Sodium in PDB 5ucn: Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Dhap

All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Dhap:
4.1.2.13;

The structure of Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Dhap, PDB code: 5ucn 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)	44.98 / 1.67
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.308, 62.612, 64.507, 82.17, 75.88, 74.17
R / Rfree (%)	17.1 / 20.8

The structure of Class II Fructose-1,6-Bisphosphate Aldolase E142A 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 E142A Variant of Helicobacter Pylori with Dhap (pdb code 5ucn). 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 E142A Variant of Helicobacter Pylori with Dhap, PDB code: 5ucn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase E142A 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 E142A Variant of Helicobacter Pylori with Dhap within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:32.3 occ:1.00 HE2 A:HIS80 2.2 19.8 1.0 HD21 A:ASN253 2.4 26.4 1.0 HE1 A:HIS210 2.7 25.9 0.5 HZ1 A:LYS251 2.7 22.4 1.0 OD1 A:ASP82 2.8 23.0 1.0 NE2 A:HIS80 3.0 16.5 1.0 HZ2 A:LYS251 3.0 22.4 1.0 HA A:ASP82 3.0 16.8 1.0 OE2 A:GLU132 3.1 17.6 1.0 ND2 A:ASN253 3.2 22.0 1.0 HE2 A:HIS210 3.2 24.9 0.5 NZ A:LYS251 3.3 18.7 1.0 CE1 A:HIS210 3.3 21.6 0.5 HB2 A:MET102 3.4 23.5 1.0 HG3 A:MET102 3.4 29.3 1.0 H A:HIS83 3.4 22.0 0.5 H A:HIS83 3.4 22.0 0.5 OE1 A:GLU132 3.5 18.5 1.0 HD22 A:ASN253 3.5 26.4 1.0 HE2 A:HIS210 3.5 26.7 0.5 CD A:GLU132 3.6 18.4 1.0 HZ3 A:LYS251 3.6 22.4 1.0 HB3 A:MET102 3.6 23.5 1.0 OE1 A:GLN47 3.7 24.1 1.0 HD2 A:HIS80 3.7 19.6 1.0 NE2 A:HIS210 3.7 22.2 0.5 CD2 A:HIS80 3.7 16.3 1.0 NE2 A:HIS210 3.8 20.8 0.5 CB A:MET102 3.8 19.6 1.0 SD A:MET102 3.8 23.1 1.0 CG A:ASP82 3.8 21.8 1.0 CG A:MET102 3.8 24.4 1.0 CA A:ASP82 3.9 14.0 1.0 HO3 A:13P404 4.1 38.2 0.3 HE22 A:GLN47 4.1 22.4 1.0 CE1 A:HIS80 4.1 16.9 1.0 HO3 A:13P404 4.1 38.2 0.3 N A:HIS83 4.1 18.3 0.5 N A:HIS83 4.1 18.3 0.5 HB2 A:ASP82 4.1 22.9 1.0 CB A:ASP82 4.2 19.1 1.0 CG A:ASN253 4.2 16.2 1.0 HD1 A:HIS83 4.3 45.2 0.5 ND1 A:HIS210 4.3 22.9 0.5 HE1 A:HIS80 4.3 20.3 1.0 OD1 A:ASN253 4.4 20.3 1.0 HG11 A:VAL208 4.4 19.4 1.0 HD2 A:HIS210 4.4 24.8 0.5 CD2 A:HIS210 4.4 20.7 0.5 CD A:GLN47 4.4 17.6 1.0 HE3 A:LYS251 4.5 18.9 1.0 CE A:LYS251 4.5 15.7 1.0 C A:ASP82 4.5 15.0 1.0 HE3 A:MET102 4.5 29.4 1.0 NE2 A:GLN47 4.5 18.6 1.0 CE1 A:HIS210 4.6 21.9 0.5 O3 A:13P404 4.6 31.9 0.3 ND1 A:HIS83 4.6 37.7 0.5 O A:LEU81 4.7 11.9 1.0 O3 A:13P404 4.7 31.9 0.3 HG2 A:MET102 4.8 29.3 1.0 HD2 A:HIS83 4.8 44.8 0.5 HE1 A:HIS210 4.8 26.2 0.5 CD2 A:HIS83 4.8 37.4 0.5 CD2 A:HIS210 4.8 20.9 0.5 CE A:MET102 4.8 24.5 1.0 HB3 A:GLU132 4.9 17.7 1.0 OD2 A:ASP82 4.9 24.0 1.0 CG A:GLU132 4.9 14.3 1.0 HE2 A:LYS251 5.0 18.9 1.0 HE1 A:HIS83 5.0 48.4 0.5 N A:ASP82 5.0 12.4 1.0 CG A:HIS80 5.0 14.8 1.0

