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Zinc in PDB 5ucn: Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Dhap

Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Dhap

All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Dhap:
4.1.2.13;

Protein crystallography data

The structure of Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Dhap, PDB code: 5ucn 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) 44.98 / 1.67
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.308, 62.612, 64.507, 82.17, 75.88, 74.17
R / Rfree (%) 17.1 / 20.8

Other elements in 5ucn:

The structure of Class II Fructose-1,6-Bisphosphate Aldolase E142A 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 E142A Variant of Helicobacter Pylori with Dhap (pdb code 5ucn). 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 E142A Variant of Helicobacter Pylori with Dhap, PDB code: 5ucn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5ucn

Go back to Zinc Binding Sites List in 5ucn
Zinc binding site 1 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase E142A 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 E142A Variant of Helicobacter Pylori with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:34.9
occ:0.50
 HE1 A:HIS83 1.7 46.8 0.5
O A:HOH541 2.2 30.9 1.0
ND1 A:HIS210 2.2 23.6 0.5
CE1 A:HIS83 2.5 39.0 0.5
NE2 A:HIS83 2.5 39.2 0.5
OE2 A:GLU134 2.6 39.0 1.0
OE1 A:GLU134 2.7 37.6 1.0
HE1 A:HIS83 2.8 48.4 0.5
CE1 A:HIS180 2.8 85.8 1.0
CE1 A:HIS210 2.9 21.9 0.5
CD A:GLU134 3.0 33.5 1.0
CE1 A:HIS83 3.0 40.3 0.5
HE1 A:HIS210 3.0 26.2 0.5
ND1 A:HIS210 3.0 22.9 0.5
NE2 A:HIS83 3.1 40.8 0.5
NE2 A:HIS180 3.3 80.8 1.0
CG A:HIS210 3.3 20.9 0.5
ZN A:ZN403 3.4 43.4 0.5
HB3 A:HIS210 3.4 26.2 0.5
CG A:HIS210 3.5 20.9 0.5
HB3 A:HIS210 3.5 26.0 0.5
HB2 A:HIS210 3.6 26.2 0.5
CE1 A:HIS210 3.7 21.6 0.5
ND1 A:HIS83 3.7 38.0 0.5
CB A:HIS210 3.7 21.8 0.5
HB2 A:HIS210 3.8 26.0 0.5
CB A:HIS210 3.8 21.7 0.5
CD2 A:HIS83 3.8 37.7 0.5
HE1 A:HIS210 4.0 25.9 0.5
HE1 A:MET102 4.0 29.4 1.0
HD1 A:HIS83 4.0 45.6 0.5
ND1 A:HIS180 4.1 87.4 1.0
NE2 A:HIS210 4.1 20.8 0.5
O A:HOH505 4.1 30.9 1.0
HD2 A:HIS83 4.2 45.3 0.5
ND1 A:HIS83 4.2 37.7 0.5
CD2 A:HIS210 4.3 20.7 0.5
CD2 A:HIS210 4.3 20.9 0.5
OD2 A:ASP104 4.4 29.2 1.0
NE2 A:HIS210 4.4 22.2 0.5
CD2 A:HIS83 4.4 37.4 0.5
CG A:GLU134 4.4 22.2 1.0
O A:HOH524 4.5 34.0 1.0
CD2 A:HIS180 4.6 85.1 1.0
CG A:HIS83 4.7 34.7 0.5
CG A:HIS83 4.7 35.7 0.5
HE3 A:MET102 4.7 29.4 1.0
HG3 A:GLU134 4.7 26.6 1.0
HB2 A:GLU134 4.8 15.6 1.0
HE2 A:HIS210 4.8 24.9 0.5
CE A:MET102 4.8 24.5 1.0
HD1 A:HIS83 4.9 45.2 0.5
CG A:ASP104 4.9 26.4 1.0
HG2 A:GLU134 5.0 26.6 1.0
HD2 A:HIS210 5.0 25.0 0.5

