Sodium in PDB 5ud4: Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Tbp

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

The structure of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Tbp, PDB code: 5ud4 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)	45.14 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.391, 62.590, 64.817, 81.98, 75.74, 74.23
R / Rfree (%)	13.4 / 17.7

The structure of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Tbp 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 Tbp (pdb code 5ud4). 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 Tbp, PDB code: 5ud4:
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 Tbp


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 Tbp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:16.4 occ:1.00 HD22 A:ASN253 2.3 11.7 1.0 HZ2 A:LYS251 2.6 11.6 1.0 HZ3 A:LYS251 2.7 11.6 1.0 OD1 A:ASP82 2.8 10.5 1.0 NE2 A:HIS80 2.9 6.9 1.0 OE2 A:GLU132 3.0 9.4 1.0 NZ A:LYS251 3.0 9.6 1.0 ND2 A:ASN253 3.1 9.8 1.0 HA A:ASP82 3.1 10.5 1.0 OE1 A:GLU132 3.3 9.6 1.0 HE2 A:HIS210 3.4 14.7 1.0 CD A:GLU132 3.4 9.3 1.0 HZ1 A:LYS251 3.4 11.6 1.0 HB2 A:MET102 3.4 10.6 1.0 HD21 A:ASN253 3.4 11.7 1.0 H A:HIS83 3.5 9.8 0.7 H A:HIS83 3.5 11.0 0.3 HD2 A:HIS80 3.6 9.4 1.0 CD2 A:HIS80 3.7 7.8 1.0 SD A:MET102 3.7 14.9 1.0 OE1 A:GLN47 3.7 10.2 1.0 CG A:ASP82 3.7 10.5 1.0 HD1 A:HIS83 3.8 12.3 0.7 NE2 A:HIS210 3.9 12.2 1.0 HB3 A:MET102 3.9 10.6 1.0 HG3 A:MET102 3.9 14.2 1.0 CB A:MET102 4.0 8.8 1.0 CE1 A:HIS80 4.0 8.6 1.0 CA A:ASP82 4.0 8.8 1.0 CG A:MET102 4.1 11.8 1.0 CG A:ASN253 4.1 8.4 1.0 HE22 A:GLN47 4.1 13.3 1.0 HB2 A:ASP82 4.2 10.8 1.0 HE1 A:HIS80 4.2 10.3 1.0 CB A:ASP82 4.2 9.0 1.0 N A:HIS83 4.2 8.2 0.7 N A:HIS83 4.2 9.1 0.3 OD1 A:ASN253 4.3 10.1 1.0 HE3 A:LYS251 4.3 12.7 1.0 CE A:LYS251 4.3 10.6 1.0 ND1 A:HIS83 4.3 10.3 0.7 HE1 A:HIS83 4.4 13.7 0.7 CD A:GLN47 4.5 9.5 1.0 HD2 A:HIS210 4.5 15.0 1.0 CD2 A:HIS210 4.5 12.5 1.0 HG13 A:VAL208 4.6 9.6 1.0 HO3 A:P6T404 4.6 22.6 1.0 O3 A:P6T404 4.6 18.9 1.0 HD2 A:HIS83 4.6 16.8 0.3 NE2 A:GLN47 4.6 11.1 1.0 CE1 A:HIS83 4.6 11.4 0.7 C A:ASP82 4.6 8.3 1.0 HG12 A:VAL208 4.7 9.6 1.0 CE1 A:HIS210 4.7 13.1 1.0 CG A:GLU132 4.8 8.8 1.0 OD2 A:ASP82 4.8 11.5 1.0 CD2 A:HIS83 4.8 14.0 0.3 O A:LEU81 4.8 8.7 1.0 HB3 A:GLU132 4.8 8.7 1.0 HE2 A:LYS251 4.8 12.7 1.0 HE1 A:HIS210 4.8 15.8 1.0 HE3 A:MET102 4.9 17.9 1.0 CG A:HIS80 4.9 8.1 1.0 HG2 A:GLU132 5.0 10.5 1.0 CE A:MET102 5.0 15.0 1.0

