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

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

The structure of Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Dhap, PDB code: 5vjf was solved by M.Coincon, J.Sygusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.49 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.518, 88.046, 90.811, 90.00, 100.39, 90.00
R / Rfree (%)	13.7 / 17.4

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

Zinc	(Zn)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Dhap (pdb code 5vjf). 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 Dhap, PDB code: 5vjf:
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 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 of Helicobacter Pylori with Dhap within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:15.5 occ:1.00 HE2 A:HIS80 2.1 2.2 1.0 HD21 A:ASN253 2.3 5.8 1.0 HZ1 A:LYS251 2.6 3.6 1.0 HZ2 A:LYS251 2.7 3.6 1.0 OE2 A:GLU132 2.8 5.7 1.0 OD1 A:ASP82 2.8 8.9 1.0 NE2 A:HIS80 2.9 1.8 1.0 HE1 A:HIS210 2.9 14.2 1.0 NZ A:LYS251 3.0 3.0 1.0 ND2 A:ASN253 3.1 4.8 1.0 HE2 A:HIS210 3.2 8.8 1.0 OE1 A:GLU132 3.3 5.1 1.0 HA A:ASP82 3.3 0.8 1.0 CD A:GLU132 3.3 3.0 1.0 HB2 A:MET102 3.3 2.1 1.0 HZ3 A:LYS251 3.3 3.6 1.0 CE1 A:HIS210 3.4 11.9 1.0 HD22 A:ASN253 3.4 5.8 1.0 NE2 A:HIS210 3.5 7.3 1.0 HD2 A:HIS80 3.6 1.0 1.0 SD A:MET102 3.6 8.7 1.0 CD2 A:HIS80 3.6 0.8 1.0 H A:HIS83 3.7 1.0 1.0 OE1 A:GLN47 3.8 5.2 1.0 CG A:ASP82 3.8 7.8 1.0 CB A:MET102 4.0 1.8 1.0 HB3 A:MET102 4.0 2.1 1.0 CE1 A:HIS80 4.0 0.9 1.0 HG11 A:VAL208 4.1 4.3 1.0 HE22 A:GLN47 4.1 6.2 1.0 HG3 A:MET102 4.1 6.5 1.0 CG A:ASN253 4.1 5.6 1.0 CG A:MET102 4.1 5.4 1.0 CA A:ASP82 4.2 0.7 1.0 HE1 A:HIS80 4.2 1.1 1.0 OD1 A:ASN253 4.3 4.7 1.0 CE A:LYS251 4.4 3.9 1.0 HB2 A:ASP82 4.4 0.8 1.0 CB A:ASP82 4.4 0.7 1.0 HE3 A:LYS251 4.4 4.7 1.0 ND1 A:HIS210 4.4 7.3 1.0 N A:HIS83 4.5 0.8 1.0 CD A:GLN47 4.5 7.3 1.0 O3 A:13P405 4.5 16.9 1.0 NE2 A:GLN47 4.6 5.1 1.0 CD2 A:HIS210 4.6 5.5 1.0 CG A:GLU132 4.7 2.5 1.0 HE3 A:MET102 4.7 14.2 1.0 HB3 A:GLU132 4.7 3.5 1.0 CE A:MET102 4.8 11.9 1.0 OD2 A:ASP82 4.8 12.6 1.0 HG2 A:GLU132 4.9 3.0 1.0 HE2 A:LYS251 4.9 4.7 1.0 O A:LEU81 4.9 1.2 1.0 CG A:HIS80 4.9 1.5 1.0 HD2 A:HIS83 4.9 12.0 1.0 C A:ASP82 4.9 4.3 1.0 CG1 A:VAL208 4.9 3.6 1.0 HE1 A:MET102 5.0 14.2 1.0

Sodium binding site 2 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase 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 of Helicobacter Pylori with Dhap within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:15.8 occ:1.00 HE2 B:HIS80 2.1 7.9 1.0 HD21 B:ASN253 2.3 6.4 1.0 HZ1 B:LYS251 2.7 5.9 1.0 HZ2 B:LYS251 2.8 5.9 1.0 OE2 B:GLU132 2.8 6.0 1.0 OD1 B:ASP82 2.8 8.4 1.0 NE2 B:HIS80 2.9 6.6 1.0 HE1 B:HIS210 2.9 24.2 1.0 ND2 B:ASN253 3.1 5.3 1.0 NZ B:LYS251 3.1 4.9 1.0 HE2 B:HIS210 3.2 7.3 1.0 OE1 B:GLU132 3.2 6.2 1.0 HA B:ASP82 3.2 6.1 1.0 HB2 B:MET102 3.3 2.0 1.0 CD B:GLU132 3.3 4.8 1.0 HD22 B:ASN253 3.4 6.4 1.0 HZ3 B:LYS251 3.4 5.9 1.0 CE1 B:HIS210 3.4 20.2 1.0 NE2 B:HIS210 3.5 6.1 1.0 HD2 B:HIS80 3.6 2.6 1.0 SD B:MET102 3.6 8.7 1.0 CD2 B:HIS80 3.6 2.1 1.0 H B:HIS83 3.7 6.4 1.0 OE1 B:GLN47 3.8 6.1 1.0 CG B:ASP82 3.9 12.3 1.0 CE1 B:HIS80 3.9 0.3 1.0 CB B:MET102 3.9 1.7 1.0 HB3 B:MET102 3.9 2.0 1.0 HG3 B:MET102 4.1 4.6 1.0 HG11 B:VAL208 4.1 4.1 1.0 HE21 B:GLN47 4.1 7.0 1.0 CG B:MET102 4.1 3.8 1.0 CG B:ASN253 4.1 2.0 1.0 CA B:ASP82 4.1 5.1 1.0 HE1 B:HIS80 4.1 0.3 1.0 OD1 B:ASN253 4.3 5.5 1.0 CB B:ASP82 4.4 4.9 1.0 CE B:LYS251 4.4 9.3 1.0 HB2 B:ASP82 4.4 5.9 1.0 HE3 B:LYS251 4.5 11.2 1.0 N B:HIS83 4.5 5.3 1.0 ND1 B:HIS210 4.5 12.3 1.0 CD B:GLN47 4.5 8.2 1.0 O3 B:13P404 4.5 19.9 1.0 NE2 B:GLN47 4.6 5.8 1.0 HE3 B:MET102 4.6 13.6 1.0 CD2 B:HIS210 4.7 6.5 1.0 CG B:GLU132 4.7 4.6 1.0 HB3 B:GLU132 4.7 6.2 1.0 CE B:MET102 4.8 11.3 1.0 O B:LEU81 4.8 2.0 1.0 OD2 B:ASP82 4.8 10.4 1.0 CG B:HIS80 4.9 2.5 1.0 C B:ASP82 4.9 5.3 1.0 HG2 B:GLU132 4.9 5.6 1.0 HE2 B:LYS251 4.9 11.2 1.0 CG1 B:VAL208 4.9 3.4 1.0 HD2 B:HIS83 4.9 13.5 1.0 ND1 B:HIS80 5.0 3.9 1.0 HE1 B:MET102 5.0 13.6 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