Zinc binding site 2 out of 4 in 5ucn

Go back to Zinc Binding Sites List in 5ucn
Zinc binding site 2 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase E142A 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 E142A Variant of Helicobacter Pylori with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:43.4
occ:0.50
 HE1 A:HIS83 1.3 48.4 0.5
NE2 A:HIS180 1.9 80.8 1.0
NE2 A:HIS83 2.0 40.8 0.5
O3 A:13P404 2.2 31.9 0.3
O3 A:13P404 2.2 31.9 0.3
CE1 A:HIS83 2.2 40.3 0.5
ND1 A:HIS210 2.2 22.9 0.5
HO3 A:13P404 2.7 38.2 0.3
O2 A:13P404 2.7 31.8 0.3
HB3 A:HIS210 2.7 26.2 0.5
CD2 A:HIS180 2.7 85.1 1.0
HO3 A:13P404 2.7 38.2 0.3
HB3 A:HIS210 2.8 26.0 0.5
O2 A:13P404 2.9 31.8 0.3
CD2 A:HIS83 2.9 37.4 0.5
CE1 A:HIS180 3.0 85.8 1.0
ND1 A:HIS83 3.0 37.7 0.5
HD1 A:HIS83 3.0 45.2 0.5
CE1 A:HIS83 3.1 39.0 0.5
HD2 A:HIS83 3.1 44.8 0.5
HD22 A:ASN253 3.1 26.4 1.0
CG A:HIS210 3.1 20.9 0.5
CG A:HIS210 3.2 20.9 0.5
CE1 A:HIS210 3.2 21.6 0.5
NE2 A:HIS83 3.3 39.2 0.5
HE1 A:HIS83 3.3 46.8 0.5
C3 A:13P404 3.3 31.9 0.3
C3 A:13P404 3.3 31.9 0.3
CB A:HIS210 3.4 21.8 0.5
C2 A:13P404 3.4 31.8 0.3
ND1 A:HIS210 3.4 23.6 0.5
ZN A:ZN402 3.4 34.9 0.5
CB A:HIS210 3.4 21.7 0.5
HE1 A:HIS210 3.4 25.9 0.5
C2 A:13P404 3.5 31.8 0.3
CD2 A:HIS210 3.7 20.7 0.5
H A:GLY211 3.8 30.2 0.3
H32 A:13P404 3.8 38.2 0.3
H32 A:13P404 3.9 38.2 0.3
H A:GLY211 3.9 30.2 0.7
ND2 A:ASN253 3.9 22.0 1.0
CE1 A:HIS210 3.9 21.9 0.5
CG A:HIS180 3.9 90.0 1.0
HA A:HIS210 4.0 20.8 0.5
ND1 A:HIS180 4.0 87.4 1.0
HA A:HIS210 4.0 20.8 0.5
HD2 A:HIS210 4.0 24.8 0.5
NE2 A:HIS210 4.1 20.8 0.5
HB2 A:HIS210 4.1 26.2 0.5
H31 A:13P404 4.1 38.2 0.3
CG A:HIS83 4.1 35.7 0.5
ND1 A:HIS83 4.1 38.0 0.5
H31 A:13P404 4.1 38.2 0.3
HB2 A:HIS210 4.2 26.0 0.5
HD21 A:ASN253 4.2 26.4 1.0
CG A:HIS83 4.2 34.7 0.5
OD1 A:ASP82 4.3 23.0 1.0
CA A:HIS210 4.3 17.4 0.5
CD2 A:HIS210 4.3 20.9 0.5
CA A:HIS210 4.3 17.4 0.5
NE2 A:HIS210 4.3 22.2 0.5
CD2 A:HIS83 4.4 37.7 0.5
HE1 A:HIS210 4.5 26.2 0.5
N A:GLY211 4.5 25.2 1.0
HB3 A:ASN253 4.6 17.9 1.0
HE2 A:HIS210 4.6 24.9 0.5
HB2 A:ASN253 4.7 17.9 1.0
C A:HIS210 4.8 19.8 0.5
C1 A:13P404 4.8 31.8 0.3
CG A:ASN253 4.9 16.2 1.0
HD1 A:HIS83 4.9 45.6 0.5
C A:HIS210 4.9 19.6 0.5
C1 A:13P404 4.9 31.8 0.3
CB A:ASN253 5.0 14.9 1.0

