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

The structure of Native E. Coli Glyceraldehyde 3-Phosphate Dehydrogenase, PDB code: 6utm 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)	46.74 / 2.14
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	77.912, 186.966, 121.751, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19.9

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

Sodium binding site 1 out of 3 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:Na402 b:42.5 occ:1.00 O A:ILE26 2.3 35.7 1.0 O A:ARG23 2.4 44.6 1.0 O A:ALA20 2.5 33.0 1.0 O A:HOH589 2.9 47.2 1.0 O A:HOH588 3.4 43.6 1.0 C A:ILE26 3.5 37.3 1.0 C A:ARG23 3.6 39.0 1.0 C A:ALA20 3.6 35.3 1.0 N A:ARG23 4.1 41.8 1.0 CA A:GLN21 4.1 38.0 1.0 CA A:GLU27 4.2 33.9 1.0 O A:GLN21 4.2 44.9 1.0 C A:GLN21 4.2 37.6 1.0 N A:GLU27 4.3 35.3 1.0 CA A:ARG23 4.3 37.4 1.0 N A:GLN21 4.3 36.1 1.0 CB A:ARG23 4.6 37.4 1.0 N A:SER24 4.6 40.0 1.0 N A:ILE26 4.6 37.5 1.0 CA A:ALA20 4.6 31.2 1.0 CA A:ILE26 4.6 34.0 1.0 CA A:SER24 4.7 42.7 1.0 CB A:ALA20 4.8 26.9 1.0 CB A:GLU27 4.8 38.7 1.0 N A:LYS22 4.9 35.8 1.0

Sodium binding site 2 out of 3 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 A:Na403 b:47.7 occ:1.00 OE2 A:GLU76 2.4 43.9 1.0 O A:HOH551 3.0 49.0 1.0 ND2 A:ASN81 3.0 44.4 1.0 N A:ASP78 3.1 39.7 1.0 N A:ARG77 3.3 32.7 1.0 CB A:ASP78 3.5 41.9 1.0 CD A:GLU76 3.5 48.4 1.0 CB A:GLU76 3.5 38.0 1.0 CA A:GLU76 3.7 37.0 1.0 O A:ASP78 3.8 38.2 1.0 CA A:ASP78 3.8 35.3 1.0 C A:GLU76 3.8 37.3 1.0 CG A:ASN81 4.0 44.2 1.0 CB A:ASN81 4.0 38.9 1.0 C A:ARG77 4.0 42.0 1.0 CG A:GLU76 4.1 42.9 1.0 CA A:ARG77 4.1 41.1 1.0 C A:ASP78 4.2 36.3 1.0 CB A:ARG77 4.5 38.8 1.0 OE1 A:GLU76 4.6 54.3 1.0 O A:GLU76 4.8 33.1 1.0 CG A:ASP78 4.9 50.2 1.0

Sodium binding site 3 out of 3 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 3 of Native E. Coli Glyceraldehyde 3-Phosphate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na804 b:37.5 occ:1.00 O B:ILE26 2.2 34.4 1.0 O B:ARG23 2.3 41.1 1.0 O B:HOH1061 2.3 45.1 1.0 O B:ALA20 2.3 33.3 1.0 O B:HOH938 2.8 48.8 1.0 O B:HOH1046 2.9 48.4 1.0 C B:ILE26 3.4 34.0 1.0 C B:ALA20 3.4 34.9 1.0 C B:ARG23 3.5 38.6 1.0 O B:HOH980 3.7 47.8 1.0 N B:ARG23 4.1 37.0 1.0 CA B:GLU27 4.1 36.6 1.0 CA B:GLN21 4.2 37.3 1.0 N B:GLU27 4.2 31.5 1.0 N B:GLN21 4.2 30.8 1.0 CA B:ARG23 4.2 41.0 1.0 C B:GLN21 4.3 34.6 1.0 O B:GLN21 4.3 39.5 1.0 CA B:ALA20 4.4 26.6 1.0 N B:SER24 4.5 37.9 1.0 N B:ILE26 4.5 33.9 1.0 CB B:ARG23 4.5 40.4 1.0 CA B:ILE26 4.5 33.1 1.0 CB B:ALA20 4.6 20.9 1.0 CA B:SER24 4.6 42.2 1.0 CB B:GLU27 4.9 37.3 1.0 N B:LYS22 4.9 32.5 1.0 C B:SER24 4.9 38.0 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