Magnesium in PDB 5t40: 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: 5t40 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)	34.70 / 1.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.368, 83.732, 74.999, 90.00, 113.54, 90.00
R / Rfree (%)	16.2 / 18.7

The binding sites of Magnesium atom in the A Novel Domain in Human Exog Converts Apoptotic Endonuclease to Dna- Repair Enzyme (pdb code 5t40). 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: 5t40:
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:Mg403 b:22.1 occ:0.96 OD1 A:ASN171 2.0 29.5 1.0 O A:HOH543 2.1 23.8 1.0 O A:HOH563 2.1 22.9 1.0 O A:HOH528 2.1 22.0 1.0 O A:HOH583 2.1 21.7 1.0 O A:HOH639 2.1 27.6 1.0 CG A:ASN171 3.1 27.9 1.0 HD21 A:ASN171 3.3 37.6 1.0 H A:HIS140 3.5 23.9 1.0 ND2 A:ASN171 3.6 31.3 1.0 HD1 A:TRP175 3.6 29.7 1.0 HB2 A:HIS140 3.6 25.8 1.0 OE2 A:GLU179 3.9 27.3 1.0 HA2 A:GLY139 3.9 29.9 1.0 O A:ASN171 4.0 26.7 1.0 HA A:ASN171 4.1 26.3 1.0 OE1 A:GLU179 4.1 27.8 1.0 N A:HIS140 4.2 19.9 1.0 OE1 A:GLN166 4.3 24.8 1.0 O A:HOH548 4.3 28.5 1.0 ND1 A:HIS140 4.3 26.5 1.0 O A:HOH629 4.3 48.8 1.0 CB A:ASN171 4.4 22.5 1.0 CD A:GLU179 4.4 29.2 1.0 HD22 A:ASN171 4.4 37.6 1.0 CD1 A:TRP175 4.5 24.7 1.0 CB A:HIS140 4.5 21.5 1.0 O A:HIS140 4.5 22.7 1.0 C A:ASN171 4.6 24.9 1.0 CA A:ASN171 4.6 21.9 1.0 O A:HOH590 4.6 45.2 1.0 CA A:GLY139 4.7 24.9 1.0 HE1 A:TRP175 4.8 30.8 1.0 HE22 A:GLN166 4.8 27.3 1.0 CA A:HIS140 4.8 20.4 1.0 CG A:HIS140 4.9 24.9 1.0 HB2 A:ASN171 4.9 27.0 1.0 HA3 A:GLY139 4.9 29.9 1.0 HB3 A:ASN171 4.9 27.0 1.0 C A:GLY139 4.9 21.9 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:Mg403 b:24.8 occ:1.00 OD1 B:ASN171 2.0 24.3 1.0 O B:HOH510 2.0 22.9 1.0 O B:HOH570 2.1 25.2 1.0 O B:HOH588 2.1 21.7 1.0 O B:HOH532 2.1 23.1 1.0 O B:HOH646 2.2 25.6 1.0 CG B:ASN171 3.1 25.1 1.0 HD21 B:ASN171 3.3 37.3 1.0 H B:HIS140 3.4 25.7 1.0 HD1 B:TRP175 3.5 28.7 1.0 ND2 B:ASN171 3.6 31.1 1.0 HD1 B:HIS140 3.6 31.0 1.0 HB2 B:HIS140 3.6 26.5 1.0 OE2 B:GLU179 3.8 24.6 1.0 HA2 B:GLY139 3.9 26.6 1.0 O B:ASN171 4.0 26.1 1.0 N B:HIS140 4.1 21.4 1.0 HA B:ASN171 4.1 25.7 1.0 OE1 B:GLU179 4.1 26.2 1.0 O B:HOH682 4.2 45.9 1.0 OE1 B:GLN166 4.2 22.2 1.0 O B:HOH537 4.3 29.1 1.0 ND1 B:HIS140 4.3 25.9 1.0 CB B:ASN171 4.4 21.0 1.0 CD1 B:TRP175 4.4 23.9 1.0 CD B:GLU179 4.4 26.4 1.0 HD22 B:ASN171 4.4 37.3 1.0 CB B:HIS140 4.5 22.1 1.0 O B:HIS140 4.5 24.3 1.0 CA B:ASN171 4.6 21.4 1.0 C B:ASN171 4.6 25.0 1.0 HE1 B:TRP175 4.7 28.1 1.0 CA B:GLY139 4.7 22.2 1.0 CA B:HIS140 4.8 22.0 1.0 HE22 B:GLN166 4.9 26.6 1.0 CG B:HIS140 4.9 24.4 1.0 C B:GLY139 4.9 20.8 1.0 HB3 B:ASN171 4.9 25.2 1.0 HB2 B:ASN171 4.9 25.2 1.0 HA3 B:GLY139 5.0 26.6 1.0 NE1 B:TRP175 5.0 23.4 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