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

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

The structure of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap, PDB code: 5ucz 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)	29.91 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.474, 86.133, 91.196, 90.00, 100.28, 90.00
R / Rfree (%)	18.4 / 22.7

The structure of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap 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 E149A Variant of Helicobacter Pylori with Dhap (pdb code 5ucz). 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 Dhap, PDB code: 5ucz:
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 Dhap


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 Dhap within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:44.4 occ:1.00 HE2 A:HIS80 2.1 32.2 1.0 HD21 A:ASN253 2.5 40.1 1.0 HE1 A:HIS210 2.5 56.6 0.5 OD1 A:ASP82 2.7 47.6 1.0 NE2 A:HIS80 2.9 26.8 1.0 HZ1 A:LYS251 2.9 35.3 1.0 HE2 A:HIS210 3.1 48.8 0.5 HA A:ASP82 3.1 29.8 1.0 HZ2 A:LYS251 3.2 35.3 1.0 CE1 A:HIS210 3.2 47.2 0.5 OE2 A:GLU132 3.2 41.4 1.0 ND2 A:ASN253 3.3 33.5 1.0 HE2 A:HIS210 3.4 49.5 0.5 HD2 A:HIS80 3.4 28.9 1.0 HB2 A:MET102 3.4 32.2 1.0 OE1 A:GLU132 3.5 34.5 1.0 OE1 A:GLN47 3.5 55.7 1.0 NZ A:LYS251 3.5 29.4 1.0 H A:HIS83 3.5 43.4 0.5 H A:HIS83 3.5 43.4 0.5 NE2 A:HIS210 3.5 40.7 0.5 CD2 A:HIS80 3.5 24.1 1.0 HD22 A:ASN253 3.6 40.1 1.0 NE2 A:HIS210 3.6 41.2 0.5 HG3 A:MET102 3.6 68.0 1.0 CD A:GLU132 3.6 41.4 1.0 HE1 A:HIS210 3.7 64.2 0.5 HO3 A:13P404 3.8 41.7 0.3 HB3 A:MET102 3.8 32.2 1.0 CG A:ASP82 3.8 41.7 1.0 SD A:MET102 3.8 41.5 1.0 HO3 A:13P404 3.8 41.8 0.3 CE1 A:HIS210 3.8 53.5 0.5 CB A:MET102 3.9 26.9 1.0 CG A:MET102 3.9 56.6 1.0 HZ3 A:LYS251 4.0 35.3 1.0 CA A:ASP82 4.0 24.8 1.0 CE1 A:HIS80 4.0 35.1 1.0 HD1 A:HIS83 4.1 85.5 0.5 CD A:GLN47 4.2 33.7 1.0 N A:HIS83 4.2 36.1 0.5 N A:HIS83 4.2 36.2 0.5 HE22 A:GLN47 4.2 41.7 1.0 CG A:ASN253 4.2 26.3 1.0 ND1 A:HIS210 4.3 44.5 0.5 HD2 A:HIS83 4.3 81.1 0.5 HE1 A:HIS80 4.3 42.1 1.0 CB A:ASP82 4.3 24.1 1.0 HG11 A:VAL208 4.4 44.6 1.0 HB2 A:ASP82 4.4 28.9 1.0 O3 A:13P404 4.4 34.7 0.3 HE3 A:LYS251 4.4 47.7 1.0 OD1 A:ASN253 4.4 26.8 1.0 CD2 A:HIS210 4.5 48.2 0.5 O3 A:13P404 4.5 34.8 0.3 NE2 A:GLN47 4.5 34.8 1.0 ND1 A:HIS83 4.6 71.2 0.5 CE A:LYS251 4.6 39.8 1.0 CD2 A:HIS83 4.6 67.6 0.5 C A:ASP82 4.7 27.5 1.0 O A:LEU81 4.7 27.6 1.0 HE3 A:MET102 4.7 65.6 1.0 OD2 A:ASP82 4.8 29.2 1.0 HD2 A:HIS210 4.8 57.9 0.5 CD2 A:HIS210 4.8 43.6 0.5 CG A:HIS80 4.8 24.0 1.0 ND1 A:HIS210 4.9 55.8 0.5 HE1 A:HIS83 4.9 87.6 0.5 HG2 A:MET102 4.9 68.0 1.0 HB3 A:GLU132 4.9 41.3 1.0 CG A:GLU132 4.9 29.4 1.0 CE A:MET102 5.0 54.6 1.0 CE1 A:HIS83 5.0 73.0 0.5