Sodium binding site 2 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase E142A 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 E142A Variant of Helicobacter Pylori with Dhap within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:31.3 occ:1.00 HE2 B:HIS80 2.1 16.6 1.0 HD21 B:ASN253 2.4 25.6 1.0 HZ1 B:LYS251 2.6 24.4 1.0 NE2 B:HIS80 2.9 13.9 1.0 OD1 B:ASP82 2.9 20.3 1.0 HE1 B:HIS210 2.9 29.3 0.5 HZ2 B:LYS251 3.0 24.4 1.0 OE2 B:GLU132 3.0 20.7 1.0 HA B:ASP82 3.1 12.8 1.0 ND2 B:ASN253 3.1 21.4 1.0 NZ B:LYS251 3.2 20.3 1.0 HE2 B:HIS210 3.2 28.9 0.5 OE1 B:GLU132 3.2 21.6 1.0 HE2 B:HIS210 3.3 29.5 0.5 HB2 B:MET102 3.3 19.6 1.0 CE1 B:HIS210 3.4 24.4 0.5 CD B:GLU132 3.4 21.6 1.0 HD22 B:ASN253 3.5 25.6 1.0 HG3 B:MET102 3.5 25.0 1.0 H B:HIS83 3.5 20.1 0.5 H B:HIS83 3.5 20.2 0.5 NE2 B:HIS210 3.6 24.6 0.5 HZ3 B:LYS251 3.6 24.4 1.0 HD2 B:HIS80 3.6 16.3 1.0 CD2 B:HIS80 3.6 13.6 1.0 HB3 B:MET102 3.7 19.6 1.0 SD B:MET102 3.7 23.3 1.0 NE2 B:HIS210 3.8 24.1 0.5 CB B:MET102 3.8 16.3 1.0 OE1 B:GLN47 3.8 19.5 1.0 CG B:MET102 3.8 20.9 1.0 HD1 B:HIS83 3.9 39.4 0.5 CG B:ASP82 3.9 21.1 1.0 CE1 B:HIS80 3.9 14.3 1.0 CA B:ASP82 4.0 10.7 1.0 HO3 B:13P404 4.0 34.6 0.3 HE22 B:GLN47 4.1 21.0 1.0 HE1 B:HIS80 4.1 17.1 1.0 CG B:ASN253 4.2 19.0 1.0 HB2 B:ASP82 4.2 16.0 1.0 HO3 B:13P404 4.2 34.6 0.3 N B:HIS83 4.3 16.8 0.5 N B:HIS83 4.3 16.8 0.5 CB B:ASP82 4.3 13.4 1.0 HG11 B:VAL208 4.3 18.8 1.0 OD1 B:ASN253 4.3 16.9 1.0 HE3 B:LYS251 4.4 24.4 1.0 CE B:LYS251 4.4 20.4 1.0 ND1 B:HIS83 4.4 32.8 0.5 CD2 B:HIS210 4.5 25.3 0.5 CE1 B:HIS210 4.5 25.6 0.5 ND1 B:HIS210 4.5 28.5 0.5 HD2 B:HIS210 4.5 30.4 0.5 HE1 B:HIS83 4.5 42.6 0.5 CD B:GLN47 4.5 17.4 1.0 HE3 B:MET102 4.6 31.4 1.0 NE2 B:GLN47 4.6 17.5 1.0 HE1 B:HIS210 4.6 30.8 0.5 O3 B:13P404 4.6 28.9 0.3 O B:LEU81 4.7 14.7 1.0 C B:ASP82 4.7 13.8 1.0 O3 B:13P404 4.7 28.9 0.3 HB3 B:GLU132 4.7 15.0 1.0 CD2 B:HIS210 4.8 25.7 0.5 CG B:GLU132 4.8 16.2 1.0 CE1 B:HIS83 4.8 35.5 0.5 HG2 B:MET102 4.8 25.0 1.0 HE2 B:LYS251 4.8 24.4 1.0 CE B:MET102 4.8 26.1 1.0 CG B:HIS80 4.9 11.8 1.0 OD2 B:ASP82 4.9 24.8 1.0 HG2 B:GLU132 4.9 19.4 1.0 ND1 B:HIS80 5.0 14.1 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