Sodium in PDB 1gvf: Structure of Tagatose-1,6-Bisphosphate Aldolase

All present enzymatic activity of Structure of Tagatose-1,6-Bisphosphate Aldolase:
4.1.2.40;

The structure of Structure of Tagatose-1,6-Bisphosphate Aldolase, PDB code: 1gvf was solved by D.R.Hall, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.45
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	72.650, 100.460, 206.660, 90.00, 90.00, 90.00
R / Rfree (%)	13.1 / 17.3

The structure of Structure of Tagatose-1,6-Bisphosphate Aldolase also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Structure of Tagatose-1,6-Bisphosphate Aldolase (pdb code 1gvf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Tagatose-1,6-Bisphosphate Aldolase, PDB code: 1gvf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Tagatose-1,6-Bisphosphate Aldolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Tagatose-1,6-Bisphosphate Aldolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na289 b:15.7 occ:1.00 O4P A:PGH287 2.3 18.4 1.0 O A:GLY181 2.3 18.2 1.0 O A:ALA179 2.4 15.3 1.0 O A:GLY209 2.6 13.7 1.0 O A:SER211 2.6 15.1 1.0 C A:GLY209 3.2 13.2 1.0 N A:GLY181 3.4 15.1 1.0 C A:GLY181 3.4 18.2 1.0 CE1 A:TYR183 3.5 18.7 1.0 CA A:GLY209 3.6 12.7 1.0 C A:ALA179 3.6 14.0 1.0 C A:SER211 3.6 13.6 1.0 OH A:TYR183 3.6 15.7 1.0 N A:SER211 3.7 13.5 1.0 CZ A:TYR183 3.7 17.0 1.0 C A:HIS180 3.8 15.6 1.0 P A:PGH287 3.8 14.7 1.0 CA A:GLY181 3.9 17.0 1.0 CB A:SER211 3.9 14.2 1.0 CA A:SER211 4.0 14.0 1.0 CA A:HIS180 4.0 15.1 1.0 N A:ALA210 4.1 13.1 1.0 N A:HIS180 4.3 15.2 1.0 C A:ALA210 4.3 12.9 1.0 CD1 A:TYR183 4.3 19.4 1.0 O A:HIS180 4.5 17.6 1.0 O2P A:PGH287 4.5 26.6 1.0 O3P A:PGH287 4.6 19.7 1.0 N A:LEU182 4.6 18.4 1.0 O1P A:PGH287 4.6 15.7 1.0 CA A:ALA210 4.6 13.2 1.0 CE2 A:TYR183 4.7 16.9 1.0 CA A:ALA179 4.8 16.1 1.0 N A:ASP212 4.8 16.0 1.0 N A:ALA179 4.8 15.6 1.0 N A:GLY209 5.0 11.9 1.0 OG A:SER211 5.0 13.7 1.0

Sodium binding site 2 out of 2 in the Structure of Tagatose-1,6-Bisphosphate Aldolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Tagatose-1,6-Bisphosphate Aldolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na289 b:16.3 occ:1.00 O B:GLY181 2.3 17.5 1.0 O3P B:PGH287 2.4 16.8 1.0 O B:ALA179 2.5 15.0 1.0 O B:SER211 2.6 16.4 1.0 O B:GLY209 2.6 15.3 1.0 C B:GLY209 3.2 15.0 1.0 C B:GLY181 3.4 18.1 1.0 N B:GLY181 3.4 17.2 1.0 CE2 B:TYR183 3.5 16.9 1.0 C B:SER211 3.6 16.7 1.0 CA B:GLY209 3.6 12.5 1.0 C B:ALA179 3.7 15.2 1.0 OH B:TYR183 3.7 16.3 1.0 N B:SER211 3.7 14.8 1.0 C B:HIS180 3.7 15.1 1.0 CZ B:TYR183 3.8 15.6 1.0 P B:PGH287 3.8 15.0 1.0 CB B:SER211 3.9 13.9 1.0 CA B:GLY181 3.9 16.2 1.0 CA B:SER211 4.0 15.5 1.0 CA B:HIS180 4.0 15.3 1.0 N B:ALA210 4.1 14.1 1.0 C B:ALA210 4.3 14.6 1.0 CD2 B:TYR183 4.3 17.5 1.0 N B:HIS180 4.3 16.6 1.0 O B:HIS180 4.5 17.8 1.0 O2P B:PGH287 4.5 19.9 1.0 N B:LEU182 4.5 19.8 1.0 O4P B:PGH287 4.6 24.5 1.0 O1P B:PGH287 4.6 15.2 1.0 CA B:ALA210 4.6 14.2 1.0 CE1 B:TYR183 4.8 17.9 1.0 N B:ASP212 4.8 16.9 1.0 CA B:ALA179 4.8 15.4 1.0 N B:ALA179 4.9 16.5 1.0 CA B:LEU182 4.9 19.4 1.0 CB B:ASP212 4.9 20.3 1.0 OG B:SER211 5.0 14.2 1.0

D.R.Hall, C.S.Bond, G.A.Leonard, C.I.Watt, A.Berry, W.N.Hunter. Structure of Tagatose-1,6-Bisphosphate Aldolase; Insight Into Chiral Discrimination, Mechanism and Specificity of Class II Aldolases J.Biol.Chem. V. 277 22018 2002.
ISSN: ISSN 0021-9258
PubMed: 11940603
DOI: 10.1074/JBC.M202464200