Sodium in PDB 5klo: Crystal Structure of Thioacyl Intermediate in 2-Aminomuconate 6- Semialdehyde Dehydrogenase N169A

The structure of Crystal Structure of Thioacyl Intermediate in 2-Aminomuconate 6- Semialdehyde Dehydrogenase N169A, PDB code: 5klo was solved by Y.Yang, I.Davis, U.Ha, Y.Wang, I.Shin, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.90 / 1.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.111, 141.724, 171.505, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.3

The binding sites of Sodium atom in the Crystal Structure of Thioacyl Intermediate in 2-Aminomuconate 6- Semialdehyde Dehydrogenase N169A (pdb code 5klo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Thioacyl Intermediate in 2-Aminomuconate 6- Semialdehyde Dehydrogenase N169A, PDB code: 5klo:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Thioacyl Intermediate in 2-Aminomuconate 6- Semialdehyde Dehydrogenase N169A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Thioacyl Intermediate in 2-Aminomuconate 6- Semialdehyde Dehydrogenase N169A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:27.7 occ:1.00 O A:GLU196 2.8 29.6 1.0 OD1 A:ASN37 2.9 30.2 1.0 O A:ILE38 2.9 31.6 1.0 O A:ASP105 3.0 30.0 1.0 O A:HOH858 3.1 33.6 1.0 O A:HOH704 3.1 43.4 1.0 N A:ILE38 3.8 31.8 1.0 C A:ILE38 3.8 32.1 1.0 C A:GLU196 3.8 29.2 1.0 C A:ASP105 3.8 29.2 1.0 CA A:ASP105 4.0 27.7 1.0 CG A:ASN37 4.0 34.2 1.0 O A:HOH813 4.1 33.7 1.0 CA A:GLU196 4.2 28.0 1.0 CB A:ASP105 4.3 28.5 1.0 CA A:ILE38 4.4 27.8 1.0 C A:ASN37 4.5 32.0 1.0 CD A:PRO40 4.5 25.0 1.0 OE1 A:GLU196 4.6 33.0 1.0 CA A:ASN37 4.7 32.0 1.0 CB A:GLU196 4.7 30.9 1.0 CD1 A:ILE46 4.7 34.0 1.0 O A:ILE345 4.7 26.2 1.0 O A:HOH754 4.8 32.9 1.0 N A:ASN39 4.8 28.3 1.0 CG A:ASP105 4.8 29.6 1.0 ND2 A:ASN37 4.8 31.9 1.0 N A:SER197 4.9 28.1 1.0 O A:HOH796 4.9 39.8 1.0 CD1 A:ILE345 5.0 27.5 1.0 CB A:ASN37 5.0 31.8 1.0 OD1 A:ASP105 5.0 29.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Thioacyl Intermediate in 2-Aminomuconate 6- Semialdehyde Dehydrogenase N169A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Thioacyl Intermediate in 2-Aminomuconate 6- Semialdehyde Dehydrogenase N169A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:30.2 occ:1.00 O B:GLU196 2.8 30.9 1.0 OD1 B:ASN37 2.9 35.0 1.0 O B:ASP105 2.9 34.0 1.0 O B:ILE38 2.9 38.7 1.0 O B:HOH710 3.1 41.4 1.0 O B:HOH836 3.1 36.9 1.0 N B:ILE38 3.7 33.9 1.0 C B:ILE38 3.8 38.9 1.0 C B:ASP105 3.8 31.5 1.0 C B:GLU196 3.9 34.9 1.0 CA B:ASP105 4.0 31.0 1.0 O B:HOH759 4.0 36.7 1.0 CG B:ASN37 4.1 33.9 1.0 CA B:ILE38 4.3 34.9 1.0 CA B:GLU196 4.3 32.7 1.0 CB B:ASP105 4.4 30.3 1.0 C B:ASN37 4.5 34.8 1.0 OE1 B:GLU196 4.5 35.1 1.0 