Sodium in PDB 4pxl: Structure of Zm ALDH2-3 (RF2C) in Complex with Nad

The structure of Structure of Zm ALDH2-3 (RF2C) in Complex with Nad, PDB code: 4pxl was solved by S.Morera, A.Vigouroux, D.Kopecny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.10 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	109.860, 126.080, 78.310, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.5

The structure of Structure of Zm ALDH2-3 (RF2C) in Complex with Nad also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Structure of Zm ALDH2-3 (RF2C) in Complex with Nad (pdb code 4pxl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Zm ALDH2-3 (RF2C) in Complex with Nad, PDB code: 4pxl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Zm ALDH2-3 (RF2C) in Complex with Nad


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Zm ALDH2-3 (RF2C) in Complex with Nad within 5.0Å range: probe atom residue distance (Å) B Occ A:Na609 b:42.3 occ:1.00 O A:GLN197 2.3 45.0 1.0 O A:HOH829 2.7 43.6 1.0 OG1 A:THR41 2.7 57.5 1.0 OD1 A:ASP110 2.8 52.8 1.0 O A:ASP110 2.8 43.4 1.0 O A:ARG42 2.8 45.6 1.0 C A:GLN197 3.5 44.2 1.0 N A:ARG42 3.6 41.4 1.0 CG A:ASP110 3.7 53.5 1.0 C A:ASP110 3.7 43.1 1.0 CA A:ASP110 3.8 38.9 1.0 C A:ARG42 3.9 47.3 1.0 CB A:THR41 4.0 49.1 1.0 CA A:GLN197 4.1 37.5 1.0 CB A:ASP110 4.2 40.2 1.0 C A:THR41 4.3 45.3 1.0 CD1 A:ILE50 4.3 54.6 1.0 CA A:ARG42 4.3 40.9 1.0 CA A:THR41 4.4 41.4 1.0 OD2 A:ASP110 4.6 64.7 1.0 CB A:GLN197 4.6 38.7 1.0 N A:THR198 4.6 40.0 1.0 O A:VAL109 4.8 44.0 1.0 CG2 A:THR41 4.9 42.6 1.0 CA A:THR198 4.9 39.2 1.0 N A:ALA111 5.0 38.6 1.0 N A:ASP110 5.0 38.5 1.0

Sodium binding site 2 out of 2 in the Structure of Zm ALDH2-3 (RF2C) in Complex with Nad


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Zm ALDH2-3 (RF2C) in Complex with Nad within 5.0Å range: probe atom residue distance (Å) B Occ B:Na604 b:56.8 occ:1.00 O B:ASP110 2.5 45.5 1.0 O B:ARG42 2.6 50.0 1.0 O B:GLN197 2.6 44.7 1.0 OG1 B:THR41 2.8 56.6 1.0 O B:HOH812 3.1 42.9 1.0 OD1 B:ASP110 3.3 57.1 1.0 C B:ASP110 3.4 45.8 1.0 N B:ARG42 3.5 44.8 1.0 CA B:ASP110 3.6 41.6 1.0 C B:ARG42 3.7 50.2 1.0 C B:GLN197 3.7 44.6 1.0 CG B:ASP110 4.0 55.5 1.0 CB B:THR41 4.1 54.0 1.0 CD1 B:ILE50 4.1 62.2 1.0 CA B:ARG42 4.2 45.2 1.0 C B:THR41 4.2 49.9 1.0 CA B:GLN197 4.3 41.0 1.0 CB B:ASP110 4.3 42.7 1.0 CA B:THR41 4.4 46.7 1.0 O B:VAL109 4.5 47.2 1.0 N B:ALA111 4.7 41.5 1.0 CB B:GLN197 4.7 41.6 1.0 N B:ASP43 4.8 47.7 1.0 CD B:PRO44 4.8 42.9 1.0 N B:THR198 4.8 40.6 1.0 N B:ASP110 4.9 41.9 1.0 O B:HOH745 4.9 43.4 1.0 OD2 B:ASP110 4.9 61.2 1.0 CG2 B:THR41 5.0 50.6 1.0

R.Koncitikova, A.Vigouroux, M.Kopecna, T.Andree, J.Bartos, M.Sebela, S.Morera, D.Kopecny. Role and Structural Characterization of Plant Aldehyde Dehydrogenases From Family 2 and Family 7. Biochem.J. 2015.
ISSN: ESSN 1470-8728
PubMed: 25734422
DOI: 10.1042/BJ20150009