Zinc in PDB 5uck: Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products

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

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

Protein crystallography data

The structure of Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products, PDB code: 5uck 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) 45.19 / 1.78
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.384, 62.843, 64.754, 82.23, 75.97, 74.40
R / Rfree (%) 19.1 / 23.2

Other elements in 5uck:

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

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products (pdb code 5uck). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products, PDB code: 5uck:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5uck

Go back to Zinc Binding Sites List in 5uck
Zinc binding site 1 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products


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 Cleavage Products within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:55.6
occ:0.70
HE1 A:HIS83 1.8 37.5 0.3
O A:HOH513 2.4 27.1 1.0
NE2 A:HIS83 2.6 31.6 0.7
ND1 A:HIS210 2.6 13.7 0.7
CE1 A:HIS83 2.6 31.3 0.3
OE2 A:GLU134 2.8 43.7 1.0
OE1 A:GLU134 2.9 42.0 1.0
NE2 A:HIS83 3.1 31.9 0.3
CD A:GLU134 3.2 39.6 1.0
CE1 A:HIS210 3.4 13.2 0.7
CE1 A:HIS83 3.4 32.5 0.7
HE1 A:HIS210 3.4 15.8 0.7
HE1 A:HIS83 3.4 39.0 0.7
NE2 A:HIS180 3.5 79.0 1.0
ND1 A:HIS210 3.5 14.2 0.3
CG A:HIS210 3.6 15.0 0.7
CD2 A:HIS83 3.7 31.1 0.7
HB3 A:HIS210 3.7 20.7 0.3
HB3 A:HIS210 3.7 20.7 0.7
ZN A:ZN403 3.8 38.2 0.3
HB2 A:HIS210 3.8 20.7 0.3
CG A:HIS210 3.8 15.2 0.3
ND1 A:HIS83 3.8 30.6 0.3
HB2 A:HIS210 3.8 20.7 0.7
HD2 A:HIS83 3.9 37.2 0.7
HE1 A:MET102 3.9 35.5 1.0
CE1 A:HIS180 4.0 84.6 1.0
CB A:HIS210 4.0 17.3 0.7
CB A:HIS210 4.0 17.3 0.3
HD1 A:HIS83 4.1 36.7 0.3
CE1 A:HIS210 4.1 13.5 0.3
O A:HOH505 4.2 26.5 1.0
O A:HOH509 4.2 28.3 1.0
O A:HOH629 4.3 30.3 1.0
OD2 A:ASP104 4.3 27.7 1.0
CD2 A:HIS180 4.3 85.8 1.0
CD2 A:HIS83 4.4 31.0 0.3
HE1 A:HIS210 4.5 16.2 0.3
CD2 A:HIS210 4.5 13.5 0.3
NE2 A:HIS210 4.5 13.2 0.7
ND1 A:HIS83 4.6 30.8 0.7
CD2 A:HIS210 4.7 12.9 0.7
CG A:GLU134 4.7 29.8 1.0
NE2 A:HIS210 4.7 12.6 0.3
CG A:HIS83 4.8 29.9 0.7
CG A:HIS83 4.8 30.2 0.3
O A:HOH503 4.9 40.0 1.0
CE A:MET102 4.9 29.6 1.0
ND1 A:HIS180 4.9 85.6 1.0
HG3 A:GLU134 5.0 35.7 1.0

Zinc binding site 2 out of 4 in 5uck

Go back to Zinc Binding Sites List in 5uck
Zinc binding site 2 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products


