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

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

The structure of Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products, PDB code: 5uck 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)	45.19 / 1.78
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.384, 62.843, 64.754, 82.23, 75.97, 74.40
R / Rfree (%)	19.1 / 23.2

The structure of Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products 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 of Helicobacter Pylori with Cleavage Products (pdb code 5uck). 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 of Helicobacter Pylori with Cleavage Products, PDB code: 5uck:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase 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 of Helicobacter Pylori with Cleavage Products within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:32.5 occ:1.00 HD21 A:ASN253 2.2 24.6 1.0 HZ1 A:LYS251 2.6 16.8 1.0 OD1 A:ASP82 2.7 24.2 1.0 HE1 A:HIS210 2.8 16.2 0.3 HZ2 A:LYS251 2.9 16.8 1.0 ND2 A:ASN253 3.0 20.5 1.0 NE2 A:HIS80 3.0 17.4 1.0 HA A:ASP82 3.0 23.4 1.0 NZ A:LYS251 3.2 14.0 1.0 OE1 A:GLN47 3.2 30.7 1.0 HD22 A:ASN253 3.3 24.6 1.0 CE1 A:HIS210 3.4 13.5 0.3 OE2 A:GLU132 3.4 23.1 1.0 HE2 A:HIS210 3.5 15.8 0.7 H A:HIS83 3.5 24.2 0.7 H A:HIS83 3.5 24.3 0.3 SD A:MET102 3.5 30.2 1.0 OE1 A:GLU132 3.5 23.9 1.0 HD2 A:HIS80 3.5 20.5 1.0 HZ3 A:LYS251 3.6 16.8 1.0 HB2 A:MET102 3.6 30.0 1.0 CD2 A:HIS80 3.7 17.1 1.0 CG A:ASP82 3.7 26.1 1.0 CD A:GLU132 3.8 21.5 1.0 HD1 A:HIS83 3.8 36.9 0.7 HO3 A:13P404 3.9 38.7 0.7 HE2 A:HIS210 3.9 15.1 0.3 CA A:ASP82 3.9 19.5 1.0 HE22 A:GLN47 3.9 27.3 1.0 NE2 A:HIS210 3.9 13.2 0.7 NE2 A:HIS210 3.9 12.6 0.3 CG A:ASN253 4.0 16.1 1.0 HB3 A:MET102 4.0 30.0 1.0 CD A:GLN47 4.0 25.8 1.0 CE1 A:HIS80 4.1 16.9 1.0 OD1 A:ASN253 4.2 15.9 1.0 CB A:MET102 4.2 25.1 1.0 CB A:ASP82 4.2 22.4 1.0 HB2 A:ASP82 4.2 26.9 1.0 N A:HIS83 4.2 20.2 0.7 N A:HIS83 4.2 20.3 0.3 CG A:MET102 4.2 29.3 1.0 ND1 A:HIS83 4.3 30.8 0.7 HE3 A:LYS251 4.3 15.2 1.0 ND1 A:HIS210 4.3 14.2 0.3 HG3 A:MET102 4.3 35.1 1.0 NE2 A:GLN47 4.3 22.8 1.0 HD2 A:HIS83 4.3 37.2 0.3 CE A:LYS251 4.4 12.7 1.0 HE1 A:HIS83 4.4 39.0 0.7 HG11 A:VAL208 4.4 21.7 1.0 HE1 A:HIS80 4.4 20.2 1.0 HD2 A:HIS210 4.4 15.4 0.7 CD2 A:HIS210 4.4 12.9 0.7 O3 A:13P404 4.5 32.3 0.7 CE1 A:HIS83 4.6 32.5 0.7 C A:ASP82 4.6 20.4 1.0 CD2 A:HIS83 4.6 31.0 0.3 OD2 A:ASP82 4.7 27.3 1.0 CE1 A:HIS210 4.7 13.2 0.7 O A:LEU81 4.8 20.3 1.0 HE2 A:LYS251 4.8 15.2 1.0 CE A:MET102 4.9 29.6 1.0 HE1 A:HIS210 4.9 15.8 0.7 NE2 A:HIS83 4.9 31.9 0.3 CG A:HIS80 4.9 17.1 1.0 N A:ASP82 5.0 18.3 1.0

