Sodium in PDB 4pz2: Structure of Zm ALDH2-6 (RF2F) in Complex with Nad

The structure of Structure of Zm ALDH2-6 (RF2F) in Complex with Nad, PDB code: 4pz2 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)	46.81 / 2.40
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	233.880, 233.880, 82.900, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 21.3

The binding sites of Sodium atom in the Structure of Zm ALDH2-6 (RF2F) in Complex with Nad (pdb code 4pz2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Zm ALDH2-6 (RF2F) in Complex with Nad, PDB code: 4pz2:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of Zm ALDH2-6 (RF2F) 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 ALDH2-6 (RF2F) in Complex with Nad within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:79.4 occ:1.00 O A:GLN211 2.4 69.1 1.0 OD1 A:ASP124 2.5 79.5 1.0 O A:ARG56 2.6 78.9 1.0 O A:ASP124 2.6 73.2 1.0 OG1 A:THR55 2.8 76.0 1.0 O A:HOH716 3.0 68.9 1.0 N A:ARG56 3.5 72.0 1.0 C A:GLN211 3.6 68.7 1.0 C A:ASP124 3.6 74.2 1.0 C A:ARG56 3.6 77.7 1.0 CG A:ASP124 3.7 77.5 1.0 CA A:ASP124 3.9 68.6 1.0 CB A:THR55 4.1 80.2 1.0 CA A:ARG56 4.1 72.4 1.0 C A:THR55 4.2 75.6 1.0 CA A:THR55 4.3 72.8 1.0 CB A:ASP124 4.3 68.9 1.0 CD1 A:ILE64 4.4 91.0 1.0 CG2 A:THR212 4.4 64.1 1.0 N A:THR212 4.5 63.5 1.0 CA A:THR212 4.5 63.1 1.0 CA A:GLN211 4.6 65.9 1.0 OD2 A:ASP124 4.6 81.3 1.0 N A:ASP57 4.8 74.5 1.0 CD A:PRO58 4.9 71.3 1.0 N A:ALA125 4.9 71.1 1.0 O A:VAL361 5.0 81.4 1.0

Sodium binding site 2 out of 4 in the Structure of Zm ALDH2-6 (RF2F) 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 ALDH2-6 (RF2F) in Complex with Nad within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:84.5 occ:1.00 O B:ASP124 2.3 78.1 1.0 O B:ARG56 2.5 79.8 1.0 O B:GLN211 2.6 77.7 1.0 OD1 B:ASP124 2.7 86.7 1.0 OG1 B:THR55 3.1 82.2 1.0 C B:ASP124 3.3 79.6 1.0 C B:ARG56 3.6 82.2 1.0 CA B:ASP124 3.7 74.3 1.0 N B:ARG56 3.7 80.2 1.0 CG B:ASP124 3.7 82.9 1.0 C B:GLN211 3.8 78.2 1.0 CB B:ASP124 4.2 74.7 1.0 CA B:ARG56 4.2 80.0 1.0 CG2 B:THR212 4.3 75.7 1.0 CD1 B:ILE64 4.4 95.2 1.0 CB B:THR55 4.5 87.1 1.0 C B:THR55 4.5 84.0 1.0 O B:VAL361 4.5 91.4 1.0 CD B:PRO58 4.5 78.3 1.0 N B:ALA125 4.6 77.7 1.0 CA B:THR212 4.6 73.2 1.0 N B:THR212 4.7 73.9 1.0 CA B:THR55 4.7 81.1 1.0 OD2 B:ASP124 4.7 90.0 1.0 N B:ASP57 4.8 80.0 1.0 CA B:GLN211 4.8 74.3 1.0 O B:LEU123 4.9 78.3 1.0 CG2 B:VAL361 5.0 84.7 1.0 N B:ASP124 5.0 74.5 1.0

Sodium binding site 3 out of 4 in the Structure of Zm ALDH2-6 (RF2F) in Complex with Nad


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Zm ALDH2-6 (RF2F) in Complex with Nad within 5.0Å range: probe atom residue distance (Å) B Occ C:Na601 b:84.5 occ:1.00 O C:ASP124 2.5 81.2 1.0 O C:ARG56 2.5 83.5 1.0 O C:GLN211 2.6 80.7 1.0 OD1 C:ASP124 2.7 83.7 1.0 OG1 C:THR55 3.0 86.4 1.0 C C:ASP124 3.5 82.8 1.0 N C:ARG56 3.6 78.0 1.0 C C:ARG56 3.6 84.5 1.0 CA C:ASP124 3.7 78.8 1.0 CG C:ASP124 3.8 83.9 1.0 C C:GLN211 3.8 80.3 1.0 CA C:ARG56 4.2 78.6 1.0 CB C:THR55 4.3 84.8 1.0 CB C:ASP124 4.3 79.0 1.0 C C:THR55 4.3 82.4 1.0 CD1 C:ILE64 4.4 94.5 1.0 CG2 C:THR212 4.4 79.3 1.0 CD C:PRO58 4.5 85.6 1.0 CA C:THR55 4.5 78.0 1.0 O C:VAL361 4.7 87.2 1.0 CA C:THR212 4.7 78.4 1.0 N C:THR212 4.7 77.8 1.0 N C:ALA125 4.7 80.1 1.0 N C:ASP57 4.8 84.1 1.0 OD2 C:ASP124 4.8 88.1 1.0 CA C:GLN211 4.8 73.3 1.0

Sodium binding site 4 out of 4 in the Structure of Zm ALDH2-6 (RF2F) in Complex with Nad


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Zm ALDH2-6 (RF2F) in Complex with Nad within 5.0Å range: probe atom residue distance (Å) B Occ D:Na601 b:0.1 occ:1.00 O D:ARG56 2.4 0.8 1.0 O D:ASP124 2.5 0.7 1.0 O D:GLN211 2.6 0.2 1.0 OD1 D:ASP124 2.6 0.7 1.0 OG1 D:THR55 3.2 0.7 1.0 C D:ARG56 3.5 0.2 1.0 C D:ASP124 3.5 0.7 1.0 N D:ARG56 3.6 0.7 1.0 CG D:ASP124 3.8 0.3 1.0 C D:GLN211 3.8 0.6 1.0 CA D:ASP124 3.9 99.6 1.0 CA D:ARG56 4.1 0.3 1.0 O D:VAL361 4.4 0.1 1.0 CB D:ASP124 4.4 99.9 1.0 C D:THR55 4.4 0.6 1.0 CD D:PRO58 4.4 0.8 1.0 CG2 D:THR212 4.5 0.7 1.0 CB D:THR55 4.5 0.6 1.0 N D:ASP57 4.6 0.3 1.0 CA D:THR55 4.6 0.5 1.0 OD2 D:ASP124 4.7 0.8 1.0 CA D:GLN211 4.7 0.3 1.0 N D:THR212 4.7 0.1 1.0 N D:ALA125 4.8 0.4 1.0 CA D:THR212 4.8 0.4 1.0 CB D:ARG56 5.0 0.9 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