Sodium in PDB 5ud1: Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori

All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori:
4.1.2.13;

The structure of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori, PDB code: 5ud1 was solved by B.Jacques, J.Sygusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.61 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.301, 64.207, 62.520, 81.37, 74.10, 75.94
R / Rfree (%)	21.3 / 26

The structure of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori (pdb code 5ud1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori, PDB code: 5ud1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:33.9 occ:1.00 NE2 A:HIS80 2.9 16.9 1.0 OE2 A:GLU132 2.9 18.9 1.0 OD1 A:ASP82 3.0 22.2 1.0 OE1 A:GLU132 3.2 21.4 1.0 CD A:GLU132 3.3 18.1 1.0 NZ A:LYS251 3.3 20.7 1.0 SD A:MET102 3.4 24.9 1.0 OE1 A:GLN47 3.4 22.6 1.0 ND2 A:ASN253 3.5 18.8 1.0 CB A:MET102 3.5 20.2 1.0 CG A:MET102 3.6 22.7 1.0 NE2 A:HIS210 3.7 36.9 1.0 CD2 A:HIS80 3.7 14.4 1.0 CE1 A:HIS80 3.9 17.1 1.0 CA A:ASP82 3.9 14.2 1.0 CG A:ASP82 4.0 21.9 1.0 N A:HIS83 4.1 16.0 0.4 N A:HIS83 4.1 15.8 0.6 CE1 A:HIS210 4.1 37.9 1.0 CD A:GLN47 4.4 17.6 1.0 CB A:ASP82 4.4 17.2 1.0 ND1 A:HIS83 4.4 21.5 0.4 O A:LEU81 4.4 13.8 1.0 CG A:ASN253 4.5 16.4 1.0 CE A:LYS251 4.5 20.4 1.0 C A:ASP82 4.5 16.0 1.0 CG A:GLU132 4.6 13.5 1.0 O A:HOH523 4.6 29.6 1.0 CD2 A:HIS210 4.6 37.5 1.0 OD1 A:ASN253 4.6 16.9 1.0 CE A:MET102 4.8 23.5 1.0 CE1 A:HIS83 4.8 22.1 0.4 NE2 A:GLN47 4.8 15.5 1.0 N A:ASP82 4.9 14.3 1.0 CG A:HIS80 4.9 16.1 1.0 CB A:GLU132 5.0 15.7 1.0 ND1 A:HIS80 5.0 14.6 1.0

Sodium binding site 2 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:25.9 occ:1.00 NE2 B:HIS80 2.9 21.8 1.0 OD1 B:ASP82 2.9 20.7 1.0 OE1 B:GLU132 3.1 23.4 1.0 SD B:MET102 3.1 32.8 1.0 NZ B:LYS251 3.2 22.7 1.0 OE2 B:GLU132 3.3 23.3 1.0 ND2 B:ASN253 3.4 22.4 1.0 CD B:GLU132 3.5 23.2 1.0 OE1 B:GLN47 3.5 27.2 1.0 NE2 B:HIS210 3.7 32.2 1.0 CB B:MET102 3.7 25.0 1.0 CG B:MET102 3.8 26.7 1.0 CD2 B:HIS80 3.8 20.2 1.0 CG B:ASP82 3.9 20.4 1.0 CE1 B:HIS80 3.9 22.3 1.0 CA B:ASP82 3.9 11.7 1.0 N B:HIS83 4.1 16.9 1.0 CB B:ASP82 4.3 13.0 1.0 CE B:LYS251 4.3 17.8 1.0 CG B:ASN253 4.4 18.4 1.0 CE1 B:HIS210 4.4 33.7 1.0 ND1 B:HIS83 4.4 25.7 1.0 CD B:GLN47 4.4 20.6 1.0 OD1 B:ASN253 4.4 14.9 1.0 CD2 B:HIS210 4.5 32.6 1.0 O B:LEU81 4.5 18.7 1.0 C B:ASP82 4.5 14.3 1.0 CE1 B:HIS83 4.7 26.9 1.0 NE2 B:GLN47 4.8 18.9 1.0 CE B:MET102 4.8 31.8 1.0 CG B:GLU132 4.8 21.6 1.0 OD2 B:ASP82 4.9 22.5 1.0 N B:ASP82 5.0 13.8 1.0

B.Jacques, M.Coincon, J.Sygusch. Active Site Remodeling During the Catalytic Cycle in Metal-Dependent Fructose-1,6-Bisphosphate Aldolases. J. Biol. Chem. V. 293 7737 2018.
ISSN: ESSN 1083-351X
PubMed: 29593097
DOI: 10.1074/JBC.RA117.001098