Zinc binding site 3 out of 4 in 5ucn

Go back to Zinc Binding Sites List in 5ucn
Zinc binding site 3 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase E142A 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 E142A Variant of Helicobacter Pylori with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:39.6
occ:0.50
 HE1 B:HIS83 1.9 39.0 0.5
O B:HOH509 2.5 29.3 1.0
CE1 B:HIS180 2.5 68.0 1.0
ND1 B:HIS210 2.5 26.1 0.5
OE1 B:GLU134 2.6 37.0 1.0
NE2 B:HIS83 2.6 32.5 0.5
CE1 B:HIS83 2.6 32.5 0.5
NE2 B:HIS180 2.7 64.2 1.0
OE2 B:GLU134 2.7 38.5 1.0
CD B:GLU134 3.0 31.8 1.0
NE2 B:HIS83 3.1 39.4 0.5
ND1 B:HIS210 3.2 28.5 0.5
HE1 B:HIS83 3.2 42.6 0.5
CE1 B:HIS83 3.3 35.5 0.5
CE1 B:HIS210 3.3 25.6 0.5
HE1 B:HIS210 3.3 30.8 0.5
CG B:HIS210 3.6 26.2 0.5
CG B:HIS210 3.6 26.1 0.5
HB3 B:HIS210 3.6 28.0 0.5
ZN B:ZN403 3.7 32.8 0.5
HB3 B:HIS210 3.7 28.0 0.5
CE1 B:HIS210 3.7 24.4 0.5
CD2 B:HIS83 3.8 33.1 0.5
ND1 B:HIS180 3.8 70.1 1.0
HB2 B:HIS210 3.9 28.0 0.5
ND1 B:HIS83 3.9 31.7 0.5
HB2 B:HIS210 3.9 28.0 0.5
CB B:HIS210 3.9 23.4 0.5
CB B:HIS210 4.0 23.3 0.5
HE1 B:MET102 4.0 31.4 1.0
HE1 B:HIS210 4.0 29.3 0.5
HD2 B:HIS83 4.1 39.7 0.5
CD2 B:HIS180 4.1 68.1 1.0
O B:HOH501 4.1 23.4 1.0
OD2 B:ASP104 4.1 28.3 1.0
HD1 B:HIS83 4.2 38.0 0.5
CD2 B:HIS210 4.4 25.7 0.5
NE2 B:HIS210 4.4 24.6 0.5
O B:HOH614 4.4 30.1 1.0
CD2 B:HIS83 4.4 32.2 0.5
NE2 B:HIS210 4.5 24.1 0.5
CG B:GLU134 4.5 25.3 1.0
ND1 B:HIS83 4.5 32.8 0.5
CD2 B:HIS210 4.6 25.3 0.5
CG B:HIS180 4.6 75.3 1.0
O B:HOH517 4.7 36.8 1.0
HG3 B:GLU134 4.7 30.4 1.0
CG B:HIS83 4.8 29.9 0.5
HB2 B:GLU134 4.8 15.1 1.0
CG B:HIS83 4.8 30.3 0.5
CG B:ASP104 4.8 26.2 1.0
CE B:MET102 4.9 26.1 1.0
HE3 B:MET102 4.9 31.4 1.0
HG2 B:GLU134 5.0 30.4 1.0

