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Zinc in PDB 5ucz: Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap

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

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

Protein crystallography data

The structure of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap, PDB code: 5ucz 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) 29.91 / 1.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.474, 86.133, 91.196, 90.00, 100.28, 90.00
R / Rfree (%) 18.4 / 22.7

Other elements in 5ucz:

The structure of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap 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 E149A Variant of Helicobacter Pylori with Dhap (pdb code 5ucz). 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 E149A Variant of Helicobacter Pylori with Dhap, PDB code: 5ucz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5ucz

Go back to Zinc Binding Sites List in 5ucz
Zinc binding site 1 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant 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 E149A Variant of Helicobacter Pylori with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:47.4
occ:0.50
HE1 A:HIS83 1.9 89.6 0.5
ZN A:ZN403 2.1 51.6 0.5
ND1 A:HIS210 2.5 55.8 0.5
OE2 A:GLU134 2.5 55.1 1.0
NE2 A:HIS83 2.6 78.6 0.5
CE1 A:HIS83 2.6 74.6 0.5
OE1 A:GLU134 2.7 71.1 1.0
HE1 A:HIS83 2.8 87.6 0.5
CD A:GLU134 2.9 52.9 1.0
CE1 A:HIS83 3.0 73.0 0.5
NE2 A:HIS83 3.0 76.7 0.5
HB3 A:HIS210 3.2 49.6 0.5
HB3 A:HIS210 3.2 49.7 0.5
ND1 A:HIS210 3.2 44.5 0.5
CG A:HIS210 3.4 42.4 0.5
CG A:HIS210 3.4 41.9 0.5
HB2 A:HIS210 3.4 49.6 0.5
HB2 A:HIS210 3.5 49.7 0.5
CE1 A:HIS210 3.5 53.5 0.5
CB A:HIS210 3.6 41.4 0.5
CB A:HIS210 3.6 41.4 0.5
HE1 A:HIS210 3.7 64.2 0.5
ND1 A:HIS83 3.8 70.5 0.5
CD2 A:HIS83 3.8 67.5 0.5
NE2 A:HIS180 3.8 73.3 1.0
CE1 A:HIS210 3.9 47.2 0.5
CD2 A:HIS210 4.1 43.6 0.5
HE1 A:MET102 4.2 65.6 1.0
HD1 A:HIS83 4.2 84.5 0.5
HD2 A:HIS83 4.3 81.0 0.5
O A:HOH501 4.3 37.2 1.0
ND1 A:HIS83 4.3 71.2 0.5
CD2 A:HIS180 4.3 74.7 1.0
HE1 A:HIS210 4.3 56.6 0.5
CD2 A:HIS83 4.4 67.6 0.5
NE2 A:HIS210 4.4 41.2 0.5
CG A:GLU134 4.4 34.7 1.0
OD2 A:ASP104 4.5 45.6 1.0
CD2 A:HIS210 4.6 48.2 0.5
NE2 A:HIS210 4.6 40.7 0.5
CE1 A:HIS180 4.7 76.5 1.0
HG3 A:GLU134 4.7 41.7 1.0
HD2 A:HIS210 4.7 52.3 0.5
CG A:HIS83 4.7 63.5 0.5
CG A:HIS83 4.8 63.2 0.5
HB2 A:GLU134 4.9 36.9 1.0
HD1 A:HIS83 4.9 85.5 0.5
HE3 A:MET102 4.9 65.6 1.0
HG2 A:GLU134 4.9 41.7 1.0
CE A:MET102 5.0 54.6 1.0

