Sodium in PDB 5tsz: Crystal Structure of Plasmodium Vivax Celtos

The structure of Crystal Structure of Plasmodium Vivax Celtos, PDB code: 5tsz was solved by N.H.Tolia, J.R.Jimah, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.76 / 3.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	158.960, 158.960, 64.090, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 23.8

The binding sites of Sodium atom in the Crystal Structure of Plasmodium Vivax Celtos (pdb code 5tsz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Plasmodium Vivax Celtos, PDB code: 5tsz:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Plasmodium Vivax Celtos


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Plasmodium Vivax Celtos within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:72.5 occ:1.00 O A:ILE168 2.4 82.5 1.0 OD1 A:ASN158 2.4 75.3 1.0 OE1 A:GLU161 2.4 96.8 1.0 OD1 A:ASP170 2.4 87.8 1.0 O A:HOH402 2.4 80.0 1.0 O A:HOH401 2.4 85.1 1.0 O A:HOH403 2.5 81.5 1.0 OE2 A:GLU161 2.5 87.0 1.0 CD A:GLU161 2.8 87.0 1.0 H A:ILE168 3.4 1.0 1.0 CG A:ASN158 3.4 79.8 1.0 HD21 A:ASN158 3.4 0.6 1.0 C A:ILE168 3.5 87.3 1.0 HB A:ILE168 3.6 97.2 1.0 CG A:ASP170 3.6 88.7 1.0 HA A:ASP170 3.7 94.4 1.0 ND2 A:ASN158 3.8 85.5 1.0 N A:ASP170 3.9 83.3 1.0 C A:PRO169 4.0 85.8 1.0 H A:ASP170 4.1 100.0 1.0 N A:ILE168 4.1 87.5 1.0 O A:PRO169 4.2 88.7 1.0 CA A:ILE168 4.2 84.1 1.0 CA A:ASP170 4.2 78.7 1.0 CG A:GLU161 4.3 75.5 1.0 CB A:ILE168 4.3 81.0 1.0 HA A:ASN158 4.3 98.8 1.0 HE1 A:TRP173 4.3 0.3 1.0 OD2 A:ASP170 4.4 92.0 1.0 N A:PRO169 4.5 91.3 1.0 CB A:ASP170 4.5 81.1 1.0 HG22 A:ILE168 4.6 0.0 1.0 CA A:PRO169 4.6 84.0 1.0 HG3 A:GLU161 4.7 90.6 1.0 HA A:PRO169 4.7 0.8 1.0 HD22 A:ASN158 4.7 0.6 1.0 HG2 A:GLU161 4.7 90.6 1.0 CB A:ASN158 4.8 80.5 1.0 HB2 A:GLU161 4.8 96.1 1.0 OE2 A:GLU129 4.8 65.8 1.0 OE1 A:GLU129 4.8 75.6 1.0 HB3 A:GLU161 5.0 96.1 1.0 CB A:GLU161 5.0 80.1 1.0 CA A:ASN158 5.0 82.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Plasmodium Vivax Celtos


