Sodium in PDB 3nv9: Crystal Structure of Entamoeba Histolytica Malic Enzyme

All present enzymatic activity of Crystal Structure of Entamoeba Histolytica Malic Enzyme:
1.1.1.40;

The structure of Crystal Structure of Entamoeba Histolytica Malic Enzyme, PDB code: 3nv9 was solved by D.Dutta, A.Chakrabarty, S.K.Ghosh, A.K.Das, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.16 / 2.25
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	117.731, 117.731, 157.615, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 24.5

The binding sites of Sodium atom in the Crystal Structure of Entamoeba Histolytica Malic Enzyme (pdb code 3nv9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Entamoeba Histolytica Malic Enzyme, PDB code: 3nv9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Entamoeba Histolytica Malic Enzyme


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 Entamoeba Histolytica Malic Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na495 b:29.0 occ:1.00 OG1 A:THR348 2.7 19.9 1.0 O A:ARG350 2.7 24.3 1.0 O A:PRO354 2.7 25.0 1.0 O A:ASN355 3.2 24.9 1.0 O A:PHE353 3.2 23.5 1.0 O A:THR348 3.3 23.7 1.0 N A:THR348 3.3 23.4 1.0 CA A:GLN356 3.4 24.6 1.0 C A:ASN355 3.4 25.4 1.0 C A:THR348 3.5 23.0 1.0 N A:GLN356 3.6 25.6 1.0 C A:PRO354 3.6 25.2 1.0 CB A:THR348 3.6 23.4 1.0 CA A:THR348 3.6 23.1 1.0 C A:PHE353 3.7 23.1 1.0 CB A:PHE353 3.7 22.4 1.0 C A:ARG350 3.8 23.6 1.0 N A:ARG350 3.9 22.7 1.0 CB A:GLN356 4.0 23.8 1.0 CG2 A:THR348 4.1 24.5 1.0 N A:ASN355 4.2 25.5 1.0 CA A:PHE353 4.2 22.7 1.0 CA A:ARG350 4.3 23.2 1.0 CA A:ASN355 4.4 25.3 1.0 N A:PRO354 4.4 24.2 1.0 N A:GLY349 4.4 23.4 1.0 C A:ALA347 4.5 23.8 1.0 O A:HOH592 4.5 21.0 1.0 N A:PHE353 4.5 21.9 1.0 CA A:PRO354 4.5 25.0 1.0 C A:GLN356 4.7 24.7 1.0 CG A:GLN356 4.7 21.8 1.0 C A:GLY349 4.7 22.8 1.0 CB A:ARG350 4.7 22.4 1.0 N A:VAL357 4.7 23.7 1.0 CA A:ALA347 4.8 23.2 1.0 CG A:PHE353 4.9 23.7 1.0 N A:GLY351 5.0 23.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Entamoeba Histolytica Malic Enzyme


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 Entamoeba Histolytica Malic Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Na496 b:35.0 occ:1.00 OG1 B:THR348 2.5 22.8 1.0 O B:PRO354 2.8 20.8 1.0 O B:ARG350 2.9 20.4 1.0 N B:THR348 3.3 21.1 1.0 O B:PHE353 3.3 22.4 1.0 O B:ASN355 3.3 22.0 1.0 CB B:THR348 3.5 22.1 1.0 O B:THR348 3.5 23.5 1.0 CB B:PHE353 3.6 23.2 1.0 C B:ASN355 3.6 21.8 1.0 C B:THR348 3.6 22.5 1.0 CA B:GLN356 3.6 22.1 1.0 CA B:THR348 3.6 21.6 1.0 C B:PHE353 3.7 23.1 1.0 N B:GLN356 3.8 21.4 1.0 C B:PRO354 3.8 22.2 1.0 CG2 B:THR348 4.0 21.4 1.0 C B:ARG350 4.0 21.1 1.0 N B:ARG350 4.1 20.8 1.0 CB B:GLN356 4.1 21.3 1.0 CA B:PHE353 4.1 23.8 1.0 N B:PHE353 4.3 23.4 1.0 O B:HOH576 4.3 24.3 1.0 N B:PRO354 4.4 22.6 1.0 N B:GLY349 4.4 20.9 1.0 C B:ALA347 4.4 21.1 1.0 N B:ASN355 4.5 21.1 1.0 CA B:ARG350 4.5 21.2 1.0 CA B:ASN355 4.6 22.1 1.0 CG B:PHE353 4.7 25.3 1.0 CG B:GLN356 4.7 23.0 1.0 CA B:PRO354 4.7 21.8 1.0 CD2 B:PHE353 4.7 25.1 1.0 C B:GLY349 4.8 22.4 1.0 CA B:ALA347 4.8 21.7 1.0 C B:GLN356 4.9 22.1 1.0 CB B:ARG350 4.9 21.0 1.0 N B:VAL357 5.0 23.8 1.0

A.Chakrabarty, D.Dutta, A.K.Das, S.K.Ghosh. Structural and Functional Characterization of Entamoeba Histolytica Malic Enzyme To Be Published.