Zinc binding site 2 out of 4 in 5ucz

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Zinc binding site 2 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant 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 E149A Variant of Helicobacter Pylori with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:51.6
occ:0.50
HE1 A:HIS83 1.3 87.6 0.5
NE2 A:HIS83 1.9 76.7 0.5
NE2 A:HIS180 1.9 73.3 1.0
CE1 A:HIS83 1.9 73.0 0.5
ZN A:ZN402 2.1 47.4 0.5
HE1 A:HIS83 2.4 89.6 0.5
ND1 A:HIS210 2.4 44.5 0.5
NE2 A:HIS83 2.4 78.6 0.5
CE1 A:HIS83 2.4 74.6 0.5
HB3 A:HIS210 2.6 49.6 0.5
HB3 A:HIS210 2.6 49.7 0.5
ND1 A:HIS210 2.6 55.8 0.5
CE1 A:HIS180 2.7 76.5 1.0
CD2 A:HIS180 2.8 74.7 1.0
CG A:HIS210 3.1 42.4 0.5
ND1 A:HIS83 3.2 71.2 0.5
CD2 A:HIS83 3.2 67.6 0.5
CG A:HIS210 3.2 41.9 0.5
CB A:HIS210 3.3 41.4 0.5
CB A:HIS210 3.3 41.4 0.5
CE1 A:HIS210 3.4 47.2 0.5
O3 A:13P404 3.4 34.7 0.3
O3 A:13P404 3.4 34.8 0.3
HD1 A:HIS83 3.6 85.5 0.5
CE1 A:HIS210 3.6 53.5 0.5
HD2 A:HIS83 3.6 81.1 0.5
ND1 A:HIS83 3.7 70.5 0.5
HE1 A:HIS210 3.7 56.6 0.5
HB2 A:HIS210 3.7 49.6 0.5
HB2 A:HIS210 3.7 49.7 0.5
CD2 A:HIS83 3.7 67.5 0.5
O2 A:13P404 3.8 34.6 0.3
ND1 A:HIS180 3.8 72.2 1.0
O2 A:13P404 3.8 34.6 0.3
HO3 A:13P404 3.8 41.8 0.3
HO3 A:13P404 3.8 41.7 0.3
CG A:HIS180 3.8 70.8 1.0
HE1 A:HIS210 3.9 64.2 0.5
CG A:HIS83 4.0 63.2 0.5
CG A:HIS83 4.0 63.5 0.5
CD2 A:HIS210 4.2 43.6 0.5
CD2 A:HIS210 4.3 48.2 0.5
HD22 A:ASN253 4.3 40.1 1.0
NE2 A:HIS210 4.3 41.2 0.5
HD1 A:HIS83 4.3 84.5 0.5
C3 A:13P404 4.4 34.7 0.3
C2 A:13P404 4.4 34.5 0.3
H A:GLY211 4.4 55.7 1.0
HD2 A:HIS83 4.4 81.0 0.5
OE1 A:GLU134 4.4 71.1 1.0
NE2 A:HIS210 4.4 40.7 0.5
C3 A:13P404 4.5 34.7 0.3
C2 A:13P404 4.5 34.6 0.3
CA A:HIS210 4.5 30.8 0.5
CA A:HIS210 4.5 30.8 0.5
OE2 A:GLU134 4.5 55.1 1.0
HA A:HIS210 4.6 37.0 0.5
HA A:HIS210 4.6 37.0 0.5
H32 A:13P404 4.6 41.6 0.3
H32 A:13P404 4.7 41.7 0.3
N A:GLY211 4.8 46.4 1.0
CD A:GLU134 4.9 52.9 1.0
ND2 A:ASN253 5.0 33.5 1.0

Zinc binding site 3 out of 4 in 5ucz

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Zinc binding site 3 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant 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 3 of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:43.4
occ:0.50
ZN B:ZN403 1.2 45.6 0.5
O B:HOH503 1.9 26.2 1.0
NE2 B:HIS83 2.0 32.5 1.0
NE2 B:HIS180 2.1 46.8 1.0
ND1 B:HIS210 2.4 26.4 1.0
CE1 B:HIS83 2.7 39.4 1.0
HE1 B:HIS83 2.7 47.2 1.0
CE1 B:HIS180 2.8 55.0 1.0
HB3 B:HIS210 2.8 34.9 1.0
HE1 B:HIS180 2.8 66.0 1.0
CD2 B:HIS83 3.2 23.8 1.0
CG B:HIS210 3.2 19.8 1.0
CD2 B:HIS180 3.2 50.1 1.0
CE1 B:HIS210 3.4 24.2 1.0
CB B:HIS210 3.4 29.1 1.0
O B:HOH642 3.5 43.5 1.0
HD2 B:HIS180 3.5 60.1 1.0
HD2 B:HIS83 3.5 28.6 1.0
HE1 B:HIS210 3.6 29.0 1.0
O3 B:13P404 3.7 29.8 0.4
HB2 B:HIS210 3.8 34.9 1.0
O3 B:13P404 3.8 29.9 0.4
ND1 B:HIS83 3.9 38.6 1.0
ND1 B:HIS180 4.0 57.8 1.0
HO3 B:13P404 4.0 35.7 0.4
OE2 B:GLU134 4.0 41.1 1.0
O2 B:13P404 4.1 29.4 0.4
CG B:HIS83 4.2 41.2 1.0
CG B:HIS180 4.2 53.0 1.0
O2 B:13P404 4.2 29.9 0.4
HO3 B:13P404 4.3 35.9 0.4
CD2 B:HIS210 4.3 30.7 1.0
NE2 B:HIS210 4.4 22.9 1.0
HE1 B:MET102 4.4 44.9 1.0
HD22 B:ASN253 4.6 30.7 1.0
HD1 B:HIS83 4.6 46.3 1.0
HD1 B:HIS180 4.7 69.3 1.0
H B:GLY211 4.7 26.4 1.0
CA B:HIS210 4.7 29.1 1.0
OE1 B:GLU134 4.8 53.6 1.0
C3 B:13P404 4.8 29.6 0.4
CD B:GLU134 4.8 38.8 1.0
HA B:HIS210 4.8 34.9 1.0
C2 B:13P404 4.8 29.3 0.4
C2 B:13P404 4.8 29.7 0.4
C3 B:13P404 4.9 29.9 0.4

