Sodium in PDB 5kll: Crystal Structure of 2-Hydroxymuconate-6-Semialdehyde Derived Tautomeric Intermediate in 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D

The structure of Crystal Structure of 2-Hydroxymuconate-6-Semialdehyde Derived Tautomeric Intermediate in 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D, PDB code: 5kll 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)	35.15 / 2.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.364, 143.055, 174.076, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 21.8

The binding sites of Sodium atom in the Crystal Structure of 2-Hydroxymuconate-6-Semialdehyde Derived Tautomeric Intermediate in 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D (pdb code 5kll). 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 2-Hydroxymuconate-6-Semialdehyde Derived Tautomeric Intermediate in 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D, PDB code: 5kll:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of 2-Hydroxymuconate-6-Semialdehyde Derived Tautomeric Intermediate in 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D


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-Hydroxymuconate-6-Semialdehyde Derived Tautomeric Intermediate in 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:33.0 occ:1.00 O A:ILE38 2.9 31.3 1.0 O A:GLU196 2.9 32.6 1.0 OD1 A:ASN37 2.9 32.7 1.0 O A:ASP105 3.1 29.8 1.0 O A:HOH937 3.1 35.8 1.0 O A:HOH706 3.1 43.1 1.0 N A:ILE38 3.7 30.6 1.0 C A:ILE38 3.8 35.0 1.0 C A:GLU196 3.8 34.7 1.0 C A:ASP105 3.9 33.4 1.0 CA A:ASP105 4.0 33.4 1.0 CG A:ASN37 4.1 37.5 1.0 O A:HOH778 4.1 30.3 1.0 CA A:GLU196 4.3 32.4 1.0 CA A:ILE38 4.3 29.0 1.0 CB A:ASP105 4.4 34.3 1.0 C A:ASN37 4.4 32.8 1.0 OE1 A:GLU196 4.5 35.2 1.0 CD1 A:ILE46 4.5 35.8 1.0 CD A:PRO40 4.5 24.7 1.0 CA A:ASN37 4.6 34.6 1.0 N A:ASN39 4.8 28.6 1.0 CB A:GLU196 4.8 28.8 1.0 CG A:ASP105 4.8 36.2 1.0 N A:SER197 4.9 30.1 1.0 O A:ILE345 4.9 26.4 1.0 O A:HOH760 4.9 35.4 1.0 CB A:ASN37 5.0 30.6 1.0 ND2 A:ASN37 5.0 37.2 1.0 OD1 A:ASP105 5.0 33.4 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of 2-Hydroxymuconate-6-Semialdehyde Derived Tautomeric Intermediate in 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D


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-Hydroxymuconate-6-Semialdehyde Derived Tautomeric Intermediate in 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:35.0 occ:1.00 O B:ASP105 3.0 32.4 1.0 O B:GLU196 3.0 34.7 1.0 OD1 B:ASN37 3.0 39.3 1.0 O B:ILE38 3.0 37.7 1.0 O B:HOH873 3.1 36.5 1.0 O B:HOH708 3.1 41.8 1.0 N B:ILE38 3.7 37.1 1.0 C B:ASP105 3.8 32.6 1.0 CA B:ASP105 3.8 36.2 1.0 C B:ILE38 3.8 38.1 1.0 C B:GLU196 3.9 38.4 1.0 CG B:ASN37 4.0 39.0 1.0 CB B:ASP105 4.2 37.2 1.0 CA B:ILE38 4.3 35.8 1.0 O B:HOH827 4.4 35.6 1.0 CD B:PRO40 4.4 31.9 1.0 CA B:GLU196 4.5 32.6 1.0 C B:ASN37 4.5 39.0 1.0 CD1 B:ILE46 4.5 38.2 1.0 OE1 B:GLU196 4.7 39.7 1.0 CA B:ASN37 4.7 35.5 1.0 ND2 B:ASN37 4.7 33.8 1.0 CG B:ASP105 4.7 41.5 1.0 N B:ASN39 4.8 33.9 1.0 O B:ILE345 4.8 29.8 1.0 CD1 B:ILE345 4.8 36.4 1.0 N B:SER197 4.9 30.2 1.0 O B:HOH775 4.9 37.0 1.0 OD1 B:ASP105 5.0 46.5 1.0 CB B:ASN37 5.0 39.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of 2-Hydroxymuconate-6-Semialdehyde Derived Tautomeric Intermediate in 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D