CD B:PRO40 4.6 33.8 1.0 CD1 B:ILE46 4.6 39.8 1.0 CA B:ASN37 4.7 35.1 1.0 O B:HOH776 4.8 41.6 1.0 O B:ILE345 4.8 29.4 1.0 N B:ASN39 4.8 33.6 1.0 CB B:GLU196 4.8 30.6 1.0 O B:HOH751 4.8 33.0 1.0 CG B:ASP105 4.8 35.2 1.0 ND2 B:ASN37 4.9 37.5 1.0 CB B:ILE38 4.9 37.5 1.0 OD1 B:ASP105 4.9 35.8 1.0 CD1 B:ILE345 4.9 31.0 1.0 N B:SER197 5.0 31.1 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Thioacyl Intermediate in 2-Aminomuconate 6- Semialdehyde Dehydrogenase N169A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Thioacyl Intermediate in 2-Aminomuconate 6- Semialdehyde Dehydrogenase N169A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na602 b:33.4 occ:1.00 O C:GLU196 2.9 33.0 1.0 OD1 C:ASN37 2.9 35.9 1.0 O C:ILE38 2.9 34.9 1.0 O C:ASP105 3.1 32.5 1.0 O C:HOH921 3.2 37.5 1.0 O C:HOH701 3.2 43.8 1.0 N C:ILE38 3.7 33.6 1.0 C C:ILE38 3.8 36.1 1.0 C C:GLU196 3.9 32.9 1.0 C C:ASP105 3.9 30.8 1.0 CA C:ASP105 4.0 30.5 1.0 CG C:ASN37 4.0 33.6 1.0 O C:HOH787 4.1 36.2 1.0 CA C:ILE38 4.3 31.8 1.0 CB C:ASP105 4.3 30.6 1.0 CA C:GLU196 4.3 30.6 1.0 C C:ASN37 4.4 34.6 1.0 CD1 C:ILE46 4.5 36.9 1.0 CD C:PRO40 4.6 29.7 1.0 OE1 C:GLU196 4.6 35.3 1.0 CA C:ASN37 4.7 34.9 1.0 ND2 C:ASN37 4.7 36.5 1.0 N C:ASN39 4.7 30.9 1.0 CB C:GLU196 4.8 31.1 1.0 O C:ILE345 4.8 27.3 1.0 CG C:ASP105 4.8 34.9 1.0 O C:HOH760 4.8 35.9 1.0 O C:HOH738 4.9 42.8 1.0 OD1 C:ASP105 4.9 36.7 1.0 CB C:ILE38 4.9 34.0 1.0 CB C:ASN37 5.0 36.2 1.0 N C:SER197 5.0 27.9 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Thioacyl Intermediate in 2-Aminomuconate 6- Semialdehyde Dehydrogenase N169A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Thioacyl Intermediate in 2-Aminomuconate 6- Semialdehyde Dehydrogenase N169A within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:37.3 occ:1.00 O D:GLU196 2.9 36.5 1.0 OD1 D:ASN37 2.9 39.4 1.0 O D:ILE38 3.0 43.2 1.0 O D:ASP105 3.1 41.9 1.0 O D:HOH701 3.1 44.2 1.0 O D:HOH885 3.2 41.8 1.0 N D:ILE38 3.7 38.8 1.0 C D:ILE38 3.8 42.1 1.0 C D:GLU196 3.9 39.9 1.0 C D:ASP105 4.0 36.2 1.0 CA D:ASP105 4.1 36.0 1.0 O D:HOH835 4.1 39.4 1.0 CG D:ASN37 4.1 40.1 1.0 CA D:ILE38 4.3 42.3 1.0 CA D:GLU196 4.3 34.8 1.0 C D:ASN37 4.4 40.8 1.0 OE1 D:GLU196 4.5 39.2 1.0 CB D:ASP105 4.5 35.6 1.0 CD D:PRO40 4.6 39.7 1.0 CA D:ASN37 4.7 37.3 1.0 CD1 D:ILE46 4.7 43.6 1.0 N D:ASN39 4.7 38.2 1.0 O D:HOH768 4.8 36.3 1.0 O D:ILE345 4.8 36.4 1.0 CB D:GLU196 4.9 35.6 1.0 CG D:ASP105 4.9 41.0 1.0 N D:SER197 4.9 34.0 1.0 CB D:ILE38 5.0 41.8 1.0 CD1 D:ILE345 5.0 32.2 1.0 ND2 D:ASN37 5.0 41.4 1.0

Y.Yang, A.Liu. Crystal Structure of 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169A in Complex with Nadh and Intermediate To Be Published.