Sodium in PDB 5klm: Crystal Structure of 2-Hydroxymuconate-6-Semialdehyde Derived Intermediate in Nad(+)-Bound 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D

The structure of Crystal Structure of 2-Hydroxymuconate-6-Semialdehyde Derived Intermediate in Nad(+)-Bound 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D, PDB code: 5klm 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)	45.62 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.378, 141.958, 171.604, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23

The binding sites of Sodium atom in the Crystal Structure of 2-Hydroxymuconate-6-Semialdehyde Derived Intermediate in Nad(+)-Bound 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D (pdb code 5klm). 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 Intermediate in Nad(+)-Bound 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D, PDB code: 5klm:
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 Intermediate in Nad(+)-Bound 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 Intermediate in Nad(+)-Bound 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:41.5 occ:1.00 O A:GLU196 2.9 38.0 1.0 O A:ILE38 2.9 42.9 1.0 OD1 A:ASN37 2.9 41.1 1.0 O A:ASP105 3.0 36.3 1.0 O A:HOH709 3.1 49.5 1.0 O A:HOH823 3.2 48.1 1.0 C A:ILE38 3.8 44.5 1.0 N A:ILE38 3.8 45.7 1.0 C A:ASP105 3.8 36.3 1.0 C A:GLU196 3.9 42.2 1.0 CA A:ASP105 3.9 38.9 1.0 CG A:ASN37 4.1 43.6 1.0 O A:HOH727 4.1 43.4 1.0 CA A:ILE38 4.3 40.6 1.0 CB A:ASP105 4.3 41.0 1.0 CA A:GLU196 4.4 39.0 1.0 CD A:PRO40 4.4 35.2 1.0 C A:ASN37 4.5 43.4 1.0 CD1 A:ILE46 4.5 45.6 1.0 OE1 A:GLU196 4.7 44.7 1.0 N A:ASN39 4.7 42.1 1.0 CA A:ASN37 4.7 46.4 1.0 O A:ILE345 4.8 36.3 1.0 ND2 A:ASN37 4.8 43.8 1.0 CG A:ASP105 4.9 41.5 1.0 CB A:GLU196 4.9 35.8 1.0 CD1 A:ILE345 5.0 34.1 1.0 CA A:ASN39 5.0 39.8 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of 2-Hydroxymuconate-6-Semialdehyde Derived Intermediate in Nad(+)-Bound 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 Intermediate in Nad(+)-Bound 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:48.5 occ:1.00 OD1 B:ASN37 2.9 48.8 1.0 O B:ASP105 3.0 45.4 1.0 O B:GLU196 3.0 46.3 1.0 O B:ILE38 3.1 52.5 1.0 O B:HOH705 3.1 52.0 1.0 O B:HOH830 3.2 52.1 1.0 N B:ILE38 3.6 50.4 1.0 C B:ILE38 3.7 52.2 1.0 C B:ASP105 3.8 45.9 1.0 CA B:ASP105 3.9 48.2 1.0 C B:GLU196 4.0 50.2 1.0 CG B:ASN37 4.1 52.8 1.0 CA B:ILE38 4.2 49.3 1.0 O B:HOH732 4.3 49.4 1.0 CD1 B:ILE46 4.3 54.9 1.0 C B:ASN37 4.4 50.8 1.0 CB B:ASP105 4.4 45.7 1.0 CA B:GLU196 4.5 46.6 1.0 CD B:PRO40 4.6 46.6 1.0 CA B:ASN37 4.6 49.6 1.0 N B:ASN39 4.7 48.0 1.0 OE1 B:GLU196 4.7 49.5 1.0 O B:ILE345 4.8 37.8 1.0 CG B:ASP105 4.8 50.7 1.0 ND2 B:ASN37 4.9 52.0 1.0 CD1 B:ILE345 4.9 42.2 1.0 CB B:ILE38 4.9 51.2 1.0 OD1 B:ASP105 4.9 53.8 1.0 CB B:ASN37 5.0 48.8 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of 2-Hydroxymuconate-6-Semialdehyde Derived Intermediate in Nad(+)-Bound 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 Intermediate in Nad(+)-Bound 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D within 5.0Å range: probe atom residue distance (Å) B Occ C:Na602 b:44.8 occ:1.00 O C:GLU196 2.9 38.4 1.0 OD1 C:ASN37 3.0 43.0 1.0 O C:ILE38 3.0 50.8 1.0 O C:ASP105 3.1 39.4 1.0 O C:HOH701 3.2 50.0 1.0 O C:HOH737 3.3 48.6 1.0 N C:ILE38 3.6 44.9 1.0 C C:ILE38 3.7 51.7 1.0 C C:ASP105 3.9 40.5 1.0 C C:GLU196 4.0 44.5 1.0 CA C:ASP105 4.0 41.0 1.0 O C:HOH714 4.1 44.4 1.0 CG C:ASN37 4.1 48.0 1.0 CA C:ILE38 4.2 48.8 1.0 CB C:ASP105 4.4 44.4 1.0 C C:ASN37 4.4 50.0 1.0 CA C:GLU196 4.4 43.0 1.0 CD1 C:ILE46 4.6 49.6 1.0 CD C:PRO40 4.6 45.2 1.0 CA C:ASN37 4.7 47.4 1.0 N C:ASN39 4.7 43.2 1.0 OE1 C:GLU196 4.7 45.5 1.0 O C:HOH804 4.7 53.4 1.0 O C:ILE345 4.8 40.5 1.0 CG C:ASP105 4.8 48.4 1.0 CB C:GLU196 4.9 41.4 1.0 CD1 C:ILE345 4.9 38.7 1.0 CB C:ILE38 5.0 47.2 1.0 ND2 C:ASN37 5.0 46.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of 2-Hydroxymuconate-6-Semialdehyde Derived Intermediate in Nad(+)-Bound 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 Intermediate in Nad(+)-Bound 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:59.3 occ:1.00 O D:ILE38 3.1 60.6 1.0 OD1 D:ASN37 3.1 49.5 1.0 O D:HOH707 3.1 57.8 1.0 O D:GLU196 3.1 53.4 1.0 N D:ILE38 3.5 56.2 1.0 O D:ASP105 3.6 51.3 1.0 C D:GLU196 3.9 55.5 1.0 C D:ILE38 3.9 57.3 1.0 CA D:GLU196 4.0 50.2 1.0 OE1 D:GLU196 4.1 55.4 1.0 C D:ASN37 4.1 56.2 1.0 CA D:ILE38 4.1 57.8 1.0 CG D:ASN37 4.2 54.7 1.0 CA D:ASN37 4.3 51.3 1.0 CB D:ILE38 4.6 58.9 1.0 CB D:GLU196 4.6 47.9 1.0 C D:ASP105 4.6 50.8 1.0 O D:GLU195 4.8 56.9 1.0 CB D:ASN37 4.8 55.4 1.0 CA D:ASP105 4.9 51.3 1.0 O D:ILE345 4.9 47.7 1.0

Y.Yang, A.Liu. Crystal Structure of 2-Aminomuconate 6-Semialdehyde Dehydrogenase N169D in Complex with Nad+, 30 Min After Soaking with Alternative Substrate To Be Published.