Sodium in PDB 5klk: Crystal Structure of 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D in Complex with Nad+ and 2-Hydroxymuconate-6-Semialdehyde

The structure of Crystal Structure of 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D in Complex with Nad+ and 2-Hydroxymuconate-6-Semialdehyde, PDB code: 5klk 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)	36.70 / 2.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.247, 142.947, 174.151, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.1

The binding sites of Sodium atom in the Crystal Structure of 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D in Complex with Nad+ and 2-Hydroxymuconate-6-Semialdehyde (pdb code 5klk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D in Complex with Nad+ and 2-Hydroxymuconate-6-Semialdehyde, PDB code: 5klk:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D in Complex with Nad+ and 2-Hydroxymuconate-6-Semialdehyde


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 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D in Complex with Nad+ and 2-Hydroxymuconate-6-Semialdehyde within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:52.5 occ:1.00 O A:GLU196 3.1 38.6 1.0 O A:ILE345 3.2 31.3 1.0 OE1 A:GLU196 3.3 42.3 1.0 O A:ASP105 3.3 39.7 1.0 O A:ILE38 3.3 37.0 1.0 O A:HOH820 3.4 38.3 1.0 CB A:GLU196 3.8 35.0 1.0 CD1 A:ILE345 3.9 32.3 1.0 CA A:GLU196 3.9 38.4 1.0 C A:GLU196 3.9 40.3 1.0 CG1 A:ILE345 3.9 32.5 1.0 C A:ILE345 4.3 33.2 1.0 OD1 A:ASN37 4.3 35.7 1.0 CD A:GLU196 4.3 45.9 1.0 C A:ILE38 4.5 41.7 1.0 C A:ASP105 4.5 38.4 1.0 CD A:PRO40 4.6 36.4 1.0 CG A:GLU196 4.7 42.2 1.0 N A:ILE38 4.7 38.8 1.0 CB A:SER346 4.9 34.7 1.0 O A:HOH758 4.9 42.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D in Complex with Nad+ and 2-Hydroxymuconate-6-Semialdehyde


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 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D in Complex with Nad+ and 2-Hydroxymuconate-6-Semialdehyde within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:49.9 occ:1.00 OD1 B:ASN37 3.1 54.2 1.0 O B:GLU196 3.1 41.0 1.0 O B:ILE38 3.1 43.8 1.0 O B:ASP105 3.1 37.8 1.0 O B:HOH705 3.2 44.8 1.0 O B:HOH929 3.2 46.8 1.0 N B:ILE38 3.5 43.9 1.0 CG B:ASN37 3.7 48.0 1.0 C B:ILE38 3.8 44.5 1.0 CA B:ASP105 3.8 38.5 1.0 C B:ASP105 3.8 36.9 1.0 ND2 B:ASN37 4.1 43.0 1.0 C B:GLU196 4.1 43.0 1.0 CA B:ILE38 4.2 42.5 1.0 CB B:ASP105 4.3 42.1 1.0 C B:ASN37 4.3 44.3 1.0 CD1 B:ILE46 4.4 46.7 1.0 O B:HOH790 4.4 41.1 1.0 CA B:ASN37 4.5 48.0 1.0 CG B:ASP105 4.5 41.7 1.0 OD1 B:ASP105 4.6 45.0 1.0 CB B:ASN37 4.6 48.4 1.0 N B:ASN39 4.7 43.1 1.0 CA B:GLU196 4.7 39.5 1.0 CD B:PRO40 4.7 38.9 1.0 O B:ALA104 5.0 37.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D in Complex with Nad+ and 2-Hydroxymuconate-6-Semialdehyde


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 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D in Complex with Nad+ and 2-Hydroxymuconate-6-Semialdehyde within 5.0Å range: probe atom residue distance (Å) B Occ C:Na603 b:52.5 occ:1.00 O C:GLU196 3.1 39.8 1.0 O C:ILE345 3.2 32.7 1.0 O C:ASP105 3.3 34.1 1.0 O C:HOH852 3.3 39.7 1.0 O C:HOH749 3.3 46.1 1.0 OE1 C:GLU196 3.4 39.1 1.0 O C:ILE38 3.4 40.9 1.0 CD1 C:ILE345 3.8 34.8 1.0 CG1 C:ILE345 3.9 32.7 1.0 CB C:GLU196 3.9 33.7 1.0 C C:GLU196 3.9 37.7 1.0 CA C:GLU196 4.0 34.8 1.0 O C:HOH775 4.2 48.5 1.0 C C:ILE345 4.3 33.3 1.0 OD1 C:ASN37 4.4 37.4 1.0 CD C:GLU196 4.4 42.7 1.0 C C:ASP105 4.4 33.2 1.0 CD C:PRO40 4.6 37.9 1.0 C C:ILE38 4.6 40.6 1.0 CG C:GLU196 4.8 34.0 1.0 CG C:PRO40 4.9 30.9 1.0 N C:ILE38 4.9 42.2 1.0 CB C:SER346 4.9 35.5 1.0 CA C:ILE345 5.0 32.1 1.0

Y.Yang, A.Liu. Crystal Structure of 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D in Ternary Complex with Nad+ and Substrate Analogue 2-Hydroxymuconate-6-Semialdehyde To Be Published.