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Plasmodium Vivax Celtos within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:59.9 occ:1.00 OD1 B:ASP170 2.4 98.5 1.0 O B:ILE168 2.4 83.3 1.0 OD1 B:ASN158 2.4 82.5 1.0 O B:HOH402 2.4 79.6 1.0 OE2 B:GLU161 2.4 85.5 1.0 OE1 B:GLU161 2.4 76.9 1.0 O B:HOH403 2.5 73.7 1.0 O B:HOH401 2.5 82.4 1.0 CD B:GLU161 2.8 77.5 1.0 H B:ILE168 3.4 0.8 1.0 C B:ILE168 3.5 84.0 1.0 HA B:ASP170 3.5 97.6 1.0 CG B:ASP170 3.5 92.4 1.0 CG B:ASN158 3.5 80.0 1.0 HB B:ILE168 3.7 99.7 1.0 O B:PRO169 3.7 83.8 1.0 C B:PRO169 3.8 84.4 1.0 HD21 B:ASN158 3.8 98.2 1.0 N B:ASP170 3.9 86.9 1.0 CA B:ASP170 4.1 81.3 1.0 ND2 B:ASN158 4.1 81.8 1.0 HA B:ASN158 4.1 84.9 1.0 N B:ILE168 4.1 85.7 1.0 H B:ASP170 4.2 0.3 1.0 CA B:ILE168 4.2 78.0 1.0 HE1 B:TRP173 4.2 94.9 1.0 OD2 B:ASP170 4.3 91.0 1.0 CG B:GLU161 4.3 74.2 1.0 CB B:ILE168 4.4 83.1 1.0 CB B:ASP170 4.4 74.0 1.0 N B:PRO169 4.5 82.8 1.0 HG3 B:LYS154 4.6 0.8 1.0 HG22 B:ILE168 4.6 96.7 1.0 CA B:PRO169 4.6 84.7 1.0 HG3 B:GLU161 4.6 89.0 1.0 OE1 B:GLU129 4.7 73.7 1.0 HA B:PRO169 4.7 0.6 1.0 HG2 B:GLU161 4.7 89.0 1.0 HB2 B:GLU161 4.8 87.8 1.0 CB B:ASN158 4.8 70.7 1.0 CA B:ASN158 4.9 70.7 1.0 OE2 B:GLU129 5.0 63.5 1.0 HD22 B:ASN158 5.0 98.2 1.0 HB3 B:GLU161 5.0 87.8 1.0 CB B:GLU161 5.0 73.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Plasmodium Vivax Celtos


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Plasmodium Vivax Celtos within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:59.6 occ:1.00 O C:ILE168 2.3 82.1 1.0 OD1 C:ASN158 2.4 68.3 1.0 OD1 C:ASP170 2.4 84.6 1.0 O C:HOH401 2.4 70.8 1.0 O C:HOH402 2.4 77.2 1.0 OE2 C:GLU161 2.4 79.7 1.0 OE1 C:GLU161 2.4 83.8 1.0 O C:HOH403 2.5 84.4 1.0 CD C:GLU161 2.7 76.7 1.0 H C:ILE168 3.4 93.7 1.0 C C:ILE168 3.4 87.5 1.0 CG C:ASN158 3.5 74.4 1.0 HB C:ILE168 3.5 96.2 1.0 CG C:ASP170 3.6 82.5 1.0 HD21 C:ASN158 3.8 93.5 1.0 HA C:ASP170 3.8 91.7 1.0 O C:PRO169 3.9 86.9 1.0 C C:PRO169 3.9 87.4 1.0 N C:ASP170 4.0 85.9 1.0 N C:ILE168 4.1 78.1 1.0 ND2 C:ASN158 4.1 77.9 1.0 CA C:ILE168 4.1 82.0 1.0 HA C:ASN158 4.1 78.3 1.0 HE1 C:TRP173 4.2 91.6 1.0 CB C:ILE168 4.2 80.2 1.0 CG C:GLU161 4.2 72.7 1.0 CA C:ASP170 4.3 76.4 1.0 H C:ASP170 4.3 0.1 1.0 OD2 C:ASP170 4.4 90.5 1.0 N C:PRO169 4.4 85.8 1.0 HG22 C:ILE168 4.5 0.3 1.0 HG3 C:GLU161 4.6 87.2 1.0 CB C:ASP170 4.6 79.0 1.0 CA C:PRO169 4.6 83.3 1.0 HA C:PRO169 4.7 100.0 1.0 OE1 C:GLU129 4.7 60.4 1.0 HG2 C:GLU161 4.7 87.2 1.0 CB C:ASN158 4.8 67.4 1.0 HB2 C:GLU161 4.8 94.4 1.0 CA C:ASN158 4.8 65.3 1.0 CG2 C:ILE168 4.9 88.6 1.0 HD22 C:ASN158 4.9 93.5 1.0 OE2 C:GLU129 4.9 59.1 1.0 HB3 C:GLU161 5.0 94.4 1.0 CB C:GLU161 5.0 78.6 1.0

J.R.Jimah, N.D.Salinas, M.Sala-Rabanal, N.G.Jones, L.D.Sibley, C.G.Nichols, P.H.Schlesinger, N.H.Tolia. Malaria Parasite Celtos Targets the Inner Leaflet of Cell Membranes For Pore-Dependent Disruption. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27906127
DOI: 10.7554/ELIFE.20621