Sodium in PDB 8q57: Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions

The structure of Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions, PDB code: 8q57 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)	61.01 / 1.70
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.734, 87.525, 104.312, 90, 107.73, 90
R / Rfree (%)	18.5 / 20.5

The structure of Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions (pdb code 8q57). 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 Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions, PDB code: 8q57:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions


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 Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:44.2 occ:1.00 O A:GLY181 2.6 38.8 1.0 O2 A:SO4302 2.8 36.1 1.0 O A:ALA179 2.8 32.3 1.0 O A:SER211 2.9 29.9 1.0 O A:GLY209 3.3 30.5 1.0 CE2 A:TYR183 3.4 37.1 1.0 O3 A:SO4302 3.4 43.0 1.0 N A:GLY181 3.5 33.2 1.0 CZ A:TYR183 3.6 41.6 1.0 C A:GLY181 3.7 42.9 1.0 C A:GLY209 3.7 27.0 1.0 S A:SO4302 3.7 34.2 1.0 CB A:SER211 3.8 31.3 1.0 C A:SER211 3.8 28.1 1.0 OH A:TYR183 3.8 36.8 1.0 CA A:GLY209 3.8 28.1 1.0 N A:SER211 3.9 26.8 1.0 CD2 A:TYR183 3.9 39.9 1.0 C A:ALA179 4.0 29.1 1.0 CA A:SER211 4.0 29.7 1.0 C A:HIS180 4.0 32.6 1.0 CA A:HIS180 4.2 29.3 0.5 CA A:HIS180 4.2 32.0 0.5 CA A:GLY181 4.2 35.8 1.0 CE1 A:TYR183 4.4 36.1 1.0 N A:HIS180 4.6 30.7 1.0 O4 A:SO4302 4.6 30.1 1.0 N A:GLY210 4.6 24.4 1.0 CG2 A:THR141 4.6 57.5 1.0 CG A:TYR183 4.7 38.9 1.0 O1 A:SO4302 4.7 33.5 1.0 C A:GLY210 4.7 27.3 1.0 OG A:SER211 4.7 28.8 1.0 CD1 A:TYR183 4.8 40.9 1.0 N A:MET182 4.9 39.5 1.0 O A:HIS180 5.0 39.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions


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 Class II Sfp Aldolase From Yersinia Aldovae (Yasqia-Zn-SO4) with Bound Sulfate Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:50.9 occ:1.00 O B:GLY181 2.7 38.5 1.0 O B:ALA179 2.8 42.4 1.0 O4 B:SO4301 2.8 41.3 1.0 O B:SER211 3.0 35.7 1.0 O B:GLY209 3.3 33.9 1.0 O2 B:SO4301 3.3 47.9 1.0 CE2 B:TYR183 3.4 43.2 1.0 N B:GLY181 3.5 35.5 1.0 C B:GLY209 3.6 34.9 1.0 CA B:GLY209 3.7 33.4 1.0 S B:SO4301 3.7 40.5 1.0 CZ B:TYR183 3.7 43.0 1.0 C B:GLY181 3.8 44.1 1.0 OH B:TYR183 3.9 37.8 1.0 C B:SER211 3.9 37.9 1.0 N B:SER211 3.9 33.7 1.0 C B:ALA179 3.9 40.4 1.0 CD2 B:TYR183 3.9 46.1 1.0 CB B:SER211 4.0 36.6 1.0 C B:HIS180 4.0 38.2 1.0 CA B:HIS180 4.1 43.6 0.5 CA B:HIS180 4.1 37.8 0.5 CA B:SER211 4.1 34.6 1.0 CA B:GLY181 4.3 35.9 1.0 N B:GLY210 4.5 32.6 1.0 CE1 B:TYR183 4.5 36.0 1.0 N B:HIS180 4.5 39.7 1.0 CG2 B:THR141 4.5 59.5 1.0 O3 B:SO4301 4.5 43.7 1.0 CG B:TYR183 4.7 38.5 1.0 C B:GLY210 4.7 38.4 1.0 O1 B:SO4301 4.8 35.7 1.0 OG B:SER211 4.9 27.9 1.0 O B:HIS180 4.9 37.1 1.0 CD1 B:TYR183 4.9 38.1 1.0 N B:MET182 5.0 43.2 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