Zinc binding site 4 out of 4 in 5ucn

Go back to Zinc Binding Sites List in 5ucn
Zinc binding site 4 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase E142A 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 E142A Variant of Helicobacter Pylori with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:32.8
occ:0.50
 HE1 B:HIS83 1.3 42.6 0.5
CE1 B:HIS83 2.0 35.5 0.5
NE2 B:HIS180 2.1 64.2 1.0
ND1 B:HIS210 2.1 28.5 0.5
NE2 B:HIS83 2.2 39.4 0.5
O3 B:13P404 2.2 28.9 0.3
CD2 B:HIS180 2.4 68.1 1.0
O3 B:13P404 2.4 28.9 0.3
HO3 B:13P404 2.7 34.6 0.3
HO3 B:13P404 2.8 34.6 0.3
HD2 B:HIS83 2.8 38.6 0.5
CD2 B:HIS83 2.8 32.2 0.5
NE2 B:HIS83 2.9 32.5 0.5
CE1 B:HIS210 2.9 24.4 0.5
O2 B:13P404 2.9 28.9 0.3
ND1 B:HIS83 3.0 32.8 0.5
HB3 B:HIS210 3.0 28.0 0.5
O2 B:13P404 3.0 28.9 0.3
HE1 B:HIS210 3.0 29.3 0.5
HB3 B:HIS210 3.1 28.0 0.5
HD1 B:HIS83 3.2 39.4 0.5
CG B:HIS210 3.2 26.1 0.5
HD22 B:ASN253 3.2 25.6 1.0
C3 B:13P404 3.3 28.9 0.3
CE1 B:HIS83 3.3 32.5 0.5
CE1 B:HIS180 3.3 68.0 1.0
CG B:HIS210 3.4 26.2 0.5
C3 B:13P404 3.4 28.9 0.3
ND1 B:HIS210 3.5 26.1 0.5
H31 B:13P404 3.5 34.7 0.3
C2 B:13P404 3.5 28.9 0.3
C2 B:13P404 3.6 28.9 0.3
CB B:HIS210 3.6 23.4 0.5
CG B:HIS180 3.7 75.3 1.0
ZN B:ZN402 3.7 39.6 0.5
CB B:HIS210 3.7 23.3 0.5
HE1 B:HIS83 3.7 39.0 0.5
H31 B:13P404 3.8 34.6 0.3
CD2 B:HIS210 3.9 25.3 0.5
ND2 B:ASN253 4.0 21.4 1.0
CD2 B:HIS83 4.0 33.1 0.5
CE1 B:HIS210 4.0 25.6 0.5
H B:GLY211 4.0 26.4 0.3
CG B:HIS83 4.1 29.9 0.5
ND1 B:HIS180 4.1 70.1 1.0
H B:GLY211 4.1 26.4 0.7
CG B:HIS83 4.1 30.3 0.5
NE2 B:HIS210 4.1 24.6 0.5
OD1 B:ASP82 4.1 20.3 1.0
HA B:HIS210 4.2 23.8 0.5
HA B:HIS210 4.2 23.8 0.5
H32 B:13P404 4.2 34.7 0.3
NE2 B:HIS210 4.2 24.1 0.5
CD2 B:HIS210 4.2 25.7 0.5
HD21 B:ASN253 4.3 25.6 1.0
ND1 B:HIS83 4.3 31.7 0.5
HD2 B:HIS210 4.3 30.4 0.5
H32 B:13P404 4.3 34.6 0.3
HB2 B:HIS210 4.4 28.0 0.5
HB2 B:HIS210 4.4 28.0 0.5
CA B:HIS210 4.5 19.8 0.5
CA B:HIS210 4.5 19.8 0.5
HE1 B:HIS210 4.5 30.8 0.5
HB3 B:ASN253 4.7 20.9 1.0
N B:GLY211 4.7 22.0 1.0
HB2 B:ASN253 4.8 20.9 1.0
HE2 B:HIS210 4.8 28.9 0.5
OD2 B:ASP82 4.8 24.8 1.0
HD2 B:HIS83 4.8 39.7 0.5
HE2 B:HIS210 4.8 29.5 0.5
CB B:HIS180 4.9 98.7 1.0
CG B:ASP82 4.9 21.1 1.0
CG B:ASN253 5.0 19.0 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 Oct 28 09:21:25 2024

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