Sodium in PDB 4xb1: Hyperthermophilic Archaeal Homoserine Dehydrogenase in Complex with Nadph

The structure of Hyperthermophilic Archaeal Homoserine Dehydrogenase in Complex with Nadph, PDB code: 4xb1 was solved by H.Sakuraba, S.Inoue, K.Yoneda, T.Ohshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.30
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	112.560, 112.560, 95.885, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.5

The binding sites of Sodium atom in the Hyperthermophilic Archaeal Homoserine Dehydrogenase in Complex with Nadph (pdb code 4xb1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hyperthermophilic Archaeal Homoserine Dehydrogenase in Complex with Nadph, PDB code: 4xb1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hyperthermophilic Archaeal Homoserine Dehydrogenase in Complex with Nadph


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hyperthermophilic Archaeal Homoserine Dehydrogenase in Complex with Nadph within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1002 b:19.9 occ:1.00 O A:VAL143 2.3 30.3 1.0 O A:ALA145 2.4 34.0 1.0 O A:THR147 2.4 22.7 1.0 OE1 A:GLU140 2.5 25.9 1.0 O A:GLU140 2.6 29.3 1.0 C A:ALA145 3.4 27.1 1.0 CD A:GLU140 3.4 32.1 1.0 C A:VAL143 3.5 25.4 1.0 C A:GLU140 3.5 29.0 1.0 C A:THR147 3.6 24.2 1.0 C A:MET144 3.6 26.9 1.0 CG A:GLU140 3.6 26.7 1.0 N A:ALA145 3.7 30.3 1.0 O A:MET144 3.7 30.3 1.0 CG2 A:ILE149 3.8 27.2 1.0 CA A:ALA145 4.0 29.3 1.0 N A:THR147 4.1 26.6 1.0 N A:ILE149 4.1 26.8 1.0 CA A:MET144 4.2 25.5 1.0 N A:MET144 4.2 24.3 1.0 CB A:MET144 4.2 27.7 1.0 N A:SER141 4.3 29.8 1.0 CA A:SER141 4.3 29.9 1.0 N A:GLY146 4.3 28.4 1.0 CA A:GLU140 4.4 27.8 1.0 C A:GLY146 4.4 29.0 1.0 CA A:PRO148 4.4 26.3 1.0 N A:VAL143 4.4 27.3 1.0 CA A:VAL143 4.5 28.1 1.0 CA A:THR147 4.5 29.3 1.0 N A:PRO148 4.5 23.8 1.0 N A:ILE150 4.5 27.2 1.0 OE2 A:GLU140 4.5 25.4 1.0 CB A:GLU140 4.6 27.5 1.0 CG1 A:ILE150 4.6 28.3 1.0 CA A:GLY146 4.6 29.9 1.0 C A:PRO148 4.7 26.0 1.0 CB A:ILE149 4.9 28.6 1.0 CB A:VAL143 4.9 31.1 1.0 CA A:ILE149 4.9 28.4 1.0 C A:SER141 4.9 26.4 1.0 O A:GLY146 5.0 24.6 1.0

Sodium binding site 2 out of 2 in the Hyperthermophilic Archaeal Homoserine Dehydrogenase in Complex with Nadph


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hyperthermophilic Archaeal Homoserine Dehydrogenase in Complex with Nadph within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1002 b:21.4 occ:1.00 O B:VAL143 2.2 29.6 1.0 O B:ALA145 2.4 37.5 1.0 O B:THR147 2.5 22.3 1.0 OE1 B:GLU140 2.5 26.8 1.0 O B:GLU140 2.6 34.3 1.0 C B:ALA145 3.4 33.8 1.0 CD B:GLU140 3.4 32.5 1.0 C B:VAL143 3.4 30.9 1.0 C B:GLU140 3.5 31.5 1.0 C B:MET144 3.6 28.4 1.0 O B:MET144 3.6 30.0 1.0 CG B:GLU140 3.6 32.3 1.0 C B:THR147 3.6 26.1 1.0 N B:ALA145 3.7 32.3 1.0 CG2 B:ILE149 3.8 29.4 1.0 N B:THR147 4.1 28.4 1.0 CA B:ALA145 4.1 32.1 1.0 N B:ILE149 4.1 25.1 1.0 CA B:MET144 4.2 31.2 1.0 CB B:MET144 4.2 28.7 1.0 N B:MET144 4.2 27.9 1.0 N B:SER141 4.3 34.3 1.0 CA B:SER141 4.3 34.1 1.0 N B:GLY146 4.3 30.9 1.0 CA B:GLU140 4.3 30.0 1.0 N B:VAL143 4.4 32.1 1.0 C B:GLY146 4.4 33.5 1.0 CA B:PRO148 4.4 26.8 1.0 CA B:VAL143 4.5 32.6 1.0 OE2 B:GLU140 4.5 26.7 1.0 N B:PRO148 4.5 24.6 1.0 CA B:THR147 4.5 29.7 1.0 CG1 B:ILE150 4.5 29.8 1.0 N B:ILE150 4.5 32.2 1.0 CB B:GLU140 4.6 28.5 1.0 CA B:GLY146 4.6 30.4 1.0 C B:PRO148 4.7 27.0 1.0 CB B:ILE149 4.9 25.9 1.0 C B:SER141 4.9 32.9 1.0 CB B:VAL143 4.9 33.3 1.0 CA B:ILE149 5.0 28.1 1.0

J.Hayashi, S.Inoue, K.Kim, K.Yoneda, Y.Kawarabayasi, T.Ohshima, H.Sakuraba. Crystal Structures of A Hyperthermophilic Archaeal Homoserine Dehydrogenase Suggest A Novel Cofactor Binding Mode For Oxidoreductases Sci Rep V. 5 11674 2015.
ISSN: ESSN 2045-2322
DOI: 10.1038/SREP11674