Sodium in PDB 4i9b: Structure of Aminoaldehyde Dehydrogenase 1 From Solanum Lycopersium (SLAMADH1) with A Thiohemiacetal Intermediate

The structure of Structure of Aminoaldehyde Dehydrogenase 1 From Solanum Lycopersium (SLAMADH1) with A Thiohemiacetal Intermediate, PDB code: 4i9b 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)	27.82 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.150, 94.790, 118.170, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21.2

The binding sites of Sodium atom in the Structure of Aminoaldehyde Dehydrogenase 1 From Solanum Lycopersium (SLAMADH1) with A Thiohemiacetal Intermediate (pdb code 4i9b). 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 Aminoaldehyde Dehydrogenase 1 From Solanum Lycopersium (SLAMADH1) with A Thiohemiacetal Intermediate, PDB code: 4i9b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Aminoaldehyde Dehydrogenase 1 From Solanum Lycopersium (SLAMADH1) with A Thiohemiacetal Intermediate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Aminoaldehyde Dehydrogenase 1 From Solanum Lycopersium (SLAMADH1) with A Thiohemiacetal Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:25.7 occ:1.00 O A:ASP99 2.2 21.1 1.0 O A:HOH778 2.3 19.5 1.0 O A:LEU189 2.5 23.4 1.0 O A:HOH866 2.5 33.1 1.0 OD1 A:ASP99 2.6 24.1 1.0 O A:ILE31 2.7 24.5 1.0 C A:ASP99 3.2 21.0 1.0 C A:LEU189 3.6 23.7 1.0 CG A:ASP99 3.7 23.5 1.0 CA A:ASP99 3.7 18.2 1.0 C A:ILE31 3.8 24.4 1.0 N A:ILE31 3.9 20.6 1.0 CB A:ASP99 4.2 19.4 1.0 O A:HOH702 4.2 20.6 1.0 CG2 A:ILE30 4.2 19.7 1.0 N A:SER100 4.4 17.7 1.0 O A:HOH790 4.4 31.3 1.0 CA A:ILE31 4.4 21.0 1.0 CD A:PRO33 4.5 21.9 1.0 N A:ALA190 4.5 19.9 1.0 CA A:ALA190 4.5 19.4 1.0 CA A:LEU189 4.5 18.6 1.0 O A:HOH792 4.6 22.5 1.0 OD2 A:ASP99 4.7 20.4 1.0 CA A:SER100 4.9 17.2 1.0 C A:ILE30 4.9 22.2 1.0 N A:ASN32 4.9 19.6 1.0 O A:HOH957 5.0 28.1 1.0 CA A:ILE30 5.0 20.6 1.0 CB A:ILE31 5.0 24.4 1.0

Sodium binding site 2 out of 2 in the Structure of Aminoaldehyde Dehydrogenase 1 From Solanum Lycopersium (SLAMADH1) with A Thiohemiacetal Intermediate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Aminoaldehyde Dehydrogenase 1 From Solanum Lycopersium (SLAMADH1) with A Thiohemiacetal Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:23.2 occ:1.00 O B:HOH733 2.2 20.8 1.0 O B:ASP99 2.3 21.4 1.0 O B:LEU189 2.4 24.0 1.0 OD1 B:ASP99 2.4 23.0 1.0 O B:HOH857 2.5 31.6 1.0 O B:ILE31 3.2 26.4 1.0 C B:ASP99 3.2 21.8 1.0 CG B:ASP99 3.5 22.3 1.0 C B:LEU189 3.6 21.7 1.0 CA B:ASP99 3.6 17.1 1.0 CB B:ASP99 4.1 18.1 1.0 O B:HOH717 4.1 16.1 1.0 N B:ILE31 4.2 20.6 1.0 C B:ILE31 4.3 25.9 1.0 CG2 B:ILE30 4.3 23.9 1.0 O B:HOH824 4.3 22.5 1.0 CA B:ALA190 4.3 16.0 1.0 N B:ALA190 4.4 17.1 1.0 N B:SER100 4.4 18.4 1.0 OD2 B:ASP99 4.5 24.3 1.0 CA B:LEU189 4.5 17.6 1.0 O B:HOH913 4.7 42.3 1.0 CD B:PRO33 4.8 22.0 1.0 CB B:ALA190 4.8 16.0 1.0 CA B:ILE31 4.8 20.5 1.0 CA B:SER100 4.8 18.6 1.0 N B:ASP99 4.9 17.8 1.0 CA B:ILE30 4.9 19.0 1.0

D.Kopecny, R.Koncitikova, M.Tylichova, A.Vigouroux, H.Moskalikova, M.Soural, M.Sebela, S.Morera. Plant ALDH10 Family: Identifying Critical Residues For Substrate Specificity and Trapping A Thiohemiacetal Intermediate. J.Biol.Chem. V. 288 9491 2013.
ISSN: ISSN 0021-9258
PubMed: 23408433
DOI: 10.1074/JBC.M112.443952