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-Hydroxymuconate-6-Semialdehyde Derived Tautomeric Intermediate in 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D within 5.0Å range: probe atom residue distance (Å) B Occ C:Na602 b:35.8 occ:1.00 O C:GLU196 2.9 31.4 1.0 O C:ILE38 3.0 35.2 1.0 OD1 C:ASN37 3.0 32.4 1.0 O C:ASP105 3.1 30.8 1.0 O C:HOH702 3.1 38.9 1.0 O C:HOH829 3.2 37.2 1.0 N C:ILE38 3.7 34.6 1.0 C C:ILE38 3.8 37.4 1.0 O C:HOH731 3.9 30.9 1.0 C C:GLU196 3.9 38.9 1.0 C C:ASP105 4.0 34.5 1.0 CA C:ASP105 4.1 33.9 1.0 CG C:ASN37 4.2 38.4 1.0 CA C:ILE38 4.3 37.1 1.0 CA C:GLU196 4.4 36.3 1.0 CB C:ASP105 4.4 39.2 1.0 C C:ASN37 4.4 36.3 1.0 OE1 C:GLU196 4.6 40.6 1.0 CD1 C:ILE46 4.6 38.5 1.0 CD C:PRO40 4.6 34.1 1.0 CA C:ASN37 4.7 34.1 1.0 O C:ILE345 4.8 30.5 1.0 N C:ASN39 4.8 34.1 1.0 O C:HOH721 4.8 37.3 1.0 CG C:ASP105 4.9 40.1 1.0 CB C:GLU196 4.9 32.6 1.0 CB C:ILE38 5.0 33.0 1.0 CD1 C:ILE345 5.0 31.4 1.0 N C:SER197 5.0 29.0 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of 2-Hydroxymuconate-6-Semialdehyde Derived Tautomeric Intermediate in 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D


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 2-Hydroxymuconate-6-Semialdehyde Derived Tautomeric Intermediate in 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:39.1 occ:1.00 O D:GLU196 3.0 36.8 1.0 OD1 D:ASN37 3.1 43.5 1.0 O D:ILE38 3.1 46.2 1.0 O D:HOH705 3.1 49.2 1.0 O D:ASP105 3.2 38.2 1.0 N D:ILE38 3.5 41.2 1.0 C D:ILE38 3.7 42.9 1.0 C D:GLU196 3.9 44.7 1.0 C D:ASP105 4.1 37.0 1.0 CA D:ILE38 4.2 41.6 1.0 O D:HOH790 4.2 41.1 1.0 CG D:ASN37 4.2 45.1 1.0 CA D:GLU196 4.2 42.5 1.0 CA D:ASP105 4.3 39.7 1.0 C D:ASN37 4.3 42.3 1.0 CA D:ASN37 4.5 40.4 1.0 CD1 D:ILE46 4.6 41.2 1.0 CB D:ASP105 4.6 39.2 1.0 OE1 D:GLU196 4.7 44.8 1.0 CD D:PRO40 4.7 38.3 1.0 N D:ASN39 4.7 35.9 1.0 CB D:GLU196 4.8 37.6 1.0 CB D:ILE38 4.8 45.8 1.0 O D:ILE345 4.9 34.3 1.0 CB D:ASN37 5.0 42.0 1.0

Y.Yang, A.Liu. Crystal Structure of 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D in Complex with Nad+, 5 Min After Soaking with Alternative Substrate To Be Published.