Sodium in PDB 5yid: Crystal Structure of Kni-10395 Bound Plasmepsin II (Pmii) From Plasmodium Falciparum

All present enzymatic activity of Crystal Structure of Kni-10395 Bound Plasmepsin II (Pmii) From Plasmodium Falciparum:
3.4.23.39;

The structure of Crystal Structure of Kni-10395 Bound Plasmepsin II (Pmii) From Plasmodium Falciparum, PDB code: 5yid was solved by V.Mishra, I.Rathore, P.Bhaumik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.00 / 2.10
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	107.600, 107.600, 72.560, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.5

The binding sites of Sodium atom in the Crystal Structure of Kni-10395 Bound Plasmepsin II (Pmii) From Plasmodium Falciparum (pdb code 5yid). 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 Crystal Structure of Kni-10395 Bound Plasmepsin II (Pmii) From Plasmodium Falciparum, PDB code: 5yid:

Sodium binding site 1 out of 1 in the Crystal Structure of Kni-10395 Bound Plasmepsin II (Pmii) From Plasmodium Falciparum


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 Kni-10395 Bound Plasmepsin II (Pmii) From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:42.0 occ:0.60 OAI A:K95401 2.1 45.5 1.0 OD2 A:ASP216 2.2 53.0 1.0 OD1 A:ASP36 2.3 45.4 1.0 OD1 A:ASP216 2.3 55.0 1.0 OAG A:K95401 2.4 39.5 1.0 CG A:ASP216 2.6 51.8 1.0 CBK A:K95401 3.1 40.7 1.0 CBR A:K95401 3.1 43.5 1.0 CG A:ASP36 3.3 46.6 1.0 CBB A:K95401 3.6 44.8 1.0 N A:GLY218 3.6 52.2 1.0 OD2 A:ASP36 3.7 45.2 1.0 N A:GLY38 3.7 49.5 1.0 CA A:GLY38 3.8 48.5 1.0 CA A:GLY218 3.8 51.3 1.0 OG1 A:THR219 3.9 47.5 1.0 CBS A:K95401 3.9 43.3 1.0 CB A:ASP216 4.1 50.8 1.0 N A:THR219 4.1 48.6 1.0 C A:GLY218 4.1 48.9 1.0 NBV A:K95401 4.4 39.2 1.0 C A:GLY38 4.5 48.6 1.0 N A:SER217 4.6 53.0 1.0 CB A:ASP36 4.6 47.2 1.0 CA A:ASP216 4.8 51.9 1.0 C A:ASP216 4.8 52.2 1.0 C A:SER217 4.9 53.7 1.0 N A:THR37 4.9 50.7 1.0 NBD A:K95401 4.9 40.4 1.0 CB A:THR219 4.9 46.4 1.0 CA A:ASP36 4.9 48.7 1.0 O A:GLY218 4.9 47.6 1.0 O A:HOH526 4.9 53.9 1.0 C A:THR37 4.9 52.1 1.0 N A:SER39 4.9 48.2 1.0 OG1 A:THR37 5.0 50.9 1.0 C A:ASP36 5.0 49.5 1.0

V.Mishra, I.Rathore, A.Arekar, L.K.Sthanam, H.Xiao, Y.Kiso, S.Sen, S.Patankar, A.Gustchina, K.Hidaka, A.Wlodawer, R.Y.Yada, P.Bhaumik. Deciphering the Mechanism of Potent Peptidomimetic Inhibitors Targeting Plasmepsins - Biochemical and Structural Insights. Febs J. V. 285 3077 2018.
ISSN: ISSN 1742-464X
PubMed: 29943906
DOI: 10.1111/FEBS.14598