Sodium in PDB 6utn: Native E. Coli Glyceraldehyde 3-Phosphate Dehydrogenase

The structure of Native E. Coli Glyceraldehyde 3-Phosphate Dehydrogenase, PDB code: 6utn was solved by A.Rodriguez-Hernandez, E.Romo-Arevalo, A.Rodriguez-Romero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.84 / 1.79
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	77.673, 187.353, 121.673, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 19.9

The binding sites of Sodium atom in the Native E. Coli Glyceraldehyde 3-Phosphate Dehydrogenase (pdb code 6utn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Native E. Coli Glyceraldehyde 3-Phosphate Dehydrogenase, PDB code: 6utn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Native E. Coli Glyceraldehyde 3-Phosphate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Native E. Coli Glyceraldehyde 3-Phosphate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:32.6 occ:1.00 O A:HOH739 2.3 50.5 1.0 O A:ILE26 2.3 21.5 1.0 O A:ARG23 2.3 34.3 1.0 O A:ALA20 2.5 22.3 1.0 O A:HOH708 2.6 46.4 1.0 O A:HOH580 2.8 35.2 1.0 C A:ARG23 3.5 31.2 1.0 C A:ILE26 3.5 23.9 1.0 C A:ALA20 3.6 22.7 1.0 O A:HOH650 3.9 27.0 1.0 N A:ARG23 4.1 29.0 1.0 O A:GLN21 4.2 30.4 1.0 CA A:GLU27 4.2 27.6 1.0 C A:GLN21 4.2 27.0 1.0 CA A:GLN21 4.2 26.3 1.0 CA A:ARG23 4.2 29.2 1.0 N A:GLU27 4.3 24.6 1.0 N A:GLN21 4.4 23.6 1.0 N A:ILE26 4.5 24.0 1.0 CB A:ARG23 4.5 28.3 1.0 N A:SER24 4.5 30.1 1.0 CA A:ILE26 4.6 23.5 1.0 CA A:ALA20 4.6 20.6 1.0 CA A:SER24 4.7 33.8 1.0 CB A:GLU27 4.8 33.7 1.0 C A:SER24 4.8 33.8 1.0 CB A:ALA20 4.8 21.1 1.0 N A:LYS22 4.8 26.7 1.0 O A:SER24 4.9 35.1 1.0

Sodium binding site 2 out of 2 in the Native E. Coli Glyceraldehyde 3-Phosphate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Native E. Coli Glyceraldehyde 3-Phosphate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:26.5 occ:1.00 O B:ARG23 2.3 32.7 1.0 O B:HOH741 2.3 44.1 1.0 O B:ILE26 2.3 23.6 1.0 O B:ALA20 2.4 20.5 1.0 O B:HOH712 2.7 41.4 1.0 O B:HOH670 3.0 42.4 1.0 C B:ARG23 3.5 31.0 1.0 C B:ILE26 3.5 25.1 1.0 C B:ALA20 3.6 20.0 1.0 O B:HOH596 4.0 36.3 1.0 N B:ARG23 4.2 29.5 1.0 CA B:GLN21 4.2 22.4 1.0 O B:GLN21 4.2 29.6 1.0 C B:GLN21 4.2 25.6 1.0 CA B:GLU27 4.3 27.6 1.0 N B:GLU27 4.3 25.8 1.0 CA B:ARG23 4.3 29.8 0.3 CA B:ARG23 4.3 29.8 0.7 N B:GLN21 4.3 20.5 1.0 N B:SER24 4.5 30.1 1.0 N B:ILE26 4.5 25.7 1.0 CA B:SER24 4.5 32.7 1.0 CA B:ALA20 4.6 16.0 1.0 CA B:ILE26 4.6 24.5 1.0 CB B:ARG23 4.6 29.3 0.3 CB B:ARG23 4.7 29.0 0.7 C B:SER24 4.7 33.0 1.0 CB B:ALA20 4.8 17.2 1.0 O B:SER24 4.9 35.8 1.0 N B:LYS22 4.9 25.1 1.0 CB B:GLU27 5.0 34.2 1.0

A.Rodriguez-Hernandez, E.Romo-Arevalo, A.Rodriguez-Romero. A Novel Substrate-Binding Site in the X-Ray Structure of An Oxidized E. Coli Glyceraldehyde 3-Phosphate Dehydrogenase Elucidated By Single-Wavelength Anomalous Dispersion Crystals V. 9 622 2019.
ISSN: ESSN 2073-4352
DOI: 10.3390/CRYST9120622