Calcium 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
Sodium	(Na)	2 atoms

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

Calcium 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 Calcium with other atoms in the Ca 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:Ca403 b:17.3 occ:1.00 O A:HOH714 2.3 26.2 1.0 OE1 A:GLU134 2.3 16.9 1.0 OD2 A:ASP104 2.3 11.5 1.0 OD1 A:ASP104 2.4 6.5 1.0 O A:HOH717 2.5 33.9 1.0 O A:HOH759 2.5 17.4 1.0 OG A:SER106 2.5 7.2 1.0 CG A:ASP104 2.7 7.1 1.0 CD A:GLU134 3.5 18.9 1.0 HE1 A:HIS83 3.5 8.5 1.0 CB A:SER106 3.7 10.8 1.0 HB3 A:SER106 3.7 12.9 1.0 H A:SER106 3.7 8.2 1.0 HD1 A:HIS83 4.1 14.1 1.0 HB3 A:GLU134 4.1 3.9 1.0 CB A:ASP104 4.2 6.1 1.0 HG2 A:GLU134 4.2 5.3 1.0 CE1 A:HIS83 4.2 7.1 1.0 O A:HOH512 4.3 18.6 1.0 CG A:GLU134 4.4 4.5 1.0 HB2 A:SER106 4.4 12.9 1.0 OE2 A:GLU134 4.4 20.7 1.0 N A:SER106 4.4 6.8 1.0 HD1 A:HIS107 4.4 20.9 1.0 ND1 A:HIS83 4.5 11.7 1.0 HB2 A:ASP104 4.5 7.4 1.0 H A:HIS107 4.5 8.9 1.0 CA A:SER106 4.6 5.9 1.0 HB3 A:ASP104 4.6 7.4 1.0 CB A:GLU134 4.7 3.2 1.0 HE1 A:MET102 4.7 14.2 1.0 N A:HIS107 4.9 7.4 1.0 HB2 A:GLU134 4.9 3.9 1.0 HA A:ASP104 4.9 6.6 1.0 O A:HOH564 5.0 18.6 1.0 HE2 A:MET102 5.0 14.2 1.0 C A:SER106 5.0 7.0 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca403 b:19.0 occ:1.00 OE1 B:GLU134 2.3 17.3 1.0 OD1 B:ASP104 2.3 12.1 1.0 OG B:SER106 2.4 10.9 1.0 O B:HOH689 2.4 27.2 1.0 O B:HOH728 2.4 25.3 1.0 O B:HOH742 2.4 16.5 1.0 OD2 B:ASP104 2.4 9.3 1.0 CG B:ASP104 2.7 9.3 1.0 CD B:GLU134 3.5 26.6 1.0 HE1 B:HIS83 3.5 12.6 1.0 CB B:SER106 3.6 7.8 1.0 HB3 B:SER106 3.6 9.4 1.0 H B:SER106 3.8 8.5 1.0 HB3 B:GLU134 4.1 9.4 1.0 HB2 B:SER106 4.2 9.4 1.0 CB B:ASP104 4.2 3.9 1.0 HD1 B:HIS83 4.2 12.6 1.0 HG2 B:GLU134 4.3 13.8 1.0 CE1 B:HIS83 4.3 10.5 1.0 OE2 B:GLU134 4.3 19.4 1.0 CG B:GLU134 4.4 11.5 1.0 HD1 B:HIS107 4.4 26.5 1.0 N B:SER106 4.4 7.1 1.0 O B:HOH545 4.4 17.6 1.0 H B:HIS107 4.5 10.0 1.0 CA B:SER106 4.5 8.8 1.0 HB2 B:ASP104 4.5 4.7 1.0 ND1 B:HIS83 4.6 10.5 1.0 HB3 B:ASP104 4.6 4.7 1.0 CB B:GLU134 4.7 7.8 1.0 HE1 B:MET102 4.8 13.6 1.0 N B:HIS107 4.8 8.3 1.0 HB2 B:GLU134 4.9 9.4 1.0 O B:HOH732 4.9 22.6 1.0 HA B:ASP104 5.0 6.4 1.0 C B:SER106 5.0 13.0 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