Sodium binding site 2 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase 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 of Helicobacter Pylori with Cleavage Products within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:32.8 occ:1.00 HE2 B:HIS80 2.1 21.6 1.0 HD21 B:ASN253 2.5 23.2 1.0 OD1 B:ASP82 2.7 26.6 1.0 HE1 B:HIS210 2.8 28.3 0.4 HZ1 B:LYS251 2.8 19.5 1.0 NE2 B:HIS80 2.9 18.0 1.0 HA B:ASP82 2.9 23.9 1.0 HZ2 B:LYS251 3.1 19.5 1.0 OE2 B:GLU132 3.2 23.6 1.0 HB2 B:MET102 3.3 26.8 1.0 ND2 B:ASN253 3.3 19.3 1.0 OE1 B:GLU132 3.4 24.5 1.0 H B:HIS83 3.4 25.2 0.6 H B:HIS83 3.4 25.2 0.4 NZ B:LYS251 3.4 16.3 1.0 SD B:MET102 3.4 28.1 1.0 CE1 B:HIS210 3.4 23.6 0.4 HD2 B:HIS80 3.5 21.1 1.0 CD B:GLU132 3.5 22.7 1.0 HE2 B:HIS210 3.5 28.5 0.6 HE2 B:HIS210 3.6 29.1 0.4 CD2 B:HIS80 3.6 17.6 1.0 CG B:ASP82 3.7 25.8 1.0 HD22 B:ASN253 3.7 23.2 1.0 OE1 B:GLN47 3.8 24.3 1.0 HB3 B:MET102 3.8 26.8 1.0 NE2 B:HIS210 3.8 24.3 0.4 CA B:ASP82 3.8 19.9 1.0 CB B:MET102 3.8 22.4 1.0 HD1 B:HIS83 3.9 34.6 0.6 HG3 B:MET102 3.9 31.8 1.0 HZ3 B:LYS251 3.9 19.5 1.0 CG B:MET102 3.9 26.6 1.0 NE2 B:HIS210 4.0 23.8 0.6 CE1 B:HIS80 4.0 18.3 1.0 N B:HIS83 4.1 21.0 0.6 N B:HIS83 4.1 21.1 0.4 CB B:ASP82 4.1 21.9 1.0 HB2 B:ASP82 4.1 26.2 1.0 HE3 B:LYS251 4.2 17.0 1.0 HE22 B:GLN47 4.2 27.2 1.0 HE1 B:HIS80 4.3 21.9 1.0 CG B:ASN253 4.3 15.4 1.0 HD2 B:HIS83 4.3 34.5 0.4 ND1 B:HIS83 4.4 28.9 0.6 CE B:LYS251 4.4 14.2 1.0 OD1 B:ASN253 4.4 15.4 1.0 O3 B:13P404 4.4 30.1 0.7 HG11 B:VAL208 4.5 21.8 1.0 CE1 B:HIS210 4.5 23.8 0.6 C B:ASP82 4.5 21.5 1.0 ND1 B:HIS210 4.5 24.9 0.4 HE1 B:HIS210 4.5 28.5 0.6 O B:LEU81 4.5 17.8 1.0 CD B:GLN47 4.5 23.8 1.0 HE1 B:HIS83 4.7 36.8 0.6 NE2 B:GLN47 4.7 22.7 1.0 OD2 B:ASP82 4.7 28.8 1.0 CD2 B:HIS83 4.7 28.8 0.4 CD2 B:HIS210 4.7 23.2 0.6 HB3 B:GLU132 4.8 19.6 1.0 HE3 B:MET102 4.8 34.7 1.0 CE B:MET102 4.8 29.0 1.0 CE1 B:HIS83 4.8 30.7 0.6 CG B:GLU132 4.8 20.1 1.0 N B:ASP82 4.8 18.1 1.0 CG B:HIS80 4.9 16.9 1.0 HG2 B:MET102 4.9 31.8 1.0 HD2 B:HIS210 4.9 27.8 0.6 HO3 B:13P404 4.9 36.0 0.7 HE2 B:LYS251 4.9 17.0 1.0 HG2 B:GLU132 5.0 24.1 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