Sodium in PDB 5gt6: Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus

The structure of Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus, PDB code: 5gt6 was solved by H.P.T.Ngo, S.H.Hong, T.H.Ho, D.K.Oh, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.57 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.527, 93.284, 145.472, 90.00, 98.05, 90.00
R / Rfree (%)	18.2 / 25.1

The binding sites of Sodium atom in the Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus (pdb code 5gt6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus, PDB code: 5gt6:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:16.9 occ:1.00 OD1 A:ASP108 2.3 15.2 1.0 O A:GLN195 2.3 16.3 1.0 O A:HOH607 2.3 15.5 1.0 O A:ASP108 2.3 16.2 1.0 O A:TYR40 2.4 18.3 1.0 OG1 A:THR39 2.8 18.1 1.0 C A:ASP108 3.3 15.4 1.0 CG A:ASP108 3.4 15.2 1.0 C A:TYR40 3.4 18.5 1.0 N A:TYR40 3.4 19.4 1.0 C A:GLN195 3.5 15.9 1.0 CA A:ASP108 3.6 15.8 1.0 CA A:TYR40 3.9 19.9 1.0 CB A:ASP108 4.1 15.4 1.0 CB A:THR39 4.1 17.7 1.0 C A:THR39 4.2 19.1 1.0 OD2 A:ASP108 4.4 15.3 1.0 N A:THR196 4.4 15.1 1.0 CA A:GLN195 4.4 16.0 1.0 CA A:THR39 4.5 19.3 1.0 N A:ASN109 4.5 14.2 1.0 CA A:THR196 4.5 14.7 1.0 N A:ASN41 4.6 18.4 1.0 CG2 A:THR196 4.6 14.4 1.0 CD A:PRO42 4.7 17.1 1.0 CG2 A:THR39 4.7 17.3 1.0 CB A:TYR40 4.8 21.4 1.0 CB A:GLN195 4.9 15.7 1.0 N A:ASP108 5.0 16.0 1.0 O A:LEU107 5.0 17.5 1.0

Sodium binding site 2 out of 4 in the Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:19.1 occ:1.00 OD1 B:ASP108 2.3 16.4 1.0 O B:HOH608 2.3 20.1 1.0 O B:TYR40 2.3 19.7 1.0 O B:ASP108 2.3 16.7 1.0 O B:GLN195 2.3 18.7 1.0 OG1 B:THR39 2.7 21.0 1.0 C B:ASP108 3.3 14.6 1.0 CG B:ASP108 3.4 14.8 1.0 C B:TYR40 3.4 18.8 1.0 N B:TYR40 3.4 18.6 1.0 C B:GLN195 3.5 18.3 1.0 CA B:ASP108 3.7 14.9 1.0 CA B:TYR40 4.0 19.5 1.0 CB B:THR39 4.0 20.2 1.0 C B:THR39 4.1 19.0 1.0 CB B:ASP108 4.1 15.0 1.0 OD2 B:ASP108 4.3 15.5 1.0 CA B:THR39 4.3 20.1 1.0 CA B:GLN195 4.4 18.0 1.0 N B:ASN109 4.5 14.0 1.0 N B:THR196 4.5 17.8 1.0 N B:ASN41 4.5 18.4 1.0 CG2 B:THR39 4.6 19.4 1.0 CD B:PRO42 4.6 16.2 1.0 CA B:THR196 4.7 17.0 1.0 CG2 B:THR196 4.7 16.3 1.0 CB B:TYR40 4.8 19.8 1.0 CB B:GLN195 4.9 18.1 1.0 O B:THR39 5.0 18.6 1.0

Sodium binding site 3 out of 4 in the Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:18.3 occ:1.00 O C:GLN195 2.3 18.8 1.0 OD1 C:ASP108 2.3 19.2 1.0 O C:HOH602 2.3 16.2 1.0 O C:TYR40 2.3 20.0 1.0 O C:ASP108 2.3 17.9 1.0 OG1 C:THR39 2.9 20.4 1.0 C C:ASP108 3.3 16.9 1.0 CG C:ASP108 3.3 18.5 1.0 C C:TYR40 3.5 19.8 1.0 C C:GLN195 3.5 18.4 1.0 N C:TYR40 3.6 20.7 1.0 CA C:ASP108 3.6 17.2 1.0 CB C:ASP108 4.1 17.8 1.0 CA C:TYR40 4.1 21.0 1.0 CB C:THR39 4.1 19.5 1.0 OD2 C:ASP108 4.3 18.8 1.0 C C:THR39 4.3 20.2 1.0 CA C:GLN195 4.4 19.7 1.0 N C:THR196 4.4 16.4 1.0 CG2 C:THR196 4.5 15.2 1.0 CA C:THR196 4.5 15.8 1.0 CA C:THR39 4.5 20.4 1.0 N C:ASN109 4.5 16.4 1.0 CG2 C:THR39 4.6 19.5 1.0 N C:ASN41 4.6 19.2 1.0 CB C:TYR40 4.9 22.3 1.0 CD C:PRO42 4.9 17.2 1.0 CG C:PRO42 4.9 17.6 1.0 CB C:GLN195 4.9 19.8 1.0 O C:LEU107 4.9 19.6 1.0 N C:ASP108 5.0 18.2 1.0

Sodium binding site 4 out of 4 in the Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ D:Na501 b:20.1 occ:1.00 O D:GLN195 2.3 19.2 1.0 OD1 D:ASP108 2.3 19.8 1.0 O D:HOH602 2.3 17.3 1.0 O D:ASP108 2.3 21.3 1.0 O D:TYR40 2.5 21.3 1.0 OG1 D:THR39 2.6 18.9 1.0 C D:ASP108 3.3 19.7 1.0 CG D:ASP108 3.3 20.7 1.0 C D:GLN195 3.5 18.8 1.0 N D:TYR40 3.5 21.0 1.0 C D:TYR40 3.6 20.8 1.0 CA D:ASP108 3.7 20.5 1.0 CB D:THR39 3.9 19.8 1.0 CA D:TYR40 4.0 22.3 1.0 CB D:ASP108 4.1 20.2 1.0 C D:THR39 4.2 20.9 1.0 OD2 D:ASP108 4.2 21.3 1.0 CG2 D:THR196 4.3 19.9 1.0 CA D:GLN195 4.4 18.7 1.0 CA D:THR39 4.4 20.6 1.0 N D:THR196 4.4 18.8 1.0 N D:ASN109 4.5 18.7 1.0 CA D:THR196 4.6 19.3 1.0 CG2 D:THR39 4.6 20.0 1.0 CD D:PRO42 4.7 18.0 1.0 N D:ASN41 4.7 19.9 1.0 CB D:GLN195 4.8 19.3 1.0 CB D:TYR40 4.8 24.1 1.0

H.P.T.Ngo, S.H.Hong, T.H.Ho, D.K.Oh, L.W.Kang. Crystal Structures of Aldehyde Dehydrogenase From Bacillus Cereus Having Atypical Bidirectional Oxidizing and Reducing Activities For All-Trans-Retinal To Be Published.