Zinc 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:

Calcium	(Ca)	2 atoms
Sodium	(Na)	2 atoms

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

Zinc 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 Zinc with other atoms in the Zn 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:Zn401 b:32.3 occ:1.00 NE2 A:HIS180 1.9 29.9 1.0 NE2 A:HIS83 2.0 17.1 1.0 ND1 A:HIS210 2.0 7.3 1.0 HE1 A:HIS180 2.5 44.9 1.0 CE1 A:HIS180 2.5 37.4 1.0 O A:HOH512 2.7 18.6 1.0 HB3 A:HIS210 2.7 4.1 1.0 CE1 A:HIS83 2.9 7.1 1.0 CG A:HIS210 3.0 6.0 1.0 CE1 A:HIS210 3.0 11.9 1.0 HE1 A:HIS83 3.0 8.5 1.0 CD2 A:HIS83 3.0 10.0 1.0 HE1 A:HIS210 3.2 14.2 1.0 CD2 A:HIS180 3.2 27.9 1.0 O3 A:13P405 3.3 16.9 1.0 HD2 A:HIS83 3.3 12.0 1.0 CB A:HIS210 3.3 3.4 1.0 O2 A:13P405 3.4 14.4 1.0 HD2 A:HIS180 3.6 33.5 1.0 ND1 A:HIS180 3.8 42.5 1.0 HB2 A:HIS210 3.8 4.1 1.0 ND1 A:HIS83 4.0 11.7 1.0 HD22 A:ASN253 4.0 5.8 1.0 NE2 A:HIS210 4.1 7.3 1.0 HD22 A:LEU138 4.1 33.4 0.5 CD2 A:HIS210 4.1 5.5 1.0 C2 A:13P405 4.1 18.2 1.0 CG A:HIS180 4.1 20.9 1.0 CG A:HIS83 4.1 9.0 1.0 C3 A:13P405 4.1 17.1 1.0 H A:GLY211 4.3 8.6 1.0 HA A:HIS210 4.5 2.5 1.0 HE1 A:MET102 4.5 14.2 1.0 HD1 A:HIS180 4.5 50.9 1.0 CA A:HIS210 4.5 2.0 1.0 OE2 A:GLU134 4.5 20.7 1.0 OD1 A:ASP82 4.7 8.9 1.0 ND2 A:ASN253 4.7 4.8 1.0 CD2 A:LEU138 4.8 27.9 0.5 HD1 A:HIS83 4.8 14.1 1.0 HD21 A:LEU138 4.8 33.4 0.5 HE2 A:HIS210 4.9 8.8 1.0 HD23 A:LEU138 4.9 33.4 0.5 N A:GLY211 4.9 7.2 1.0 HD2 A:HIS210 4.9 6.6 1.0 HD21 A:ASN253 5.0 5.8 1.0 O A:HOH714 5.0 26.2 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn401 b:35.7 occ:1.00 NE2 B:HIS180 2.0 21.7 1.0 NE2 B:HIS83 2.0 17.3 1.0 ND1 B:HIS210 2.0 12.3 1.0 HE1 B:HIS180 2.4 31.5 1.0 CE1 B:HIS180 2.5 26.3 1.0 O B:HOH545 2.6 17.6 1.0 HB3 B:HIS210 2.7 5.1 1.0 CE1 B:HIS83 2.9 10.5 1.0 CE1 B:HIS210 3.0 20.2 1.0 CG B:HIS210 3.0 8.4 1.0 CD2 B:HIS83 3.0 11.3 1.0 HE1 B:HIS83 3.1 12.6 1.0 HE1 B:HIS210 3.2 24.2 1.0 O3 B:13P404 3.2 19.9 1.0 HD2 B:HIS83 3.2 13.5 1.0 CD2 B:HIS180 3.3 34.5 1.0 CB B:HIS210 3.3 4.2 1.0 O2 B:13P404 3.5 15.6 1.0 HD2 B:HIS180 3.7 41.4 1.0 ND1 B:HIS180 3.7 40.1 1.0 HB2 B:HIS210 3.8 5.1 1.0 C3 B:13P404 4.0 19.8 1.0 C2 B:13P404 4.1 19.6 1.0 ND1 B:HIS83 4.1 10.5 1.0 HD22 B:ASN253 4.1 6.4 1.0 NE2 B:HIS210 4.1 6.1 1.0 CD2 B:HIS210 4.1 6.5 1.0 CG B:HIS83 4.1 8.9 1.0 CG B:HIS180 4.1 22.5 1.0 HD22 B:LEU138 4.3 42.9 0.5 H B:GLY211 4.4 6.8 1.0 HD1 B:HIS180 4.4 48.1 1.0 HA B:HIS210 4.4 6.0 1.0 O B:HOH806 4.5 37.2 0.5 HE1 B:MET102 4.5 13.6 1.0 CA B:HIS210 4.5 5.0 1.0 HD21 B:LEU138 4.6 42.9 0.5 OE2 B:GLU134 4.6 19.4 1.0 OD1 B:ASP82 4.7 8.4 1.0 ND2 B:ASN253 4.8 5.3 1.0 CD2 B:LEU138 4.8 35.8 0.5 HD1 B:HIS83 4.8 12.6 1.0 HE2 B:HIS210 4.9 7.3 1.0 HD23 B:LEU138 4.9 42.9 0.5 O B:HOH728 4.9 25.3 1.0 N B:GLY211 4.9 5.7 1.0 HD2 B:HIS210 5.0 7.8 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