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Calcium in PDB 5ud0: Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Cleavage Products

Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Cleavage Products

All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Cleavage Products:
4.1.2.13;

Protein crystallography data

The structure of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Cleavage Products, PDB code: 5ud0 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) 29.88 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.258, 85.386, 91.082, 90.00, 100.20, 90.00
R / Rfree (%) 17.8 / 22.3

Other elements in 5ud0:

The structure of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Cleavage Products also contains other interesting chemical elements:

Zinc (Zn) 3 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Cleavage Products (pdb code 5ud0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Cleavage Products, PDB code: 5ud0:

Calcium binding site 1 out of 1 in 5ud0

Go back to Calcium Binding Sites List in 5ud0
Calcium binding site 1 out of 1 in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Cleavage Products


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 E149A Variant of Helicobacter Pylori with Cleavage Products within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:23.2
occ:0.85
 HG B:SER106 1.9 29.9 1.0
OD2 B:ASP104 2.2 19.0 1.0
O B:HOH565 2.2 33.6 1.0
OE1 B:GLU134 2.2 24.6 1.0
OD1 B:ASP104 2.3 21.6 1.0
OG B:SER106 2.4 24.9 1.0
O B:HOH643 2.4 24.5 1.0
O B:HOH634 2.6 47.6 1.0
CG B:ASP104 2.6 18.1 1.0
CD B:GLU134 3.4 21.3 1.0
HE1 B:HIS83 3.5 29.3 1.0
CB B:SER106 3.6 26.7 1.0
HB3 B:SER106 3.6 32.1 1.0
H B:SER106 3.6 26.6 1.0
HB3 B:GLU134 4.1 21.3 1.0
HG2 B:GLU134 4.1 19.6 1.0
CB B:ASP104 4.1 22.6 1.0
OE2 B:GLU134 4.2 22.9 1.0
O B:HOH761 4.2 57.5 1.0
HB2 B:SER106 4.2 32.1 1.0
CG B:GLU134 4.2 16.3 1.0
CE1 B:HIS83 4.3 24.4 1.0
HD1 B:HIS83 4.3 34.6 1.0
N B:SER106 4.3 22.2 1.0
O B:HOH502 4.3 14.4 1.0
H B:HIS107 4.4 26.7 1.0
HB2 B:ASP104 4.4 27.1 1.0
CA B:SER106 4.4 22.2 1.0
HB3 B:ASP104 4.5 27.1 1.0
ND1 B:HIS83 4.6 28.9 1.0
CB B:GLU134 4.6 17.7 1.0
N B:HIS107 4.7 22.3 1.0
HE1 B:MET102 4.8 30.5 1.0
C B:SER106 4.8 24.2 1.0
HA B:ASP104 4.8 21.4 1.0
HB2 B:GLU134 4.9 21.3 1.0
CA B:ASP104 4.9 17.8 1.0
O B:HOH664 5.0 28.5 1.0

Reference:

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
Page generated: Mon Jul 15 11:28:54 2024

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