Sodium in PDB 5ud2: Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Dhap

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

The structure of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Dhap, PDB code: 5ud2 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)	35.79 / 1.78
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.407, 63.089, 64.789, 82.51, 75.96, 74.39
R / Rfree (%)	19.3 / 21.6

The structure of Class II Fructose-1,6-Bisphosphate Aldolase H180Q 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 H180Q Variant of Helicobacter Pylori with Dhap (pdb code 5ud2). 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 with Dhap, PDB code: 5ud2:
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 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 H180Q Variant of Helicobacter Pylori with Dhap within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:25.3 occ:0.95 HE2 A:HIS80 2.3 11.0 1.0 HD21 A:ASN253 2.3 13.4 1.0 HE1 A:HIS210 2.7 19.9 0.3 OD1 A:ASP82 2.8 19.4 1.0 HZ1 A:LYS251 2.9 16.8 1.0 OE2 A:GLU132 3.0 11.2 1.0 ND2 A:ASN253 3.1 11.1 1.0 NE2 A:HIS80 3.1 9.2 1.0 HA A:ASP82 3.1 16.6 1.0 HZ2 A:LYS251 3.1 16.8 1.0 HE2 A:HIS210 3.2 20.1 0.3 HE2 A:HIS210 3.2 20.9 0.7 CE1 A:HIS210 3.2 16.6 0.3 HD22 A:ASN253 3.3 13.4 1.0 H A:HIS83 3.3 20.0 0.7 HB2 A:MET102 3.4 15.8 1.0 H A:HIS83 3.4 19.6 0.3 OE1 A:GLU132 3.4 11.6 1.0 NZ A:LYS251 3.4 14.0 1.0 NE2 A:HIS210 3.4 16.7 0.3 CD A:GLU132 3.5 11.7 1.0 SD A:MET102 3.5 18.5 1.0 OE1 A:GLN47 3.5 19.7 1.0 NE2 A:HIS210 3.7 17.4 0.7 HD1 A:HIS83 3.7 29.2 0.7 HO3 A:13P404 3.7 34.0 1.0 HG3 A:MET102 3.7 19.3 1.0 HB3 A:MET102 3.8 15.8 1.0 CG A:ASP82 3.8 19.3 1.0 HD2 A:HIS80 3.8 11.6 1.0 CD2 A:HIS80 3.8 9.6 1.0 HZ3 A:LYS251 3.8 16.8 1.0 CB A:MET102 3.9 13.2 1.0 CG A:MET102 3.9 16.1 1.0 CA A:ASP82 4.0 13.9 1.0 N A:HIS83 4.1 16.7 0.7 N A:HIS83 4.1 16.3 0.3 CE1 A:HIS80 4.1 9.7 1.0 CG A:ASN253 4.2 11.5 1.0 HB2 A:ASP82 4.2 19.2 1.0 ND1 A:HIS83 4.2 24.3 0.7 CB A:ASP82 4.2 16.0 1.0 HG11 A:VAL208 4.3 10.3 1.0 HE1 A:HIS80 4.3 11.6 1.0 CE1 A:HIS210 4.3 15.6 0.7 HE22 A:GLN47 4.4 19.3 1.0 O3 A:13P404 4.4 28.3 1.0 ND1 A:HIS210 4.4 17.2 0.3 HE1 A:HIS83 4.4 30.1 0.7 CD2 A:HIS210 4.4 16.9 0.7 HE1 A:HIS210 4.4 18.7 0.7 OD1 A:ASN253 4.4 11.5 1.0 CD A:GLN47 4.5 18.2 1.0 HE3 A:LYS251 4.5 15.2 1.0 HD2 A:HIS210 4.5 20.2 0.7 C A:ASP82 4.6 13.0 1.0 CE1 A:HIS83 4.6 25.0 0.7 CE A:LYS251 4.6 12.7 1.0 CD2 A:HIS210 4.7 17.1 0.3 O A:LEU81 4.7 11.4 1.0 HE3 A:MET102 4.8 23.2 1.0 NE2 A:GLN47 4.8 16.1 1.0 CG A:GLU132 4.8 12.7 1.0 HB3 A:GLU132 4.8 15.6 1.0 OD2 A:ASP82 4.8 20.2 1.0 CE A:MET102 4.8 19.3 1.0 HG2 A:MET102 4.9 19.3 1.0 HG2 A:GLU132 5.0 15.3 1.0 CD2 A:HIS83 5.0 25.2 0.3

