Magnesium in PDB 5dku: C-Terminal His Tagged Appol Exonuclease Mutant

All present enzymatic activity of C-Terminal His Tagged Appol Exonuclease Mutant:
2.7.7.7;

The structure of C-Terminal His Tagged Appol Exonuclease Mutant, PDB code: 5dku was solved by M.E.Milton, R.B.Honzatko, J.Y.Choe, S.W.Nelson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.92 / 2.90
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	146.382, 146.382, 165.671, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 23.2

The binding sites of Magnesium atom in the C-Terminal His Tagged Appol Exonuclease Mutant (pdb code 5dku). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the C-Terminal His Tagged Appol Exonuclease Mutant, PDB code: 5dku:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the C-Terminal His Tagged Appol Exonuclease Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of C-Terminal His Tagged Appol Exonuclease Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:63.8 occ:1.00 O A:HOH804 2.1 42.6 1.0 O A:HOH834 2.1 48.2 1.0 O A:HOH847 2.1 65.2 1.0 OD1 A:ASN82 2.1 42.2 1.0 O A:HOH837 2.1 59.7 1.0 O A:HOH817 2.1 47.8 1.0 HD21 A:ASN82 3.0 60.1 1.0 CG A:ASN82 3.0 45.5 1.0 ND2 A:ASN82 3.3 50.1 1.0 H A:ILE83 3.8 47.2 1.0 O A:ILE83 3.9 44.9 1.0 O A:HOH810 4.1 27.1 1.0 HE22 A:GLN84 4.1 84.2 1.0 HD22 A:ASN82 4.1 60.1 1.0 CB A:ASN82 4.3 27.9 1.0 HB3 A:GLN138 4.3 47.8 1.0 HA A:ASN82 4.4 43.0 1.0 OD2 A:ASP143 4.4 53.3 1.0 NE2 A:GLN84 4.5 70.1 1.0 HB2 A:ASN82 4.5 33.4 1.0 N A:ILE83 4.6 39.3 1.0 O A:HOH842 4.6 35.1 1.0 O A:GLN138 4.7 38.2 1.0 HE21 A:GLN84 4.7 84.2 1.0 HB3 A:ASP215 4.7 56.1 1.0 CA A:ASN82 4.8 35.8 1.0 HD22 A:LEU178 4.9 65.0 1.0 C A:ILE83 4.9 34.8 1.0 O A:HOH851 5.0 22.7 1.0

Magnesium binding site 2 out of 2 in the C-Terminal His Tagged Appol Exonuclease Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of C-Terminal His Tagged Appol Exonuclease Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:62.5 occ:1.00 OD1 B:ASN82 2.1 52.6 1.0 O B:HOH834 2.1 40.4 1.0 O B:HOH839 2.1 49.7 1.0 O B:HOH807 2.1 53.4 1.0 O B:HOH823 2.1 43.7 1.0 O B:HOH808 2.1 51.9 1.0 CG B:ASN82 3.2 42.1 1.0 HD21 B:ASN82 3.5 56.4 1.0 H B:ILE83 3.7 37.8 1.0 O B:ILE83 3.8 33.2 1.0 ND2 B:ASN82 3.8 47.0 1.0 OD2 B:ASP143 3.9 46.9 1.0 O B:HOH816 3.9 33.8 1.0 HA B:ASN82 4.1 59.5 1.0 HB3 B:GLN138 4.3 35.4 1.0 CB B:ASN82 4.4 44.1 1.0 O B:GLN138 4.4 56.6 1.0 N B:ILE83 4.4 31.5 1.0 O B:HOH813 4.5 50.2 1.0 OD1 B:ASP143 4.5 57.2 1.0 CG B:ASP143 4.6 46.7 1.0 HB2 B:ASN82 4.6 52.9 1.0 HD22 B:ASN82 4.6 56.4 1.0 OE1 B:GLN84 4.7 61.1 1.0 CA B:ASN82 4.7 49.6 1.0 C B:ILE83 4.8 30.2 1.0 O B:HOH842 5.0 47.3 1.0

M.E.Milton, J.Y.Choe, R.B.Honzatko, S.W.Nelson. Crystal Structure of the Apicoplast Dna Polymerase From Plasmodium Falciparum: the First Look at A Plastidic A-Family Dna Polymerase. J.Mol.Biol. V. 428 3920 2016.
ISSN: ESSN 1089-8638
PubMed: 27487482
DOI: 10.1016/J.JMB.2016.07.016