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 Cleavage Products within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:38.2
occ:0.30
HE1 A:HIS83 1.3 39.0 0.7
NE2 A:HIS180 2.0 79.0 1.0
CE1 A:HIS83 2.0 32.5 0.7
NE2 A:HIS83 2.1 31.9 0.3
ND1 A:HIS210 2.3 14.2 0.3
O3 A:13P404 2.3 32.3 0.7
O1 A:G3H405 2.7 20.2 0.3
HB3 A:HIS210 2.7 20.7 0.7
O2 A:13P404 2.7 43.1 0.7
HB3 A:HIS210 2.7 20.7 0.3
HD2 A:HIS83 2.8 37.2 0.3
CD2 A:HIS83 2.8 31.0 0.3
HO3 A:13P404 2.9 38.7 0.7
NE2 A:HIS83 2.9 31.6 0.7
CD2 A:HIS180 2.9 85.8 1.0
ND1 A:HIS83 3.0 30.8 0.7
CE1 A:HIS180 3.0 84.6 1.0
HD1 A:HIS83 3.2 36.9 0.7
H11 A:G3H405 3.2 24.9 0.3
HD22 A:ASN253 3.2 24.6 1.0
CG A:HIS210 3.2 15.2 0.3
CE1 A:HIS83 3.3 31.3 0.3
CG A:HIS210 3.3 15.0 0.7
CE1 A:HIS210 3.3 13.5 0.3
CB A:HIS210 3.4 17.3 0.3
CB A:HIS210 3.4 17.3 0.7
ND1 A:HIS210 3.5 13.7 0.7
O1 A:G3H405 3.5 20.2 0.3
HE1 A:HIS210 3.5 16.2 0.3
C3 A:13P404 3.5 36.1 0.7
C2 A:13P404 3.5 40.4 0.7
HE1 A:HIS83 3.6 37.5 0.3
C1 A:G3H405 3.7 20.8 0.3
ZN A:ZN402 3.8 55.6 0.7
C1 A:G3H405 3.8 20.3 0.3
CD2 A:HIS210 3.8 12.9 0.7
H A:GLY211 3.9 29.1 1.0
ND2 A:ASN253 4.0 20.5 1.0
ND1 A:HIS180 4.0 85.6 1.0
CD2 A:HIS83 4.0 31.1 0.7
CE1 A:HIS210 4.0 13.2 0.7
CG A:HIS180 4.0 89.9 1.0
CG A:HIS83 4.0 30.2 0.3
CG A:HIS83 4.1 29.9 0.7
H11 A:G3H405 4.1 24.3 0.3
HA A:HIS210 4.1 23.8 0.7
HB2 A:HIS210 4.1 20.7 0.3
H32 A:13P404 4.1 43.3 0.7
HB2 A:HIS210 4.1 20.7 0.7
HA A:HIS210 4.1 23.9 0.3
OD1 A:ASP82 4.2 24.2 1.0
HD2 A:HIS210 4.2 15.4 0.7
NE2 A:HIS210 4.2 13.2 0.7
H31 A:13P404 4.2 43.3 0.7
ND1 A:HIS83 4.2 30.6 0.3
HD21 A:ASN253 4.2 24.6 1.0
CA A:HIS210 4.4 19.8 0.7
CA A:HIS210 4.4 20.0 0.3
CD2 A:HIS210 4.4 13.5 0.3
NE2 A:HIS210 4.4 12.6 0.3
HB3 A:ASN253 4.5 14.5 1.0
N A:GLY211 4.6 24.3 1.0
HE1 A:HIS210 4.6 15.8 0.7
HB2 A:ASN253 4.8 14.5 1.0
HE2 A:HIS210 4.8 15.8 0.7
HD2 A:HIS83 4.8 37.2 0.7
CG A:ASN253 4.9 16.1 1.0
C1 A:13P404 5.0 39.8 0.7
OD2 A:ASP82 5.0 27.3 1.0
C A:HIS210 5.0 23.1 0.3
C A:HIS210 5.0 23.2 0.7
CB A:ASN253 5.0 12.1 1.0

Zinc binding site 3 out of 4 in 5uck

Go back to Zinc Binding Sites List in 5uck
Zinc binding site 3 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:48.4
occ:0.60
HE1 B:HIS83 2.1 34.8 0.4
OE2 B:GLU134 2.4 46.5 1.0
O B:HOH530 2.5 28.9 1.0
ND1 B:HIS210 2.7 22.5 0.6
NE2 B:HIS83 2.8 29.9 0.6
CE1 B:HIS83 2.8 29.1 0.4
OE1 B:GLU134 2.8 46.3 1.0
CE1 B:HIS180 2.8 68.6 1.0
CD B:GLU134 2.9 42.2 1.0
NE2 B:HIS180 3.2 65.0 1.0
NE2 B:HIS83 3.2 30.5 0.4
HE1 B:HIS83 3.3 36.8 0.6
CE1 B:HIS83 3.4 30.7 0.6
ND1 B:HIS210 3.5 24.9 0.4
HB3 B:HIS210 3.6 26.4 0.4
HB3 B:HIS210 3.6 26.5 0.6
CE1 B:HIS210 3.6 23.8 0.6
CG B:HIS210 3.6 23.7 0.4
CG B:HIS210 3.7 23.8 0.6
HB2 B:HIS210 3.7 26.5 0.6
HB2 B:HIS210 3.7 26.4 0.4
ZN B:ZN403 3.7 32.1 0.4
HE1 B:HIS210 3.7 28.5 0.6
CB B:HIS210 3.8 22.1 0.4
CB B:HIS210 3.9 22.1 0.6
CD2 B:HIS83 4.0 29.3 0.6
HE1 B:MET102 4.0 34.7 1.0
CE1 B:HIS210 4.1 23.6 0.4
ND1 B:HIS180 4.1 68.9 1.0
ND1 B:HIS83 4.1 28.6 0.4
O B:HOH507 4.2 23.2 1.0
HD2 B:HIS83 4.3 35.1 0.6
CD2 B:HIS210 4.3 24.0 0.4
CG B:GLU134 4.4 30.7 1.0
HD1 B:HIS83 4.5 34.3 0.4
HE1 B:HIS210 4.5 28.3 0.4
CD2 B:HIS180 4.5 68.7 1.0
NE2 B:HIS210 4.5 24.3 0.4
CD2 B:HIS83 4.5 28.8 0.4
ND1 B:HIS83 4.7 28.9 0.6
HG3 B:GLU134 4.7 36.8 1.0
OD2 B:ASP104 4.7 27.3 1.0
NE2 B:HIS210 4.8 23.8 0.6
CD2 B:HIS210 4.8 23.2 0.6
HD2 B:HIS210 4.8 28.7 0.4
HG2 B:GLU134 4.9 36.8 1.0
CE B:MET102 4.9 29.0 1.0
HB2 B:GLU134 5.0 25.3 1.0
CG B:HIS180 5.0 69.5 1.0
CG B:HIS83 5.0 28.0 0.6
CG B:HIS83 5.0 28.0 0.4

