Sodium in PDB 7sxl: Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag

All present enzymatic activity of Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag:
2.7.7.7;

The structure of Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag, PDB code: 7sxl was solved by N.Nieto, P.Chheda, R.Kerns, S.Nelson, R.Honzatko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.91 / 2.70
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	145.369, 145.369, 164.944, 90, 90, 120
R / Rfree (%)	19.1 / 22.4

The structure of Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Sodium atom in the Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag (pdb code 7sxl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag, PDB code: 7sxl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:53.0 occ:1.00 O A:GLN138 2.5 49.5 1.0 OD1 A:ASN82 2.5 50.3 1.0 OD2 A:ASP143 2.5 58.9 1.0 O A:HOH974 2.5 48.7 1.0 O A:HOH841 2.5 49.0 1.0 HB3 A:GLN138 3.3 60.3 1.0 H A:GLN138 3.4 58.9 1.0 CG A:ASP143 3.4 57.6 1.0 CG A:ASN82 3.5 49.5 1.0 O A:HOH871 3.5 43.5 1.0 O A:HOH931 3.6 51.6 1.0 C A:GLN138 3.6 50.8 1.0 OD1 A:ASP143 3.6 58.6 1.0 HG23 A:ILE137 3.7 64.2 1.0 HA A:ASN82 3.8 66.7 1.0 HB2 A:ASN139 4.0 56.4 1.0 HG22 A:ILE137 4.0 64.2 1.0 N A:GLN138 4.0 49.0 1.0 CB A:GLN138 4.0 50.2 1.0 HD21 A:ASN82 4.1 60.9 1.0 H A:ILE83 4.1 63.3 1.0 CA A:GLN138 4.1 47.6 1.0 ND2 A:ASN82 4.2 50.8 1.0 O A:HOH922 4.3 48.2 1.0 CG2 A:ILE137 4.3 53.5 1.0 HG3 A:GLN138 4.3 57.1 1.0 CB A:ASN82 4.4 50.9 1.0 HB2 A:ASN82 4.4 61.1 1.0 O A:ASN139 4.6 49.5 1.0 CA A:ASN82 4.6 55.6 1.0 CG A:GLN138 4.7 47.6 1.0 HG21 A:ILE137 4.7 64.2 1.0 N A:ASN139 4.7 52.0 1.0 CB A:ASP143 4.8 54.3 1.0 HB2 A:GLN138 4.8 60.3 1.0 HG12 A:ILE83 4.8 64.1 1.0 HG2 A:GLN138 4.8 57.1 1.0 CB A:ASN139 4.9 47.0 1.0 HB2 A:ASP143 4.9 65.1 1.0 N A:ILE83 4.9 52.8 1.0 O A:LEU81 4.9 52.8 1.0 HD22 A:ASN82 4.9 60.9 1.0 OD1 A:ASN139 4.9 62.5 1.0 HA A:ILE137 5.0 60.0 1.0

Sodium binding site 2 out of 2 in the Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag within 5.0Å range: probe atom residue distance (Å) B Occ B:Na702 b:56.3 occ:1.00 O B:GLN138 2.5 55.7 1.0 O B:HOH952 2.5 52.3 1.0 O B:HOH825 2.5 47.7 1.0 OD1 B:ASN82 2.5 54.6 1.0 OD2 B:ASP143 2.5 62.9 1.0 OD1 B:ASP143 3.2 60.1 1.0 CG B:ASP143 3.2 58.0 1.0 HB3 B:GLN138 3.4 58.3 1.0 CG B:ASN82 3.5 53.1 1.0 H B:GLN138 3.5 60.9 1.0 HG23 B:ILE137 3.6 64.4 1.0 C B:GLN138 3.6 52.1 1.0 O B:HOH880 3.6 53.6 1.0 HA B:ASN82 3.7 67.0 1.0 O B:HOH818 3.8 56.7 1.0 HB2 B:ASN139 3.8 64.7 1.0 H B:ILE83 3.9 66.8 1.0 HG22 B:ILE137 4.0 64.4 1.0 N B:GLN138 4.1 50.8 1.0 CB B:GLN138 4.1 48.6 1.0 CA B:GLN138 4.2 50.0 1.0 CG2 B:ILE137 4.2 53.6 1.0 HD21 B:ASN82 4.2 65.0 1.0 O B:HOH886 4.3 57.1 1.0 ND2 B:ASN82 4.3 54.2 1.0 HG3 B:GLN138 4.3 61.3 1.0 CB B:ASN82 4.4 55.8 1.0 CA B:ASN82 4.4 55.8 1.0 HB2 B:ASN82 4.5 66.9 1.0 O B:ASN139 4.5 52.4 1.0 HG21 B:ILE137 4.6 64.4 1.0 CB B:ASP143 4.6 51.0 1.0 HG12 B:ILE83 4.7 67.1 1.0 CG B:GLN138 4.7 51.1 1.0 N B:ILE83 4.7 55.6 1.0 N B:ASN139 4.7 50.7 1.0 CB B:ASN139 4.8 53.9 1.0 O B:LEU81 4.8 54.0 1.0 HB2 B:ASP143 4.8 61.1 1.0 HG2 B:GLN138 4.9 61.3 1.0 HB2 B:GLN138 4.9 58.3 1.0

P.R.Chheda, N.Nieto, S.Kaur, J.M.Beck, J.R.Beck, R.Honzatko, R.J.Kerns, S.W.Nelson. Promising Antimalarials Targeting Apicoplast Dna Polymerase From Plasmodium Falciparum. Eur.J.Med.Chem. V. 243 14751 2022.
ISSN: ISSN 0223-5234
PubMed: 36191407
DOI: 10.1016/J.EJMECH.2022.114751