Sodium in PDB 8q59: Crystal Structure of Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp)

The structure of Crystal Structure of Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp), PDB code: 8q59 was solved by M.Sharma, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.637, 87.739, 91.008, 90, 110.66, 90
R / Rfree (%)	18.7 / 21.2

The structure of Crystal Structure of Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp) also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp) (pdb code 8q59). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp), PDB code: 8q59:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp)


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 Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:50.8 occ:1.00 O3 A:JP9303 2.6 41.2 0.9 O A:SER211 2.7 36.3 1.0 O A:GLY181 2.8 39.2 1.0 O A:GLY209 3.0 37.3 1.0 O A:ALA179 3.0 33.6 1.0 CE2 A:TYR183 3.2 45.2 1.0 C A:GLY209 3.4 31.1 1.0 C A:SER211 3.6 39.5 1.0 CZ A:TYR183 3.6 39.6 1.0 N A:SER211 3.6 33.6 1.0 O4 A:JP9303 3.7 43.9 0.9 CA A:GLY209 3.7 30.5 1.0 N A:GLY181 3.7 37.7 1.0 P1 A:JP9303 3.8 33.9 0.9 CB A:SER211 3.8 34.8 1.0 OH A:TYR183 3.8 39.9 1.0 CD2 A:TYR183 3.8 42.9 1.0 CA A:SER211 3.8 35.0 1.0 C A:GLY181 3.9 41.0 1.0 C A:ALA179 4.2 33.2 1.0 C A:HIS180 4.3 43.1 1.0 N A:GLY210 4.3 32.8 1.0 CA A:HIS180 4.4 37.9 1.0 CA A:GLY181 4.4 39.5 1.0 C A:GLY210 4.4 38.4 1.0 CE1 A:TYR183 4.5 34.8 1.0 CG A:TYR183 4.6 44.1 1.0 O2 A:JP9303 4.7 37.8 0.9 OG A:SER211 4.8 30.3 1.0 N A:HIS180 4.8 32.7 1.0 N A:GLY212 4.8 38.7 1.0 O5 A:JP9303 4.8 39.0 0.9 CD1 A:TYR183 4.9 39.6 1.0 CA A:GLY210 4.9 32.5 1.0 CG2 A:THR141 5.0 63.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp)


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 Metal-Dependent Class II Sulfofructose Phosphate Aldolase From Yersinia Aldovae in Complex with Sulfofructose Phosphate (Yasqia-Zn-Sfp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:58.9 occ:1.00 O B:ALA179 2.7 37.1 1.0 O3 B:JP9303 2.7 43.7 0.8 O B:GLY181 2.7 44.1 1.0 O B:SER211 3.0 43.8 1.0 O B:GLY209 3.1 45.9 1.0 CE2 B:TYR183 3.3 39.1 1.0 C B:GLY209 3.5 44.5 1.0 N B:GLY181 3.6 41.4 1.0 O4 B:JP9303 3.6 42.9 0.8 CZ B:TYR183 3.6 38.5 1.0 CA B:GLY209 3.6 44.0 1.0 P1 B:JP9303 3.8 33.8 0.8 OH B:TYR183 3.8 42.8 1.0 C B:GLY181 3.8 45.8 1.0 C B:ALA179 3.9 39.6 1.0 CD2 B:TYR183 3.9 40.5 1.0 C B:SER211 3.9 43.1 1.0 N B:SER211 3.9 36.3 1.0 CB B:SER211 3.9 41.9 1.0 C B:HIS180 4.0 43.6 1.0 CA B:SER211 4.1 44.6 1.0 CA B:HIS180 4.1 42.4 1.0 CA B:GLY181 4.3 42.0 1.0 CE1 B:TYR183 4.4 43.6 1.0 N B:GLY210 4.4 42.6 1.0 N B:HIS180 4.5 38.7 1.0 CG B:TYR183 4.6 41.8 1.0 O2 B:JP9303 4.6 34.9 0.8 C B:GLY210 4.7 43.6 1.0 CG2 B:THR141 4.7 61.0 1.0 CD1 B:TYR183 4.8 43.0 1.0 O5 B:JP9303 4.8 37.5 0.8 OG B:SER211 4.9 44.8 1.0 O B:HIS180 4.9 43.5 1.0 N B:ALA179 5.0 41.5 1.0

M.Sharma, A.Kaur, N.M.Soler, J.P.Lingford, R.Epa, E.D.Goddard-Borger, G.J.Davies, S.J.Williams. Defining the Molecular Architecture, Metal Dependence, and Distribution of Metal-Dependent Class II Sulfofructose-1-Phosphate Aldolases. J.Biol.Chem. 05338 2023.
ISSN: ESSN 1083-351X
PubMed: 37838169
DOI: 10.1016/J.JBC.2023.105338