E:DT2 4.0 37.5 1.0 O B:ASN171 4.0 31.3 1.0 H5'' E:DT2 4.0 37.2 1.0 C4' E:DT2 4.1 30.7 1.0 O E:HOH205 4.1 35.1 1.0 OE1 B:GLN166 4.1 28.2 1.0 HB3 B:ALA140 4.1 35.5 1.0 OE1 B:GLU179 4.1 29.8 1.0 CD1 B:TRP175 4.2 25.5 1.0 OP2 E:DG3 4.2 30.0 1.0 CA B:GLY139 4.3 26.3 1.0 CB B:ASN171 4.4 27.9 1.0 H3' E:DT2 4.4 36.9 1.0 C2' E:DT2 4.4 31.2 1.0 CD B:GLU179 4.5 30.4 1.0 HA3 B:GLY139 4.5 31.6 1.0 CA B:ASN171 4.5 27.3 1.0 HE22 B:GLN166 4.5 32.1 1.0 C B:GLY139 4.6 25.9 1.0 C B:ASN171 4.6 30.5 1.0 HD22 B:ASN171 4.6 36.9 1.0 C5' E:DT2 4.6 31.0 1.0 HE1 B:TRP175 4.7 33.1 1.0 CA B:ALA140 4.8 26.0 1.0 CD B:GLN166 4.8 28.7 1.0 C B:ALA140 4.8 27.0 1.0 CB B:ALA140 4.9 29.6 1.0 NE1 B:TRP175 4.9 27.6 1.0 HB3 B:TRP175 4.9 32.2 1.0 HB2 B:ASN171 4.9 33.5 1.0 NE2 B:GLN166 4.9 26.7 1.0 H2' E:DT2 5.0 37.5 1.0 HB3 B:ASN171 5.0 33.5 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