Sodium in PDB 7og3: Ired-88

The structure of Ired-88, PDB code: 7og3 was solved by M.Faller, E.Koch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.72 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.856, 75.746, 97.081, 90, 90, 90
R / Rfree (%)	20.6 / 23.2

The binding sites of Sodium atom in the Ired-88 (pdb code 7og3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ired-88, PDB code: 7og3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ired-88


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ired-88 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:22.0 occ:1.00 O A:GLY126 2.3 19.0 1.0 O A:ASN102 2.4 23.2 1.0 OD1 A:ASP125 2.4 23.5 1.0 OH A:TYR79 2.5 26.4 1.0 O A:ASN100 2.5 20.7 1.0 CG A:ASP125 3.2 25.7 1.0 C A:GLY126 3.4 19.1 1.0 CG1 A:VAL175 3.5 21.6 1.0 OD2 A:ASP125 3.5 26.3 1.0 C A:ASN102 3.5 22.7 1.0 N A:ASN102 3.5 21.6 1.0 N A:GLY126 3.6 22.4 1.0 C A:ASN100 3.6 20.1 1.0 CZ A:TYR79 3.7 26.7 1.0 C A:LEU101 3.8 21.6 1.0 OD1 A:ASN100 4.0 23.3 1.0 CA A:ASN102 4.0 22.7 1.0 CA A:LEU101 4.1 19.5 1.0 CA A:GLY126 4.1 21.2 1.0 N A:LEU101 4.2 19.5 1.0 CE1 A:TYR79 4.3 26.2 1.0 CG A:ASN100 4.3 23.9 1.0 CB A:ASP125 4.4 24.9 1.0 O A:LEU101 4.4 22.6 1.0 CB A:ASN102 4.5 24.2 1.0 C A:ASP125 4.5 23.5 1.0 CB A:ASN100 4.5 21.5 1.0 N A:ALA127 4.5 19.0 1.0 CA A:ASP125 4.6 24.2 1.0 N A:SER103 4.6 21.5 1.0 O A:HOH661 4.6 24.2 1.0 CA A:ASN100 4.6 20.3 1.0 CE2 A:TYR79 4.8 26.4 1.0 CA A:ALA127 4.8 19.0 1.0 CA A:SER103 4.9 22.1 1.0 CB A:VAL175 5.0 21.2 1.0

Sodium binding site 2 out of 2 in the Ired-88


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ired-88 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:19.6 occ:1.00 O B:GLY126 2.3 22.7 1.0 O B:ASN102 2.3 24.2 1.0 OD1 B:ASP125 2.4 23.3 1.0 OH B:TYR79 2.4 29.4 1.0 O B:ASN100 2.6 22.7 1.0 CG B:ASP125 3.2 25.3 1.0 C B:GLY126 3.4 23.1 1.0 OD2 B:ASP125 3.5 26.9 1.0 CG1 B:VAL175 3.5 20.6 1.0 C B:ASN102 3.5 23.9 1.0 N B:ASN102 3.6 22.1 1.0 N B:GLY126 3.6 23.5 1.0 C B:ASN100 3.7 21.4 1.0 CZ B:TYR79 3.7 27.7 1.0 C B:LEU101 3.9 22.0 1.0 OD1 B:ASN100 4.1 23.3 1.0 CA B:ASN102 4.1 23.8 1.0 CA B:LEU101 4.1 21.8 1.0 CA B:GLY126 4.1 23.8 1.0 CE1 B:TYR79 4.2 26.3 1.0 N B:LEU101 4.3 21.0 1.0 CG B:ASN100 4.4 23.3 1.0 CB B:ASP125 4.4 24.8 1.0 O B:LEU101 4.4 22.5 1.0 N B:ALA127 4.5 23.1 1.0 C B:ASP125 4.5 24.5 1.0 CB B:ASN102 4.5 27.3 1.0 CB B:ASN100 4.5 19.5 1.0 N B:SER103 4.6 23.4 1.0 CA B:ASP125 4.6 25.1 1.0 CA B:ASN100 4.7 20.4 1.0 CE2 B:TYR79 4.7 26.1 1.0 CA B:ALA127 4.8 23.0 1.0 O B:HOH616 4.8 19.0 1.0 CA B:SER103 4.9 23.5 1.0 CB B:VAL175 5.0 19.6 1.0

E.J.Ma, E.Siirola, C.Moore, A.Kummer, M.Stoeckli, M.Faller, C.Bouquet, F.Eggimann, M.Ligibel, D.Huynh, G.Cutler, L.Siegrist, R.A.Lewis, A.C.Acker, E.Freund, E.Koch, M.Vogel, H.Schlingensiepen, E.J.Oakeley, R.Snajdrova. Machine-Directed Evolution of An Imine Reductase For Activity and Stereoselectivity Acs Catalysis 12433 2021.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.1C02786