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


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 Dhap within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:28.4 occ:1.00 HE2 B:HIS80 2.0 21.3 1.0 HD21 B:ASN253 2.4 30.7 1.0 HZ1 B:LYS251 2.6 20.5 1.0 OD1 B:ASP82 2.7 20.7 1.0 HE1 B:HIS210 2.8 29.0 1.0 NE2 B:HIS80 2.8 17.8 1.0 HZ2 B:LYS251 3.0 20.5 1.0 HA B:ASP82 3.1 14.5 1.0 ND2 B:ASN253 3.2 25.6 1.0 OE1 B:GLN47 3.2 28.6 1.0 NZ B:LYS251 3.2 17.1 1.0 CE1 B:HIS210 3.4 24.2 1.0 OE2 B:GLU132 3.4 21.1 1.0 HD2 B:HIS80 3.4 15.7 1.0 HD22 B:ASN253 3.5 30.7 1.0 HB2 B:MET102 3.5 24.3 1.0 HZ3 B:LYS251 3.5 20.5 1.0 CD2 B:HIS80 3.5 13.1 1.0 OE1 B:GLU132 3.6 21.3 1.0 H B:HIS83 3.6 21.2 1.0 HE2 B:HIS210 3.7 27.5 1.0 CG B:ASP82 3.7 25.7 1.0 CD B:GLU132 3.8 26.5 1.0 NE2 B:HIS210 3.8 22.9 1.0 SD B:MET102 3.9 28.1 1.0 HB3 B:MET102 3.9 24.3 1.0 CE1 B:HIS80 4.0 14.1 1.0 CA B:ASP82 4.0 12.1 1.0 HO3 B:13P404 4.0 35.7 0.4 HG3 B:MET102 4.0 25.2 1.0 HE22 B:GLN47 4.0 21.9 1.0 CB B:MET102 4.0 20.2 1.0 HO3 B:13P404 4.0 35.9 0.4 CD B:GLN47 4.0 17.7 1.0 CG B:ASN253 4.2 16.5 1.0 CG B:MET102 4.2 21.0 1.0 HB2 B:ASP82 4.2 18.2 1.0 CB B:ASP82 4.2 15.2 1.0 HE1 B:HIS80 4.2 16.9 1.0 N B:HIS83 4.3 17.7 1.0 HG11 B:VAL208 4.4 19.1 1.0 NE2 B:GLN47 4.4 18.2 1.0 OD1 B:ASN253 4.4 19.8 1.0 ND1 B:HIS210 4.4 26.4 1.0 CE B:LYS251 4.5 23.9 1.0 HE3 B:LYS251 4.5 28.7 1.0 O3 B:13P404 4.6 29.9 0.4 O3 B:13P404 4.6 29.8 0.4 HE3 B:MET102 4.6 44.9 1.0 C B:ASP82 4.7 14.3 1.0 O B:LEU81 4.7 15.8 1.0 OD2 B:ASP82 4.7 24.7 1.0 HD2 B:HIS83 4.8 28.6 1.0 CG B:HIS80 4.8 11.8 1.0 CE B:MET102 4.9 37.4 1.0 HE2 B:LYS251 4.9 28.7 1.0 ND1 B:HIS80 5.0 15.4 1.0 HB3 B:GLU132 5.0 18.1 1.0 N B:ASP82 5.0 15.6 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