Sodium in PDB 5dkt: N-Terminal His Tagged Appol Exonuclease Mutant

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

The structure of N-Terminal His Tagged Appol Exonuclease Mutant, PDB code: 5dkt 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)	47.35 / 2.90
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.775, 141.775, 148.759, 90.00, 90.00, 120.00
R / Rfree (%)	26.5 / 30

The binding sites of Sodium atom in the N-Terminal His Tagged Appol Exonuclease Mutant (pdb code 5dkt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the N-Terminal His Tagged Appol Exonuclease Mutant, PDB code: 5dkt:

Sodium binding site 1 out of 1 in the N-Terminal His Tagged Appol Exonuclease Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of N-Terminal His Tagged Appol Exonuclease Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na710 b:28.6 occ:1.00 O A:HOH819 2.5 24.9 1.0 OD1 A:ASN82 2.5 30.6 1.0 O A:HOH822 2.5 33.1 1.0 O A:HOH816 2.5 23.6 1.0 O A:HOH844 2.5 34.7 1.0 HD21 A:ASN82 2.9 34.4 1.0 OE1 A:GLN84 3.2 44.8 1.0 CG A:ASN82 3.3 28.4 1.0 ND2 A:ASN82 3.4 28.7 1.0 O1 A:SO4702 3.9 60.1 0.7 O A:ILE83 4.1 37.0 1.0 HD22 A:ASN82 4.2 34.4 1.0 CD A:GLN84 4.4 45.2 1.0 HB3 A:ASP215 4.6 63.8 1.0 CB A:ASN82 4.7 27.8 1.0 HG3 A:GLN84 4.8 61.1 1.0 H A:ILE83 4.9 35.4 1.0 HB3 A:GLN138 4.9 44.7 1.0 HB2 A:ASP215 4.9 63.8 1.0 O1 A:SO4703 5.0 47.2 0.7

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