Sodium binding site 2 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Tbp


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 Tbp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:16.8 occ:1.00 HE2 B:HIS80 2.1 7.4 1.0 HD21 B:ASN253 2.3 10.4 1.0 HZ1 B:LYS251 2.6 11.5 1.0 HZ2 B:LYS251 2.8 11.5 1.0 OD1 B:ASP82 2.8 9.7 1.0 NE2 B:HIS80 2.9 6.2 1.0 OE2 B:GLU132 2.9 10.0 1.0 NZ B:LYS251 3.0 9.6 1.0 ND2 B:ASN253 3.1 8.7 1.0 HA B:ASP82 3.1 10.4 1.0 OE1 B:GLU132 3.3 9.8 1.0 HE2 B:HIS210 3.3 13.2 1.0 CD B:GLU132 3.4 10.0 1.0 HZ3 B:LYS251 3.4 11.5 1.0 HB2 B:MET102 3.4 11.6 1.0 HD22 B:ASN253 3.5 10.4 1.0 H B:HIS83 3.6 10.0 0.7 H B:HIS83 3.6 10.9 0.3 HD2 B:HIS80 3.6 7.0 1.0 CD2 B:HIS80 3.7 5.9 1.0 OE1 B:GLN47 3.7 9.6 1.0 SD B:MET102 3.7 14.6 1.0 CG B:ASP82 3.8 10.5 1.0 HD1 B:HIS83 3.8 12.5 0.7 NE2 B:HIS210 3.8 11.0 1.0 HB3 B:MET102 3.9 11.6 1.0 CE1 B:HIS80 4.0 6.8 1.0 CB B:MET102 4.0 9.6 1.0 HG3 B:MET102 4.0 14.2 1.0 CA B:ASP82 4.0 8.6 1.0 CG B:MET102 4.1 11.9 1.0 CG B:ASN253 4.1 8.0 1.0 HE21 B:GLN47 4.1 11.9 1.0 HE1 B:HIS80 4.2 8.2 1.0 HB2 B:ASP82 4.2 11.3 1.0 CB B:ASP82 4.2 9.4 1.0 N B:HIS83 4.3 8.4 0.7 N B:HIS83 4.3 9.1 0.3 ND1 B:HIS83 4.3 10.4 0.7 HE1 B:HIS83 4.3 12.6 0.7 OD1 B:ASN253 4.3 9.4 1.0 CE B:LYS251 4.3 8.3 1.0 HE3 B:LYS251 4.4 10.0 1.0 HD2 B:HIS210 4.4 14.1 1.0 CD2 B:HIS210 4.4 11.8 1.0 CD B:GLN47 4.5 9.4 1.0 HG13 B:VAL208 4.5 9.4 1.0 CE1 B:HIS83 4.5 10.5 0.7 NE2 B:GLN47 4.6 9.9 1.0 HG12 B:VAL208 4.6 9.4 1.0 O3 B:P6T404 4.6 14.6 1.0 CE1 B:HIS210 4.6 12.7 1.0 C B:ASP82 4.7 9.0 1.0 CG B:GLU132 4.7 8.2 1.0 HO3 B:P6T404 4.7 17.5 1.0 HD2 B:HIS83 4.7 14.8 0.3 O B:LEU81 4.7 7.1 1.0 HB3 B:GLU132 4.8 8.1 1.0 OD2 B:ASP82 4.8 12.2 1.0 HE1 B:HIS210 4.8 15.2 1.0 HE2 B:LYS251 4.8 10.0 1.0 CD2 B:HIS83 4.9 12.3 0.3 HG2 B:GLU132 4.9 9.8 1.0 HE3 B:MET102 4.9 18.9 1.0 CG B:HIS80 4.9 6.4 1.0 CE B:MET102 5.0 15.7 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