Zinc 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:

Sodium

(Na)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori, PDB code: 5ucs:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn402 b:22.5 occ:1.00 HE1 A:HIS83 1.3 26.7 0.1 OE1 A:GLU134 2.1 24.2 1.0 NE2 A:HIS180 2.1 22.6 1.0 NE2 A:HIS83 2.1 19.0 0.9 ND1 A:HIS210 2.2 19.4 1.0 CE1 A:HIS83 2.2 22.2 0.1 O A:HOH584 2.3 22.3 1.0 OE2 A:GLU134 2.6 28.4 1.0 CD A:GLU134 2.7 24.2 1.0 NE2 A:HIS83 2.9 21.1 0.1 CE1 A:HIS210 3.0 21.6 1.0 CD2 A:HIS180 3.0 28.3 1.0 HE1 A:HIS210 3.0 26.0 1.0 CE1 A:HIS83 3.0 20.2 0.9 CE1 A:HIS180 3.1 23.5 1.0 HD2 A:HIS180 3.1 34.0 1.0 HE1 A:HIS83 3.1 24.3 0.9 CD2 A:HIS83 3.2 16.1 0.9 ND1 A:HIS83 3.3 23.6 0.1 HE1 A:HIS180 3.3 28.2 1.0 CG A:HIS210 3.3 17.7 1.0 HD2 A:HIS83 3.4 19.4 0.9 HB3 A:HIS210 3.5 22.2 1.0 HD1 A:HIS83 3.6 28.3 0.1 O A:HOH501 3.6 27.7 1.0 HE1 A:MET102 3.6 23.0 1.0 HB2 A:HIS210 3.8 22.2 1.0 CB A:HIS210 3.8 18.5 1.0 O A:HOH709 4.1 30.5 1.0 CG A:HIS180 4.1 24.6 1.0 ND1 A:HIS83 4.2 23.4 0.9 NE2 A:HIS210 4.2 17.7 1.0 CG A:GLU134 4.2 18.9 1.0 CD2 A:HIS83 4.2 15.1 0.1 O A:HOH561 4.2 30.0 1.0 ND1 A:HIS180 4.2 25.2 1.0 CG A:HIS83 4.3 18.6 0.9 OD2 A:ASP104 4.3 20.4 1.0 CG A:HIS83 4.4 19.0 0.1 CD2 A:HIS210 4.4 19.4 1.0 HB2 A:GLU134 4.4 22.9 1.0 CE A:MET102 4.5 19.2 1.0 HE3 A:MET102 4.5 23.0 1.0 HA3 A:GLY181 4.5 37.9 1.0 HG3 A:GLU134 4.6 22.7 1.0 HG2 A:GLU134 4.6 22.7 1.0 CG A:ASP104 4.8 17.4 1.0 O A:HOH618 4.8 30.4 1.0 CB A:GLU134 4.8 19.1 1.0 HE2 A:HIS210 4.9 21.3 1.0 HD1 A:HIS83 4.9 28.0 0.9 HB3 A:GLU134 4.9 22.9 1.0 HD2 A:HIS83 4.9 18.2 0.1 HD1 A:HIS180 5.0 30.2 1.0 HB2 A:ASP104 5.0 21.4 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn402 b:19.8 occ:1.00 HE1 B:HIS83 1.3 24.1 0.1 NE2 B:HIS180 2.0 18.5 1.0 OE1 B:GLU134 2.1 18.4 1.0 NE2 B:HIS83 2.1 16.8 0.9 CE1 B:HIS83 2.1 20.1 0.1 ND1 B:HIS210 2.2 15.8 1.0 O B:HOH613 2.3 18.5 1.0 OE2 B:GLU134 2.7 27.4 1.0 CD B:GLU134 2.7 17.4 1.0 NE2 B:HIS83 2.9 16.7 0.1 CE1 B:HIS210 2.9 15.0 1.0 CE1 B:HIS83 3.0 19.4 0.9 CD2 B:HIS180 3.0 19.1 1.0 HE1 B:HIS210 3.0 18.1 1.0 CE1 B:HIS180 3.0 21.7 1.0 HE1 B:HIS83 3.1 23.3 0.9 HD2 B:HIS180 3.1 22.9 1.0 CD2 B:HIS83 3.2 18.7 0.9 HE1 B:HIS180 3.2 26.1 1.0 ND1 B:HIS83 3.3 17.9 0.1 CG B:HIS210 3.3 14.3 1.0 HD2 B:HIS83 3.4 22.5 0.9 HD1 B:HIS83 3.5 21.5 0.1 HB3 B:HIS210 3.6 20.4 1.0 HE1 B:MET102 3.7 19.8 1.0 O B:HOH502 3.8 45.3 1.0 HB2 B:HIS210 3.8 20.4 1.0 CB B:HIS210 3.8 16.9 1.0 ND1 B:HIS180 4.1 20.2 1.0 O B:HOH730 4.1 26.5 1.0 CG B:HIS180 4.1 21.5 1.0 ND1 B:HIS83 4.1 17.1 0.9 CD2 B:HIS83 4.1 16.5 0.1 NE2 B:HIS210 4.1 15.2 1.0 O B:HOH620 4.1 25.4 1.0 CG B:GLU134 4.2 18.2 1.0 CG B:HIS83 4.3 15.7 0.9 CG B:HIS83 4.3 17.8 0.1 OD2 B:ASP104 4.3 19.1 1.0 CD2 B:HIS210 4.3 13.7 1.0 HB2 B:GLU134 4.4 20.5 1.0 CE B:MET102 4.5 16.5 1.0 HE3 B:MET102 4.5 19.8 1.0 HA3 B:GLY181 4.6 47.5 1.0 HG3 B:GLU134 4.6 21.9 1.0 HG2 B:GLU134 4.6 21.9 1.0 O B:HOH562 4.6 29.0 1.0 CB B:GLU134 4.8 17.1 1.0 CG B:ASP104 4.8 17.3 1.0 HD1 B:HIS180 4.9 24.2 1.0 HE2 B:HIS210 4.9 18.2 1.0 HD1 B:HIS83 4.9 20.6 0.9 HB3 B:GLU134 4.9 20.5 1.0 HD2 B:HIS83 4.9 19.9 0.1 O B:HOH733 4.9 32.1 1.0 HB2 B:ASP104 5.0 16.2 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