Sodium in PDB 7sxq: 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: 7sxq 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)	19.97 / 2.50
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	143.999, 143.999, 165.006, 90, 90, 120
R / Rfree (%)	20.1 / 22.5

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

Chlorine

(Cl)

6 atoms

The binding sites of Sodium atom in the Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag (pdb code 7sxq). 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: 7sxq:
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:Na706 b:58.6 occ:1.00 O A:GLN138 2.5 54.2 1.0 OD1 A:ASN82 2.5 52.5 1.0 OD2 A:ASP143 2.5 55.3 1.0 O A:HOH941 2.5 58.1 1.0 O A:HOH897 2.5 50.4 1.0 O A:HOH991 2.5 51.0 1.0 CG A:ASP143 3.3 57.2 1.0 HB3 A:GLN138 3.4 62.8 1.0 OD1 A:ASP143 3.4 59.4 1.0 H A:GLN138 3.4 62.3 1.0 CG A:ASN82 3.4 54.2 1.0 C A:GLN138 3.6 53.0 1.0 O A:HOH913 3.6 52.7 1.0 HG23 A:ILE137 3.6 63.4 1.0 HA A:ASN82 3.7 65.5 1.0 HB2 A:ASN139 3.8 65.1 1.0 O A:HOH830 3.9 56.7 1.0 H A:ILE83 4.0 67.8 1.0 HG22 A:ILE137 4.1 63.4 1.0 O A:HOH824 4.1 57.9 1.0 N A:GLN138 4.1 51.9 1.0 HD21 A:ASN82 4.1 67.4 1.0 CB A:GLN138 4.1 52.3 1.0 HG3 A:GLN138 4.2 61.1 1.0 CA A:GLN138 4.2 50.6 1.0 ND2 A:ASN82 4.2 56.1 1.0 CG2 A:ILE137 4.3 52.8 1.0 CB A:ASN82 4.4 53.6 1.0 HB2 A:ASN82 4.4 64.3 1.0 CA A:ASN82 4.5 54.6 1.0 CG A:GLN138 4.6 50.9 1.0 O A:ASN139 4.6 54.5 1.0 HG21 A:ILE137 4.7 63.4 1.0 CB A:ASN139 4.7 54.3 1.0 CB A:ASP143 4.7 54.6 1.0 N A:ASN139 4.7 52.8 1.0 N A:ILE83 4.8 56.5 1.0 HG12 A:ILE83 4.8 66.8 1.0 HG2 A:GLN138 4.8 61.1 1.0 O A:LEU81 4.9 54.0 1.0 HB2 A:ASP143 4.9 65.5 1.0 HD22 A:ASN82 4.9 67.4 1.0 HB2 A:GLN138 4.9 62.8 1.0 OD1 A:ASN139 4.9 57.2 1.0 HD2 A:PHE142 5.0 67.8 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:Na707 b:56.9 occ:1.00 OD2 B:ASP143 2.5 57.5 1.0 O B:HOH997 2.5 53.1 1.0 O B:HOH831 2.5 53.0 1.0 OD1 B:ASN82 2.5 57.9 1.0 O B:GLN138 2.5 55.1 1.0 H B:GLN138 3.3 63.1 1.0 CG B:ASP143 3.3 57.2 1.0 HB3 B:GLN138 3.3 61.9 1.0 OD1 B:ASP143 3.4 59.2 1.0 CG B:ASN82 3.5 58.1 1.0 HG23 B:ILE137 3.6 66.4 1.0 HA B:ASN82 3.6 69.9 1.0 C B:GLN138 3.6 53.5 1.0 O B:HOH829 3.7 52.6 1.0 HG22 B:ILE137 3.8 66.4 1.0 H B:ILE83 3.9 71.3 1.0 N B:GLN138 4.0 52.6 1.0 HB2 B:ASN139 4.0 62.7 1.0 CB B:GLN138 4.1 51.6 1.0 CA B:GLN138 4.1 51.2 1.0 O B:HOH966 4.1 59.0 1.0 CG2 B:ILE137 4.1 55.3 1.0 HD21 B:ASN82 4.2 70.4 1.0 HG3 B:GLN138 4.2 63.3 1.0 ND2 B:ASN82 4.2 58.6 1.0 CB B:ASN82 4.4 57.3 1.0 CA B:ASN82 4.4 58.2 1.0 O B:HOH823 4.5 59.6 1.0 HB2 B:ASN82 4.5 68.8 1.0 HG21 B:ILE137 4.6 66.4 1.0 CG B:GLN138 4.6 52.8 1.0 O B:LEU81 4.7 58.5 1.0 N B:ILE83 4.7 59.5 1.0 O B:ASN139 4.7 53.4 1.0 CB B:ASP143 4.7 52.5 1.0 HG12 B:ILE83 4.7 71.3 1.0 HG2 B:GLN138 4.8 63.3 1.0 N B:ASN139 4.8 53.5 1.0 HB2 B:ASP143 4.9 63.0 1.0 HB2 B:GLN138 4.9 61.9 1.0 HA B:ILE137 4.9 64.6 1.0 CB B:ASN139 4.9 52.2 1.0 O B:ILE83 5.0 61.9 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