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Zinc 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:

Calcium (Ca) 1 atom
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 Cleavage Products (pdb code 5ud0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Cleavage Products, PDB code: 5ud0:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5ud0

Go back to Zinc Binding Sites List in 5ud0
Zinc binding site 1 out of 3 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 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 Cleavage Products within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:30.4
occ:0.86
 NE2 A:HIS180 1.8 29.3 1.0
OE1 A:GLU134 2.1 36.8 1.0
NE2 A:HIS83 2.2 36.7 1.0
OE2 A:GLU134 2.4 34.5 1.0
ND1 A:HIS210 2.4 50.1 1.0
O A:HOH580 2.5 29.9 1.0
CD A:GLU134 2.6 40.8 1.0
CE1 A:HIS180 2.8 46.5 1.0
CD2 A:HIS180 2.9 39.8 1.0
CE1 A:HIS83 3.1 45.0 1.0
CD2 A:HIS83 3.2 29.6 1.0
HE1 A:HIS83 3.2 54.0 1.0
CE1 A:HIS210 3.3 41.5 1.0
HE1 A:HIS210 3.3 49.8 1.0
HD2 A:HIS83 3.4 35.5 1.0
CG A:HIS210 3.5 30.1 1.0
HB3 A:HIS210 3.6 39.1 1.0
HE1 A:MET102 3.6 35.9 1.0
HB2 A:HIS210 3.6 39.1 1.0
CB A:HIS210 3.8 32.6 1.0
ND1 A:HIS180 3.9 39.7 1.0
CG A:HIS180 4.0 38.4 1.0
O A:HOH502 4.1 33.4 1.0
CG A:GLU134 4.1 23.2 1.0
ND1 A:HIS83 4.2 27.1 1.0
O A:HOH539 4.3 41.8 1.0
OD2 A:ASP104 4.3 27.8 1.0
CG A:HIS83 4.3 24.9 1.0
HB2 A:GLU134 4.4 32.5 1.0
NE2 A:HIS210 4.4 24.4 1.0
HG3 A:GLU134 4.4 27.8 1.0
CE A:MET102 4.5 29.9 1.0
CD2 A:HIS210 4.6 51.1 1.0
HE3 A:MET102 4.6 35.9 1.0
HG2 A:GLU134 4.6 27.8 1.0
CG A:ASP104 4.7 22.1 1.0
O A:HOH611 4.7 37.2 1.0
CB A:GLU134 4.8 27.1 1.0
OD1 A:ASP104 4.9 25.3 1.0
HB3 A:GLU134 5.0 32.5 1.0
HD1 A:HIS83 5.0 32.6 1.0

Zinc binding site 2 out of 3 in 5ud0

Go back to Zinc Binding Sites List in 5ud0
Zinc binding site 2 out of 3 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 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 Cleavage Products within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:22.1
occ:0.71
 ZN B:ZN403 1.7 28.3 0.3
NE2 B:HIS83 1.8 18.5 1.0
NE2 B:HIS180 2.0 26.9 1.0
O B:HOH502 2.1 14.4 1.0
ND1 B:HIS210 2.1 24.6 1.0
HE1 B:HIS180 2.6 45.1 1.0
CE1 B:HIS180 2.6 37.5 1.0
CE1 B:HIS83 2.7 24.4 1.0
HE1 B:HIS83 2.8 29.3 1.0
HB3 B:HIS210 2.8 22.7 1.0
CD2 B:HIS83 3.0 23.0 1.0
CE1 B:HIS210 3.0 25.7 1.0
CG B:HIS210 3.0 22.0 1.0
HE1 B:HIS210 3.2 30.9 1.0
CD2 B:HIS180 3.2 45.0 1.0
HD2 B:HIS83 3.3 27.6 1.0
CB B:HIS210 3.4 18.9 1.0
HD2 B:HIS180 3.6 54.0 1.0
HB2 B:HIS210 3.8 22.7 1.0
ND1 B:HIS83 3.8 28.9 1.0
ND1 B:HIS180 3.9 38.7 1.0
O2 B:13P405 3.9 23.7 0.9
O3 B:13P405 4.0 23.4 0.9
CG B:HIS83 4.0 24.0 1.0
OE2 B:GLU134 4.1 22.9 1.0
NE2 B:HIS210 4.1 16.6 1.0
CD2 B:HIS210 4.1 17.4 1.0
CG B:HIS180 4.2 30.6 1.0
O1 B:G3H406 4.2 23.7 0.2
H11 B:G3H406 4.3 28.7 0.4
HO3 B:13P405 4.3 28.1 0.9
HE1 B:MET102 4.3 30.5 1.0
HD22 B:ASN253 4.4 16.8 1.0
HD1 B:HIS180 4.6 46.4 1.0
HD1 B:HIS83 4.6 34.6 1.0
H32 B:13P405 4.6 28.3 0.9
C3 B:13P405 4.7 23.6 0.9
CA B:HIS210 4.7 18.4 1.0
H B:GLY211 4.7 23.8 1.0
HA B:HIS210 4.7 22.1 1.0
OE1 B:GLU134 4.8 24.6 1.0
C2 B:13P405 4.8 23.8 0.9
O B:HOH565 4.8 33.6 1.0
CD B:GLU134 4.8 21.3 1.0
HE2 B:HIS210 4.9 20.0 1.0
HD2 B:HIS210 5.0 20.8 1.0

