Sodium in PDB 4oub: A 2.20 Angstroms X-Ray Crystal Structure of E268A 2-Aminomucaonate 6- Semialdehyde Dehydrogenase Catalytic Intermediate From Pseudomonas Fluorescens

The structure of A 2.20 Angstroms X-Ray Crystal Structure of E268A 2-Aminomucaonate 6- Semialdehyde Dehydrogenase Catalytic Intermediate From Pseudomonas Fluorescens, PDB code: 4oub was solved by L.Huo, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.00 / 2.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.329, 141.345, 173.530, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22.5

The binding sites of Sodium atom in the A 2.20 Angstroms X-Ray Crystal Structure of E268A 2-Aminomucaonate 6- Semialdehyde Dehydrogenase Catalytic Intermediate From Pseudomonas Fluorescens (pdb code 4oub). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the A 2.20 Angstroms X-Ray Crystal Structure of E268A 2-Aminomucaonate 6- Semialdehyde Dehydrogenase Catalytic Intermediate From Pseudomonas Fluorescens, PDB code: 4oub:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the A 2.20 Angstroms X-Ray Crystal Structure of E268A 2-Aminomucaonate 6- Semialdehyde Dehydrogenase Catalytic Intermediate From Pseudomonas Fluorescens


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A 2.20 Angstroms X-Ray Crystal Structure of E268A 2-Aminomucaonate 6- Semialdehyde Dehydrogenase Catalytic Intermediate From Pseudomonas Fluorescens within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:38.6 occ:1.00 O A:HOH780 2.4 34.2 1.0 O A:HOH750 2.5 33.2 1.0 OD1 A:ASN37 2.5 32.5 1.0 O A:ILE38 2.7 40.3 1.0 O A:GLU196 2.7 33.6 1.0 O A:ASP105 2.9 37.1 1.0 N A:ILE38 3.6 37.1 1.0 C A:ILE38 3.7 37.5 1.0 CG A:ASN37 3.7 36.4 1.0 C A:ASP105 3.8 31.4 1.0 C A:GLU196 3.8 34.2 1.0 CA A:ASP105 4.0 32.2 1.0 CA A:ILE38 4.2 35.7 1.0 CA A:GLU196 4.3 34.5 1.0 OE1 A:GLU196 4.3 41.8 1.0 C A:ASN37 4.3 36.2 1.0 CD1 A:ILE46 4.4 44.9 1.0 O A:HOH875 4.4 39.6 1.0 CB A:ASP105 4.4 35.0 1.0 ND2 A:ASN37 4.5 37.4 1.0 CA A:ASN37 4.5 34.9 1.0 CD A:PRO40 4.6 35.4 1.0 N A:ASN39 4.7 35.3 1.0 CB A:GLU196 4.7 35.2 1.0 CB A:ASN37 4.7 38.3 1.0 O A:ILE345 4.8 32.6 1.0 CB A:ILE38 4.8 41.2 1.0 O A:HOH732 4.8 32.4 1.0 CG A:ASP105 4.9 35.7 1.0 N A:SER197 4.9 32.0 1.0 N A:THR106 5.0 34.1 1.0

Sodium binding site 2 out of 4 in the A 2.20 Angstroms X-Ray Crystal Structure of E268A 2-Aminomucaonate 6- Semialdehyde Dehydrogenase Catalytic Intermediate From Pseudomonas Fluorescens


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A 2.20 Angstroms X-Ray Crystal Structure of E268A 2-Aminomucaonate 6- Semialdehyde Dehydrogenase Catalytic Intermediate From Pseudomonas Fluorescens within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:40.2 occ:1.00 O B:HOH715 2.5 33.6 1.0 OD1 B:ASN37 2.5 36.1 1.0 O B:GLU196 2.5 35.3 1.0 O B:ILE38 2.7 36.2 1.0 O B:HOH876 2.8 40.8 1.0 O B:ASP105 3.1 34.2 1.0 N B:ILE38 3.6 41.6 1.0 C B:ILE38 3.6 40.0 1.0 C B:GLU196 3.7 34.9 1.0 CG B:ASN37 3.7 35.2 1.0 C B:ASP105 4.0 29.5 1.0 CA B:ASP105 4.0 31.5 1.0 O B:HOH828 4.1 37.2 1.0 CA B:ILE38 4.2 38.3 1.0 CA B:GLU196 4.2 32.9 1.0 CB B:ASP105 4.3 34.6 1.0 C B:ASN37 4.4 38.8 1.0 OE1 B:GLU196 4.5 41.6 1.0 ND2 B:ASN37 4.5 33.6 1.0 CA B:ASN37 4.6 35.0 1.0 CB B:GLU196 4.7 33.3 1.0 N B:ASN39 4.7 34.6 1.0 CD1 B:ILE46 4.7 37.3 1.0 N B:SER197 4.8 29.7 1.0 CD B:PRO40 4.8 30.8 1.0 CB B:ASN37 4.8 36.8 1.0 O B:HOH833 4.8 37.1 1.0 CG B:ASP105 4.9 40.9 1.0 O B:ILE345 4.9 29.5 1.0 CB B:ILE38 4.9 38.7 1.0 OD1 B:ASP105 4.9 36.5 1.0

