Sodium in PDB 5k4v: Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nad+ Refined to 2.2 Angstroms

All present enzymatic activity of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nad+ Refined to 2.2 Angstroms:
1.1.1.103;

The structure of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nad+ Refined to 2.2 Angstroms, PDB code: 5k4v was solved by E.A.Adjogatse, P.T.Erskine, J.B.Cooper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.23 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.399, 131.530, 55.020, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 22.5

The binding sites of Sodium atom in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nad+ Refined to 2.2 Angstroms (pdb code 5k4v). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nad+ Refined to 2.2 Angstroms, PDB code: 5k4v:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nad+ Refined to 2.2 Angstroms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nad+ Refined to 2.2 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1411 b:53.5 occ:1.00 O A:HOH1540 2.7 42.5 1.0 OD1 A:ASP1187 2.8 31.3 1.0 O A:HOH1523 2.9 26.5 1.0 O7N A:NAD1401 3.3 36.4 1.0 CE A:MET1081 3.5 51.9 1.0 C7N A:NAD1401 3.6 35.5 1.0 OE1 A:GLN1013 3.7 24.2 1.0 N7N A:NAD1401 3.8 35.8 1.0 OG1 A:THR1186 3.9 25.0 1.0 CG A:ASP1187 3.9 31.5 1.0 CB A:PRO1181 3.9 31.6 1.0 SD A:MET1081 4.0 53.4 1.0 CA A:GLY1184 4.1 27.4 1.0 N A:GLY1184 4.3 28.8 1.0 OD2 A:ASP1187 4.4 32.5 1.0 C3N A:NAD1401 4.6 34.5 1.0 O2N A:NAD1401 4.6 34.7 1.0 OXT A:ACT1407 4.7 46.2 1.0 CA A:PRO1181 4.7 31.7 1.0 N A:GLY1182 4.7 33.9 1.0 N A:ASP1187 4.8 25.7 1.0 C A:GLY1184 4.8 26.3 1.0 CD A:GLN1013 5.0 23.5 1.0

Sodium binding site 2 out of 2 in the Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nad+ Refined to 2.2 Angstroms


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Three-Dimensional Structure of L-Threonine 3-Dehydrogenase From Trypanosoma Brucei Bound to Nad+ Refined to 2.2 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1409 b:52.8 occ:1.00 OD1 C:ASP1187 2.5 33.2 1.0 O C:HOH1530 2.6 29.2 1.0 O C:HOH1525 3.0 25.3 1.0 O C:HOH1507 3.3 32.9 1.0 CE C:MET1081 3.6 52.1 1.0 OE1 C:GLN1013 3.6 31.9 1.0 CB C:PRO1181 3.6 35.7 1.0 CG C:ASP1187 3.6 31.2 1.0 O7N C:NAD1401 3.8 26.5 1.0 N7N C:NAD1401 3.8 24.4 1.0 OG1 C:THR1186 4.0 24.8 1.0 C7N C:NAD1401 4.1 25.3 1.0 N C:GLY1184 4.1 25.5 1.0 CA C:GLY1184 4.2 25.9 1.0 OD2 C:ASP1187 4.3 37.2 1.0 N C:GLY1182 4.4 29.2 1.0 SD C:MET1081 4.5 46.8 1.0 CA C:PRO1181 4.5 34.1 1.0 N C:ASP1187 4.5 25.8 1.0 C C:GLY1184 4.7 25.6 1.0 CD C:GLN1013 4.7 30.2 1.0 CA C:ASP1187 4.8 27.4 1.0 CB C:ASP1187 4.8 29.3 1.0 CG C:PRO1181 4.9 35.4 1.0 C C:PRO1181 4.9 31.7 1.0 C C:THR1186 4.9 24.3 1.0 O2N C:NAD1401 4.9 29.1 1.0 O C:GLY1184 5.0 22.7 1.0

E.Adjogatse, P.Erskine, S.A.Wells, J.M.Kelly, J.D.Wilden, A.W.E.Chan, D.Selwood, A.Coker, S.Wood, J.B.Cooper. Structure and Function of L-Threonine-3-Dehydrogenase From the Parasitic Protozoan Trypanosoma Brucei Revealed By X-Ray Crystallography and Geometric Simulations. Acta Crystallogr D Struct V. 74 861 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30198897
DOI: 10.1107/S2059798318009208