Zinc binding site 4 out of 4 in 5uck

Go back to Zinc Binding Sites List in 5uck
Zinc binding site 4 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:32.1
occ:0.40
HE1 B:HIS83 1.2 36.8 0.6
HO3 B:13P404 1.8 36.0 0.7
CE1 B:HIS83 2.0 30.7 0.6
NE2 B:HIS180 2.0 65.0 1.0
NE2 B:HIS83 2.1 30.5 0.4
ND1 B:HIS210 2.1 24.9 0.4
O3 B:13P404 2.5 30.1 0.7
CD2 B:HIS180 2.6 68.7 1.0
O2 B:13P404 2.7 37.7 0.7
HD2 B:HIS83 2.7 34.5 0.4
CD2 B:HIS83 2.7 28.8 0.4
ND1 B:HIS83 2.9 28.9 0.6
NE2 B:HIS83 2.9 29.9 0.6
HB3 B:HIS210 2.9 26.5 0.6
CE1 B:HIS210 3.0 23.6 0.4
HB3 B:HIS210 3.0 26.4 0.4
HD1 B:HIS83 3.0 34.6 0.6
HE1 B:HIS210 3.1 28.3 0.4
CE1 B:HIS180 3.1 68.6 1.0
H11 B:G3H405 3.1 22.4 0.3
CG B:HIS210 3.2 23.7 0.4
CE1 B:HIS83 3.2 29.1 0.4
HD22 B:ASN253 3.3 23.2 1.0
O1 B:G3H405 3.4 18.5 0.3
O1 B:G3H405 3.4 18.2 0.3
C2 B:13P404 3.4 36.4 0.7
ND1 B:HIS210 3.4 22.5 0.6
C3 B:13P404 3.5 32.6 0.7
CG B:HIS210 3.5 23.8 0.6
CB B:HIS210 3.6 22.1 0.4
CB B:HIS210 3.6 22.1 0.6
C1 B:G3H405 3.6 18.7 0.3
HE1 B:HIS83 3.6 34.8 0.4
ZN B:ZN402 3.7 48.4 0.6
CG B:HIS180 3.9 69.5 1.0
H32 B:13P404 3.9 39.1 0.7
CG B:HIS83 4.0 28.0 0.4
CD2 B:HIS83 4.0 29.3 0.6
CG B:HIS83 4.0 28.0 0.6
ND1 B:HIS180 4.1 68.9 1.0
CE1 B:HIS210 4.1 23.8 0.6
ND2 B:ASN253 4.1 19.3 1.0
H B:GLY211 4.1 31.4 1.0
CD2 B:HIS210 4.1 23.2 0.6
NE2 B:HIS210 4.2 24.3 0.4
ND1 B:HIS83 4.2 28.6 0.4
OD1 B:ASP82 4.2 26.6 1.0
HB2 B:HIS210 4.3 26.5 0.6
CD2 B:HIS210 4.3 24.0 0.4
HA B:HIS210 4.3 26.6 0.4
HA B:HIS210 4.3 26.7 0.6
HB2 B:HIS210 4.3 26.4 0.4
HD21 B:ASN253 4.3 23.2 1.0
H31 B:13P404 4.4 39.1 0.7
NE2 B:HIS210 4.4 23.8 0.6
HE1 B:HIS210 4.5 28.5 0.6
CA B:HIS210 4.5 22.2 0.4
CA B:HIS210 4.6 22.3 0.6
C1 B:G3H405 4.6 19.0 0.3
HD2 B:HIS210 4.6 27.8 0.6
HO2 B:G3H405 4.7 23.5 0.3
HB3 B:ASN253 4.7 18.7 1.0
N B:GLY211 4.8 26.2 1.0
OD2 B:ASP82 4.8 28.8 1.0
HD2 B:HIS83 4.8 35.1 0.6
C1 B:13P404 4.9 37.9 0.7
HE2 B:HIS210 4.9 29.1 0.4
CG B:ASP82 4.9 25.8 1.0
O2 B:G3H405 5.0 19.6 0.3
HD1 B:HIS83 5.0 34.3 0.4

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: Wed Dec 16 11:00:57 2020

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