Sodium in PDB 5gtk: Nad+ Complex Structure of Aldehyde Dehydrogenase From Bacillus Cereus

The structure of Nad+ Complex Structure of Aldehyde Dehydrogenase From Bacillus Cereus, PDB code: 5gtk 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)	47.93 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.222, 93.253, 145.149, 90.00, 97.86, 90.00
R / Rfree (%)	16.5 / 23.3

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

Sodium binding site 1 out of 3 in the Nad+ Complex 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 Nad+ Complex Structure of Aldehyde Dehydrogenase From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:14.5 occ:1.00 O A:GLN195 2.2 12.2 1.0 O A:HOH718 2.4 9.4 1.0 OD1 A:ASP108 2.5 10.5 1.0 O A:TYR40 2.6 14.1 1.0 O A:ASP108 2.6 10.2 1.0 OG1 A:THR39 3.0 14.5 1.0 C A:GLN195 3.4 12.4 1.0 CG A:ASP108 3.5 10.1 1.0 C A:ASP108 3.5 10.5 1.0 N A:TYR40 3.6 16.5 1.0 C A:TYR40 3.6 14.8 1.0 CA A:ASP108 3.9 10.3 1.0 CA A:TYR40 4.1 16.6 1.0 CA A:GLN195 4.1 13.1 1.0 OD2 A:ASP108 4.2 9.9 1.0 CB A:ASP108 4.2 10.2 1.0 CB A:THR39 4.3 15.0 1.0 C A:THR39 4.4 15.6 1.0 N A:THR196 4.4 11.6 1.0 CG2 A:THR196 4.5 10.9 1.0 CB A:GLN195 4.5 13.3 1.0 CA A:THR39 4.6 15.8 1.0 CA A:THR196 4.6 11.1 1.0 CD A:PRO42 4.7 12.2 1.0 N A:ASN109 4.7 10.5 1.0 N A:ASN41 4.8 13.7 1.0 CB A:TYR40 4.8 18.1 1.0 CG2 A:THR39 4.9 14.8 1.0

Sodium binding site 2 out of 3 in the Nad+ Complex 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 Nad+ Complex Structure of Aldehyde Dehydrogenase From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:17.7 occ:1.00 O B:GLN195 2.3 11.8 1.0 O B:HOH689 2.4 6.8 1.0 O B:TYR40 2.6 14.5 1.0 OD1 B:ASP108 2.6 15.5 1.0 O B:ASP108 2.6 13.0 1.0 OG1 B:THR39 3.3 14.3 1.0 C B:GLN195 3.5 11.8 1.0 C B:ASP108 3.5 13.3 1.0 CG B:ASP108 3.6 14.6 1.0 C B:TYR40 3.6 14.3 1.0 N B:TYR40 3.6 14.7 1.0 CA B:ASP108 3.8 13.6 1.0 CA B:TYR40 4.1 15.4 1.0 CB B:ASP108 4.2 14.1 1.0 CA B:GLN195 4.3 12.3 1.0 OD2 B:ASP108 4.3 14.5 1.0 C B:THR39 4.4 13.9 1.0 CB B:THR39 4.4 13.9 1.0 N B:THR196 4.5 11.2 1.0 CD B:PRO42 4.6 12.2 1.0 CG2 B:THR196 4.7 10.7 1.0 CA B:THR39 4.7 14.4 1.0 N B:ASN41 4.7 13.5 1.0 CB B:GLN195 4.7 12.2 1.0 CA B:THR196 4.7 10.9 1.0 N B:ASN109 4.7 12.8 1.0 CB B:TYR40 4.8 17.0 1.0 O B:HOH676 4.9 14.9 1.0 CD2 B:LEU48 4.9 13.6 1.0 CG2 B:THR39 4.9 13.6 1.0

Sodium binding site 3 out of 3 in the Nad+ Complex 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 Nad+ Complex Structure of Aldehyde Dehydrogenase From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ D:Na502 b:21.8 occ:1.00 O D:GLN195 2.4 14.0 1.0 OD1 D:ASP108 2.5 16.2 1.0 O D:TYR40 2.5 16.9 1.0 O D:ASP108 2.5 15.7 1.0 O D:HOH623 2.6 2.7 1.0 OG1 D:THR39 2.9 13.5 1.0 CG D:ASP108 3.5 16.3 1.0 C D:ASP108 3.5 15.1 1.0 C D:TYR40 3.5 16.6 1.0 N D:TYR40 3.5 16.0 1.0 C D:GLN195 3.6 13.2 1.0 CA D:ASP108 3.8 15.1 1.0 CA D:TYR40 4.0 17.2 1.0 CB D:ASP108 4.2 15.3 1.0 OD2 D:ASP108 4.2 17.7 1.0 CB D:THR39 4.2 14.1 1.0 C D:THR39 4.3 14.7 1.0 CA D:GLN195 4.4 13.4 1.0 CD D:PRO42 4.4 14.9 1.0 N D:THR196 4.6 12.7 1.0 CG2 D:THR196 4.6 12.3 1.0 CA D:THR39 4.6 14.4 1.0 N D:ASN109 4.7 14.8 1.0 N D:ASN41 4.7 16.5 1.0 CA D:THR196 4.7 12.2 1.0 CB D:GLN195 4.7 13.4 1.0 CB D:TYR40 4.8 18.4 1.0 CG2 D:THR39 4.9 14.0 1.0 CD2 D:LEU48 5.0 16.5 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.