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

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

The structure of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori, PDB code: 5ucs 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)	29.94 / 1.41
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.056, 82.826, 91.095, 90.00, 99.64, 90.00
R / Rfree (%)	16.4 / 18.8

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

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori (pdb code 5ucs). 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, PDB code: 5ucs:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:25.1 occ:1.00 HD21 A:ASN253 2.3 20.0 1.0 HZ1 A:LYS251 2.7 22.0 1.0 OD1 A:ASP82 2.8 17.8 1.0 NE2 A:HIS80 2.9 16.9 1.0 HA A:ASP82 3.0 16.2 1.0 HZ2 A:LYS251 3.1 22.0 1.0 ND2 A:ASN253 3.1 16.7 1.0 OE2 A:GLU132 3.2 19.6 1.0 NZ A:LYS251 3.3 18.3 1.0 HE2 A:HIS210 3.3 21.3 1.0 H A:HIS83 3.3 18.5 0.1 H A:HIS83 3.3 18.4 0.9 HB2 A:MET102 3.4 23.9 1.0 OE1 A:GLN47 3.5 20.1 1.0 HD22 A:ASN253 3.5 20.0 1.0 HG3 A:MET102 3.6 27.6 1.0 OE1 A:GLU132 3.6 18.2 1.0 HZ3 A:LYS251 3.6 22.0 1.0 CD A:GLU132 3.7 18.5 1.0 HB3 A:MET102 3.7 23.9 1.0 HD2 A:HIS80 3.7 17.6 1.0 CD2 A:HIS80 3.7 14.6 1.0 NE2 A:HIS210 3.8 17.7 1.0 CG A:ASP82 3.8 16.6 1.0 SD A:MET102 3.8 21.6 1.0 HD1 A:HIS83 3.8 28.0 0.9 CB A:MET102 3.9 19.9 1.0 CA A:ASP82 3.9 13.4 1.0 CG A:MET102 3.9 23.0 1.0 CE1 A:HIS80 4.0 20.2 1.0 HD2 A:HIS83 4.0 18.2 0.1 HE22 A:GLN47 4.0 17.2 1.0 HE1 A:HIS210 4.0 26.0 1.0 N A:HIS83 4.1 15.4 0.1 N A:HIS83 4.1 15.4 0.9 CG A:ASN253 4.1 18.1 1.0 CE1 A:HIS210 4.1 21.6 1.0 HE1 A:HIS80 4.2 24.2 1.0 ND1 A:HIS83 4.2 23.4 0.9 CB A:ASP82 4.2 15.4 1.0 HE1 A:HIS83 4.2 24.3 0.9 HB2 A:ASP82 4.2 18.5 1.0 CD A:GLN47 4.3 17.9 1.0 OD1 A:ASN253 4.3 18.6 1.0 CD2 A:HIS83 4.3 15.1 0.1 CE1 A:HIS83 4.4 20.2 0.9 NE2 A:GLN47 4.5 14.3 1.0 HG11 A:VAL208 4.5 22.6 1.0 C A:ASP82 4.5 14.6 1.0 HE3 A:LYS251 4.6 24.0 1.0 CE A:LYS251 4.6 20.0 1.0 HE3 A:MET102 4.6 23.0 1.0 O A:HOH621 4.6 23.9 1.0 NE2 A:HIS83 4.7 21.1 0.1 O A:LEU81 4.7 13.6 1.0 CD2 A:HIS210 4.7 19.4 1.0 CE A:MET102 4.9 19.2 1.0 HG2 A:MET102 4.9 27.6 1.0 OD2 A:ASP82 4.9 18.6 1.0 HB3 A:GLU132 4.9 20.4 1.0 N A:ASP82 4.9 14.8 1.0 HE2 A:LYS251 5.0 24.0 1.0 CG A:HIS80 5.0 14.6 1.0 CG A:GLU132 5.0 16.4 1.0

Sodium binding site 2 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase E149A 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 E149A Variant of Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:23.0 occ:1.00 HD21 B:ASN253 2.4 17.6 1.0 HZ1 B:LYS251 2.6 16.8 1.0 NE2 B:HIS80 2.8 12.1 1.0 OD1 B:ASP82 2.9 15.7 1.0 HZ2 B:LYS251 2.9 16.8 1.0 HA B:ASP82 3.0 15.6 1.0 NZ B:LYS251 3.1 14.0 1.0 OE2 B:GLU132 3.2 17.9 1.0 ND2 B:ASN253 3.2 14.7 1.0 HE2 B:HIS210 3.3 18.2 1.0 H B:HIS83 3.4 15.4 0.1 H B:HIS83 3.4 15.6 0.9 HB2 B:MET102 3.4 16.9 1.0 HZ3 B:LYS251 3.5 16.8 1.0 OE1 B:GLN47 3.5 16.6 1.0 OE1 B:GLU132 3.5 16.2 1.0 HG3 B:MET102 3.5 22.0 1.0 HD22 B:ASN253 3.6 17.6 1.0 CD B:GLU132 3.6 17.2 1.0 HD2 B:HIS80 3.7 14.3 1.0 CD2 B:HIS80 3.7 11.9 1.0 HB3 B:MET102 3.7 16.9 1.0 NE2 B:HIS210 3.8 15.2 1.0 CB B:MET102 3.9 14.1 1.0 CE1 B:HIS80 3.9 12.6 1.0 SD B:MET102 3.9 18.8 1.0 CG B:MET102 3.9 18.3 1.0 HD1 B:HIS83 3.9 20.6 0.9 CA B:ASP82 3.9 13.0 1.0 CG B:ASP82 3.9 16.3 1.0 HD2 B:HIS83 4.1 19.9 0.1 HE1 B:HIS80 4.1 15.2 1.0 N B:HIS83 4.1 12.8 0.1 N B:HIS83 4.1 13.0 0.9 HE22 B:GLN47 4.1 15.7 1.0 HE1 B:HIS210 4.1 18.1 1.0 CG B:ASN253 4.2 14.0 1.0 CE1 B:HIS210 4.2 15.0 1.0 ND1 B:HIS83 4.3 17.1 0.9 OD1 B:ASN253 4.3 16.4 1.0 CD B:GLN47 4.3 14.9 1.0 CB B:ASP82 4.3 15.1 1.0 HB2 B:ASP82 4.3 18.2 1.0 HE1 B:HIS83 4.3 23.3 0.9 CD2 B:HIS83 4.4 16.5 0.1 HG11 B:VAL208 4.4 18.3 1.0 CE B:LYS251 4.4 16.4 1.0 HE3 B:LYS251 4.4 19.7 1.0 CE1 B:HIS83 4.5 19.4 0.9 HE3 B:MET102 4.5 19.8 1.0 C B:ASP82 4.5 14.4 1.0 NE2 B:GLN47 4.5 13.1 1.0 O B:LEU81 4.7 13.9 1.0 NE2 B:HIS83 4.7 16.7 0.1 CD2 B:HIS210 4.7 13.7 1.0 O B:HOH671 4.8 24.4 1.0 HB3 B:GLU132 4.8 15.1 1.0 HE2 B:LYS251 4.8 19.7 1.0 HG2 B:MET102 4.9 22.0 1.0 CE B:MET102 4.9 16.5 1.0 CG B:GLU132 4.9 16.3 1.0 CG B:HIS80 4.9 12.7 1.0 ND1 B:HIS80 5.0 13.6 1.0 N B:ASP82 5.0 12.6 1.0 OD2 B:ASP82 5.0 17.8 1.0 HD2 B:HIS210 5.0 16.4 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