Zinc binding site 3 out of 3 in 5ud0

Go back to Zinc Binding Sites List in 5ud0
Zinc binding site 3 out of 3 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 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 Cleavage Products within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:28.3
occ:0.29
 ZN B:ZN402 1.7 22.1 0.7
NE2 B:HIS180 2.0 26.9 1.0
ND1 B:HIS210 2.3 24.6 1.0
O3 B:13P405 2.4 23.4 0.9
CE1 B:HIS180 2.4 37.5 1.0
HE1 B:HIS180 2.4 45.1 1.0
NE2 B:HIS83 2.5 18.5 1.0
O2 B:13P405 2.6 23.7 0.9
HD2 B:HIS83 2.8 27.6 1.0
HO3 B:13P405 2.9 28.1 0.9
CD2 B:HIS83 3.0 23.0 1.0
C3 B:13P405 3.0 23.6 0.9
H32 B:13P405 3.0 28.3 0.9
HB3 B:HIS210 3.0 22.7 1.0
O1 B:G3H406 3.1 23.7 0.2
CD2 B:HIS180 3.1 45.0 1.0
H11 B:G3H406 3.2 28.7 0.4
CE1 B:HIS210 3.2 25.7 1.0
C2 B:13P405 3.2 23.8 0.9
HD22 B:ASN253 3.2 16.8 1.0
CG B:HIS210 3.3 22.0 1.0
HE1 B:HIS210 3.4 30.9 1.0
ND1 B:HIS180 3.5 38.7 1.0
HD2 B:HIS180 3.6 54.0 1.0
CB B:HIS210 3.6 18.9 1.0
O B:HOH502 3.7 14.4 1.0
CE1 B:HIS83 3.8 24.4 1.0
CG B:HIS180 3.9 30.6 1.0
H B:GLY211 3.9 23.8 1.0
ND2 B:ASN253 4.0 14.0 1.0
H31 B:13P405 4.1 28.3 0.9
C1 B:G3H406 4.1 23.9 0.4
OD1 B:ASP82 4.2 18.9 1.0
HD1 B:HIS180 4.2 46.4 1.0
HA B:HIS210 4.2 22.1 1.0
HE1 B:HIS83 4.2 29.3 1.0
C1 B:G3H406 4.3 23.7 0.2
CG B:HIS83 4.3 24.0 1.0
HD21 B:ASN253 4.3 16.8 1.0
NE2 B:HIS210 4.3 16.6 1.0
HB2 B:HIS210 4.4 22.7 1.0
CD2 B:HIS210 4.4 17.4 1.0
CA B:HIS210 4.5 18.4 1.0
HB3 B:ASN253 4.5 18.9 1.0
N B:GLY211 4.6 19.9 1.0
C1 B:13P405 4.6 23.4 0.9
ND1 B:HIS83 4.7 28.9 1.0
HB2 B:ASN253 4.7 18.9 1.0
O1 B:G3H406 4.8 23.9 0.4
OD2 B:ASP82 4.8 21.2 1.0
O2 B:G3H406 4.8 23.8 0.2
CG B:ASP82 4.9 18.1 1.0
O2 B:G3H406 4.9 23.9 0.4
CB B:ASN253 4.9 15.7 1.0
CG B:ASN253 4.9 14.1 1.0
H11 B:13P405 5.0 28.1 0.9
H11 B:G3H406 5.0 28.5 0.2

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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