Sodium binding site 3 out of 4 in the A 2.20 Angstroms X-Ray Crystal Structure of E268A 2-Aminomucaonate 6- Semialdehyde Dehydrogenase Catalytic Intermediate From Pseudomonas Fluorescens


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of A 2.20 Angstroms X-Ray Crystal Structure of E268A 2-Aminomucaonate 6- Semialdehyde Dehydrogenase Catalytic Intermediate From Pseudomonas Fluorescens within 5.0Å range: probe atom residue distance (Å) B Occ C:Na602 b:48.7 occ:1.00 O C:HOH775 2.4 43.4 1.0 O C:GLU196 2.6 45.6 1.0 O C:HOH702 2.6 52.6 1.0 O C:ILE38 2.7 47.3 1.0 OD1 C:ASN37 2.8 53.4 1.0 O C:ASP105 3.2 45.5 1.0 C C:GLU196 3.6 50.6 1.0 N C:ILE38 3.6 48.5 1.0 C C:ILE38 3.7 49.1 1.0 CA C:GLU196 3.9 46.3 1.0 CG C:ASN37 4.0 50.7 1.0 CA C:ILE38 4.1 51.2 1.0 C C:ASP105 4.2 41.4 1.0 OE1 C:GLU196 4.3 52.8 1.0 CB C:GLU196 4.3 43.7 1.0 CA C:ASP105 4.4 45.4 1.0 C C:ASN37 4.5 48.7 1.0 CB C:ILE38 4.6 52.2 1.0 O C:ILE345 4.7 44.2 1.0 CA C:ASN37 4.7 46.7 1.0 N C:SER197 4.8 44.0 1.0 N C:ASN39 4.8 47.3 1.0 CB C:ASP105 4.8 49.3 1.0 CD C:PRO40 4.8 48.5 1.0 ND2 C:ASN37 4.9 51.6 1.0 CD1 C:ILE345 4.9 41.7 1.0 CB C:ASN37 5.0 50.4 1.0

Sodium binding site 4 out of 4 in the A 2.20 Angstroms X-Ray Crystal Structure of E268A 2-Aminomucaonate 6- Semialdehyde Dehydrogenase Catalytic Intermediate From Pseudomonas Fluorescens


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of A 2.20 Angstroms X-Ray Crystal Structure of E268A 2-Aminomucaonate 6- Semialdehyde Dehydrogenase Catalytic Intermediate From Pseudomonas Fluorescens within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:48.2 occ:1.00 O D:HOH763 2.6 39.5 1.0 O D:ILE38 2.6 38.6 1.0 O D:GLU196 2.7 33.8 1.0 O D:ASP105 2.9 31.3 1.0 OD1 D:ASN37 3.2 34.0 1.0 O D:HOH826 3.6 43.0 1.0 C D:GLU196 3.7 37.9 1.0 C D:ILE38 3.8 40.2 1.0 OE1 D:GLU196 3.9 39.2 1.0 CA D:GLU196 3.9 35.7 1.0 C D:ASP105 4.0 30.7 1.0 N D:ILE38 4.0 35.1 1.0 O D:ILE345 4.2 28.0 1.0 CB D:GLU196 4.2 36.0 1.0 CD D:PRO40 4.4 32.3 1.0 CA D:ILE38 4.4 37.4 1.0 CA D:ASP105 4.4 33.3 1.0 CG D:ASN37 4.4 36.1 1.0 CD1 D:ILE345 4.6 29.9 1.0 O D:HOH876 4.6 42.8 1.0 CB D:ASP105 4.8 38.3 1.0 CB D:ILE38 4.8 39.1 1.0 C D:ASN37 4.9 33.8 1.0 N D:ASN39 4.9 35.5 1.0 CG1 D:ILE345 4.9 31.7 1.0 O D:HOH815 4.9 35.2 1.0 N D:SER197 4.9 37.3 1.0 CD D:GLU196 4.9 43.3 1.0

L.Huo, I.Davis, F.Liu, H.Iwaki, Y.Hasegawa, A.Liu. Crystallographic and Spectroscopic Snapshots Reveal A Dehydrogenase in Action Nat Commun 2014.
ISSN: ESSN 2041-1723
DOI: 10.1038/NCOMMS6935