Sodium in PDB 5ud0: Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Cleavage Products

All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Cleavage Products:
4.1.2.13;

The structure of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Cleavage Products, PDB code: 5ud0 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)	29.88 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.258, 85.386, 91.082, 90.00, 100.20, 90.00
R / Rfree (%)	17.8 / 22.3

The structure of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Cleavage Products also contains other interesting chemical elements:

Zinc	(Zn)	3 atoms
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Cleavage Products (pdb code 5ud0). 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 E149A Variant of Helicobacter Pylori with Cleavage Products, PDB code: 5ud0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Cleavage Products


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 E149A Variant of Helicobacter Pylori with Cleavage Products within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:32.4 occ:1.00 HD21 A:ASN253 2.3 29.7 1.0 NE2 A:HIS80 2.8 25.6 1.0 HZ1 A:LYS251 2.9 22.6 1.0 OD1 A:ASP82 2.9 24.6 1.0 HA A:ASP82 3.0 16.8 1.0 OE2 A:GLU132 3.1 27.7 1.0 HZ2 A:LYS251 3.1 22.6 1.0 ND2 A:ASN253 3.2 24.7 1.0 HB2 A:MET102 3.4 27.5 1.0 HE2 A:HIS210 3.4 29.3 1.0 NZ A:LYS251 3.4 18.8 1.0 H A:HIS83 3.4 27.1 1.0 OE1 A:GLN47 3.4 29.7 1.0 OE1 A:GLU132 3.4 26.7 1.0 HD22 A:ASN253 3.5 29.7 1.0 CD A:GLU132 3.5 25.2 1.0 CD2 A:HIS80 3.6 18.2 1.0 HE1 A:HIS210 3.6 49.8 1.0 HD2 A:HIS80 3.6 21.8 1.0 SD A:MET102 3.7 26.4 1.0 HB3 A:MET102 3.7 27.5 1.0 NE2 A:HIS210 3.7 24.4 1.0 HG3 A:MET102 3.7 33.7 1.0 HZ3 A:LYS251 3.7 22.6 1.0 CE1 A:HIS80 3.8 20.9 1.0 CB A:MET102 3.8 22.9 1.0 CE1 A:HIS210 3.8 41.5 1.0 CG A:ASP82 3.9 20.1 1.0 CA A:ASP82 3.9 14.0 1.0 CG A:MET102 3.9 28.1 1.0 HE1 A:HIS80 4.0 25.0 1.0 N A:HIS83 4.1 22.6 1.0 HE22 A:GLN47 4.1 24.3 1.0 CG A:ASN253 4.1 17.4 1.0 HD1 A:HIS83 4.2 32.6 1.0 OD1 A:ASN253 4.3 19.9 1.0 CD A:GLN47 4.3 20.7 1.0 CB A:ASP82 4.3 17.5 1.0 HB2 A:ASP82 4.3 21.0 1.0 HG11 A:VAL208 4.3 33.3 1.0 ND1 A:HIS83 4.4 27.1 1.0 HE1 A:HIS83 4.5 54.0 1.0 C A:ASP82 4.5 22.2 1.0 NE2 A:GLN47 4.5 20.2 1.0 CE1 A:HIS83 4.6 45.0 1.0 HE3 A:LYS251 4.6 25.1 1.0 O A:LEU81 4.6 18.7 1.0 CE A:LYS251 4.6 20.9 1.0 HE3 A:MET102 4.7 35.9 1.0 CD2 A:HIS210 4.7 51.1 1.0 HB3 A:GLU132 4.8 27.0 1.0 CG A:HIS80 4.8 17.3 1.0 ND1 A:HIS210 4.8 50.1 1.0 CG A:GLU132 4.8 21.6 1.0 CE A:MET102 4.9 29.9 1.0 ND1 A:HIS80 4.9 20.3 1.0 HG2 A:MET102 4.9 33.7 1.0 OD2 A:ASP82 4.9 24.1 1.0 N A:ASP82 4.9 15.6 1.0

Sodium binding site 2 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Cleavage Products


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 E149A Variant of Helicobacter Pylori with Cleavage Products within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:22.4 occ:1.00 HE2 B:HIS80 2.0 20.9 1.0 HD21 B:ASN253 2.3 16.8 1.0 HZ1 B:LYS251 2.5 14.9 1.0 HZ2 B:LYS251 2.8 14.9 1.0 OD1 B:ASP82 2.8 18.9 1.0 NE2 B:HIS80 2.9 17.4 1.0 HE1 B:HIS210 2.9 30.9 1.0 NZ B:LYS251 3.0 12.4 1.0 ND2 B:ASN253 3.1 14.0 1.0 HA B:ASP82 3.1 15.7 1.0 OE2 B:GLU132 3.2 19.3 1.0 HE2 B:HIS210 3.3 20.0 1.0 HZ3 B:LYS251 3.3 14.9 1.0 HB2 B:MET102 3.3 17.8 1.0 CE1 B:HIS210 3.4 25.7 1.0 OE1 B:GLU132 3.4 16.6 1.0 HD22 B:ASN253 3.4 16.8 1.0 H B:HIS83 3.5 16.5 1.0 NE2 B:HIS210 3.6 16.6 1.0 CD B:GLU132 3.6 14.6 1.0 OE1 B:GLN47 3.6 15.4 1.0 HD2 B:HIS80 3.7 16.4 1.0 CD2 B:HIS80 3.7 13.7 1.0 SD B:MET102 3.7 20.7 1.0 HB3 B:MET102 3.8 17.8 1.0 CG B:ASP82 3.9 18.1 1.0 CB B:MET102 3.9 14.8 1.0 CE1 B:HIS80 3.9 21.0 1.0 HG3 B:MET102 4.0 25.5 1.0 CA B:ASP82 4.0 13.1 1.0 HE22 B:GLN47 4.1 16.5 1.0 CG B:MET102 4.1 21.2 1.0 HE1 B:HIS80 4.1 25.2 1.0 CG B:ASN253 4.2 14.1 1.0 HO3 B:13P405 4.2 28.1 0.9 N B:HIS83 4.3 13.8 1.0 HG11 B:VAL208 4.3 16.1 1.0 CB B:ASP82 4.3 16.9 1.0 HB2 B:ASP82 4.3 20.3 1.0 CE B:LYS251 4.3 15.5 1.0 OD1 B:ASN253 4.4 16.6 1.0 CD B:GLN47 4.4 14.5 1.0 HE3 B:LYS251 4.4 18.6 1.0 O3 B:13P405 4.4 23.4 0.9 ND1 B:HIS210 4.4 24.6 1.0 HE3 B:MET102 4.5 30.5 1.0 NE2 B:GLN47 4.5 13.7 1.0 HD2 B:HIS83 4.6 27.6 1.0 O B:LEU81 4.6 14.6 1.0 C B:ASP82 4.7 10.8 1.0 CE B:MET102 4.7 25.4 1.0 CD2 B:HIS210 4.7 17.4 1.0 HE2 B:LYS251 4.8 18.6 1.0 HB3 B:GLU132 4.9 20.2 1.0 CG B:GLU132 4.9 14.1 1.0 OD2 B:ASP82 4.9 21.2 1.0 CG B:HIS80 4.9 10.4 1.0 CD2 B:HIS83 5.0 23.0 1.0 HE1 B:MET102 5.0 30.5 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