Manganese in PDB 5t3v: 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: 5t3v 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)	49.71 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.340, 83.436, 74.771, 90.00, 113.42, 90.00
R / Rfree (%)	17.6 / 22.4

The binding sites of Manganese atom in the A Novel Domain in Human Exog Converts Apoptotic Endonuclease to Dna- Repair Enzyme (pdb code 5t3v). 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: 5t3v:
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:69.0 occ:1.00 O A:HOH522 1.9 69.7 1.0 OD1 A:ASN171 2.1 60.3 1.0 O A:HOH505 2.1 40.2 1.0 O A:HOH507 2.2 51.0 1.0 O A:HOH506 2.3 72.2 1.0 O A:HOH510 2.5 49.6 1.0 HD21 A:ASN171 2.9 71.1 1.0 CG A:ASN171 3.0 57.7 1.0 ND2 A:ASN171 3.3 59.3 1.0 H A:HIS140 3.4 57.9 1.0 HB2 A:HIS140 3.7 56.4 1.0 HA2 A:GLY139 3.8 66.0 1.0 HD1 A:TRP175 3.9 64.3 1.0 O A:HOH521 4.0 32.3 1.0 N A:HIS140 4.1 48.2 1.0 OE1 A:GLU179 4.1 60.8 1.0 ND1 A:HIS140 4.2 52.2 1.0 HD22 A:ASN171 4.2 71.1 1.0 O A:ASN171 4.2 45.9 1.0 OE2 A:GLU179 4.3 63.4 1.0 CB A:ASN171 4.4 55.9 1.0 CB A:HIS140 4.5 47.0 1.0 OE1 A:GLN166 4.5 43.2 1.0 HA A:ASN171 4.5 64.1 1.0 CD A:GLU179 4.6 61.0 1.0 CD1 A:TRP175 4.7 53.6 1.0 CA A:GLY139 4.7 55.0 1.0 O A:HIS140 4.7 48.9 1.0 C A:ASN171 4.8 48.8 1.0 HE1 A:TRP175 4.8 62.4 1.0 CG A:HIS140 4.8 51.6 1.0 HB2 A:ASN171 4.8 67.0 1.0 CA A:HIS140 4.8 45.5 1.0 CA A:ASN171 4.8 53.4 1.0 C A:GLY139 4.9 51.7 1.0 HA3 A:GLY139 4.9 66.0 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:61.2 occ:1.00 OD1 B:ASN171 2.0 78.8 1.0 O B:HOH518 2.3 43.0 1.0 O B:HOH511 2.3 56.7 1.0 O B:HOH508 2.3 65.7 1.0 O B:HOH536 2.4 49.9 1.0 O B:HOH512 2.4 64.9 1.0 CG B:ASN171 3.0 70.7 1.0 HD21 B:ASN171 3.1 89.3 1.0 H B:HIS140 3.4 55.4 1.0 ND2 B:ASN171 3.4 74.5 1.0 HD1 B:TRP175 3.6 58.5 1.0 HA2 B:GLY139 3.8 57.9 1.0 HB2 B:HIS140 3.8 55.8 1.0 OE2 B:GLU179 3.9 57.0 1.0 N B:HIS140 4.1 46.1 1.0 O B:ASN171 4.2 47.8 1.0 ND1 B:HIS140 4.3 53.4 1.0 OE1 B:GLU179 4.3 64.7 1.0 HD22 B:ASN171 4.3 89.3 1.0 OE1 B:GLN166 4.3 43.5 1.0 HA B:ASN171 4.3 65.8 1.0 O B:HOH502 4.3 42.5 1.0 CB B:ASN171 4.4 63.2 1.0 CD1 B:TRP175 4.5 48.7 1.0 CD B:GLU179 4.5 59.0 1.0 CA B:GLY139 4.6 48.2 1.0 CB B:HIS140 4.6 46.5 1.0 O B:HIS140 4.6 37.9 1.0 C B:ASN171 4.7 49.3 1.0 HA3 B:GLY139 4.7 57.9 1.0 CA B:ASN171 4.7 54.8 1.0 HB2 B:ASN171 4.7 75.8 1.0 C B:GLY139 4.8 47.1 1.0 HE1 B:TRP175 4.8 58.5 1.0 HE22 B:GLN166 4.9 53.8 1.0 CA B:HIS140 4.9 43.1 1.0 CG B:HIS140 4.9 49.4 1.0 HB3 B:ASN171 5.0 75.8 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