Zinc binding site 4 out of 4 in 5ucz

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Zinc binding site 4 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant 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 4 of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:45.6
occ:0.50
ZN B:ZN402 1.2 43.4 0.5
NE2 B:HIS180 1.9 46.8 1.0
NE2 B:HIS83 2.1 32.5 1.0
ND1 B:HIS210 2.1 26.4 1.0
HE1 B:HIS180 2.2 66.0 1.0
CE1 B:HIS180 2.3 55.0 1.0
O3 B:13P404 2.5 29.8 0.4
O3 B:13P404 2.6 29.9 0.4
HB3 B:HIS210 2.8 34.9 1.0
CD2 B:HIS83 2.8 23.8 1.0
HO3 B:13P404 2.9 35.7 0.4
HD2 B:HIS83 2.9 28.6 1.0
CE1 B:HIS210 3.0 24.2 1.0
O B:HOH503 3.1 26.2 1.0
HO3 B:13P404 3.1 35.9 0.4
CG B:HIS210 3.1 19.8 1.0
O2 B:13P404 3.2 29.4 0.4
CE1 B:HIS83 3.2 39.4 1.0
HE1 B:HIS210 3.2 29.0 1.0
CD2 B:HIS180 3.3 50.1 1.0
O2 B:13P404 3.3 29.9 0.4
CB B:HIS210 3.4 29.1 1.0
HE1 B:HIS83 3.5 47.2 1.0
HD22 B:ASN253 3.5 30.7 1.0
ND1 B:HIS180 3.6 57.8 1.0
C3 B:13P404 3.6 29.6 0.4
C3 B:13P404 3.7 29.9 0.4
HD2 B:HIS180 3.8 60.1 1.0
C2 B:13P404 3.8 29.3 0.4
C2 B:13P404 3.8 29.7 0.4
H32 B:13P404 4.0 35.5 0.4
HB2 B:HIS210 4.1 34.9 1.0
H32 B:13P404 4.1 35.8 0.4
CG B:HIS83 4.1 41.2 1.0
CG B:HIS180 4.1 53.0 1.0
NE2 B:HIS210 4.2 22.9 1.0
ND1 B:HIS83 4.2 38.6 1.0
CD2 B:HIS210 4.2 30.7 1.0
H B:GLY211 4.2 26.4 1.0
HD1 B:HIS180 4.3 69.3 1.0
ND2 B:ASN253 4.3 25.6 1.0
HA B:HIS210 4.4 34.9 1.0
H31 B:13P404 4.5 35.5 0.4
OD1 B:ASP82 4.5 20.7 1.0
HD21 B:ASN253 4.5 30.7 1.0
CA B:HIS210 4.5 29.1 1.0
O B:HOH642 4.6 43.5 1.0
H31 B:13P404 4.6 35.8 0.4
HE1 B:MET102 4.8 44.9 1.0
H12 B:13P404 4.8 34.9 0.4
N B:GLY211 4.9 22.0 1.0
HE2 B:HIS210 4.9 27.5 1.0
C1 B:13P404 5.0 29.1 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: Mon Oct 28 09:21:25 2024

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