Sodium binding site 2 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q 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 H180Q Variant of Helicobacter Pylori with Dhap within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:21.8 occ:0.91 HE2 B:HIS80 2.1 12.1 1.0 HD21 B:ASN253 2.4 15.1 1.0 HZ1 B:LYS251 2.8 18.1 1.0 HZ2 B:LYS251 2.8 18.1 1.0 HE1 B:HIS210 2.8 20.7 0.5 OE2 B:GLU132 2.9 17.7 1.0 NE2 B:HIS80 2.9 10.1 1.0 OD1 B:ASP82 3.0 14.2 1.0 ND2 B:ASN253 3.1 12.6 1.0 HA B:ASP82 3.2 10.7 1.0 HE2 B:HIS210 3.2 22.0 0.5 NZ B:LYS251 3.2 15.1 1.0 HB2 B:MET102 3.2 16.5 1.0 OE1 B:GLU132 3.3 13.8 1.0 HE2 B:HIS210 3.3 22.0 0.5 CE1 B:HIS210 3.4 17.3 0.5 CD B:GLU132 3.4 14.8 1.0 HD22 B:ASN253 3.4 15.1 1.0 HG3 B:MET102 3.4 19.8 1.0 H B:HIS83 3.5 16.0 0.5 H B:HIS83 3.5 16.0 0.5 OE1 B:GLN47 3.6 20.2 1.0 NE2 B:HIS210 3.6 18.3 0.5 HD2 B:HIS80 3.6 12.2 1.0 HZ3 B:LYS251 3.6 18.1 1.0 CD2 B:HIS80 3.7 10.2 1.0 HB3 B:MET102 3.7 16.5 1.0 NE2 B:HIS210 3.7 18.3 0.5 CB B:MET102 3.7 13.8 1.0 SD B:MET102 3.7 18.5 1.0 CG B:MET102 3.8 16.4 1.0 HD1 B:HIS83 3.9 25.0 0.5 CE1 B:HIS80 4.0 10.7 1.0 CG B:ASP82 4.0 13.1 1.0 CA B:ASP82 4.1 8.9 1.0 HO3 B:13P404 4.1 35.7 1.0 HG11 B:VAL208 4.2 12.3 1.0 CG B:ASN253 4.2 12.5 1.0 HE1 B:HIS80 4.2 12.8 1.0 HB2 B:ASP82 4.3 11.6 1.0 N B:HIS83 4.3 13.3 0.5 N B:HIS83 4.3 13.3 0.5 CE1 B:HIS210 4.3 18.4 0.5 HE1 B:HIS210 4.3 22.1 0.5 CB B:ASP82 4.3 9.6 1.0 HE3 B:LYS251 4.4 16.5 1.0 ND1 B:HIS83 4.4 20.8 0.5 CD B:GLN47 4.4 17.3 1.0 HE22 B:GLN47 4.4 18.1 1.0 OD1 B:ASN253 4.4 12.1 1.0 ND1 B:HIS210 4.5 17.9 0.5 CE B:LYS251 4.5 13.7 1.0 CD2 B:HIS210 4.5 18.2 0.5 HE1 B:HIS83 4.5 21.2 0.5 O3 B:13P404 4.6 29.8 1.0 O B:LEU81 4.6 6.2 1.0 HD2 B:HIS210 4.7 21.8 0.5 CG B:GLU132 4.7 13.1 1.0 HB3 B:GLU132 4.7 14.9 1.0 C B:ASP82 4.7 10.6 1.0 HE3 B:MET102 4.7 22.9 1.0 HG2 B:MET102 4.7 19.8 1.0 CE1 B:HIS83 4.8 17.7 0.5 CD2 B:HIS210 4.8 17.6 0.5 NE2 B:GLN47 4.8 15.1 1.0 HG2 B:GLU132 4.8 15.8 1.0 CG B:HIS80 4.9 9.9 1.0 CE B:MET102 4.9 19.1 1.0 HE2 B:LYS251 5.0 16.5 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