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Zinc in PDB 5ud1: Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori

Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori

All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori:
4.1.2.13;

Protein crystallography data

The structure of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori, PDB code: 5ud1 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) 28.61 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.301, 64.207, 62.520, 81.37, 74.10, 75.94
R / Rfree (%) 21.3 / 26

Other elements in 5ud1:

The structure of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori 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 H180Q Variant of Helicobacter Pylori (pdb code 5ud1). 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 H180Q Variant of Helicobacter Pylori, PDB code: 5ud1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5ud1

Go back to Zinc Binding Sites List in 5ud1
Zinc binding site 1 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori


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 H180Q Variant of Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:34.5
occ:0.44
 O A:HOH531 2.2 28.4 1.0
O A:HOH566 2.2 36.3 1.0
OE2 A:GLU134 2.6 32.9 1.0
NE2 A:HIS83 2.6 21.1 0.4
CE1 A:HIS83 2.8 21.3 0.6
ND1 A:HIS210 2.8 38.6 1.0
OE1 A:GLU134 2.9 33.1 1.0
CD A:GLU134 3.1 27.8 1.0
CE1 A:HIS83 3.2 22.1 0.4
NE2 A:HIS83 3.4 22.7 0.6
CG A:HIS210 3.6 36.1 1.0
CB A:HIS210 3.7 30.9 1.0
CE1 A:HIS210 3.8 37.9 1.0
O A:HOH504 3.8 26.4 1.0
ZN A:ZN403 3.8 53.4 0.6
CD2 A:HIS83 3.9 21.5 0.4
ND1 A:HIS83 3.9 21.8 0.6
ND1 A:HIS83 4.5 21.5 0.4
O A:HOH514 4.6 41.9 1.0
CG A:GLU134 4.6 25.8 1.0
OD2 A:ASP104 4.7 28.4 1.0
CD2 A:HIS83 4.7 21.9 0.6
CG A:HIS83 4.8 21.6 0.4
CD2 A:HIS210 4.8 37.5 1.0
NE2 A:HIS210 4.9 36.9 1.0
CG A:HIS83 4.9 21.7 0.6

Zinc binding site 2 out of 4 in 5ud1

Go back to Zinc Binding Sites List in 5ud1
Zinc binding site 2 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori


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 H180Q Variant of Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:53.4
occ:0.56
 O A:HOH566 2.3 36.3 1.0
NE2 A:HIS83 2.3 22.7 0.6
O A:HOH523 2.5 29.6 1.0
CE1 A:HIS83 2.7 22.1 0.4
CD2 A:HIS83 3.2 21.9 0.6
CE1 A:HIS83 3.4 21.3 0.6
CB A:HIS210 3.5 30.9 1.0
NE2 A:HIS83 3.5 21.1 0.4
ND1 A:HIS83 3.5 21.5 0.4
CG A:HIS210 3.6 36.1 1.0
ND1 A:HIS210 3.7 38.6 1.0
ZN A:ZN402 3.8 34.5 0.4
N A:GLY211 3.9 36.5 1.0
O A:HOH576 4.1 31.9 1.0
CA A:HIS210 4.2 28.2 1.0
ND2 A:ASN253 4.2 18.8 1.0
CG A:HIS83 4.4 21.7 0.6
CD2 A:HIS210 4.5 37.5 1.0
ND1 A:HIS83 4.5 21.8 0.6
C A:HIS210 4.5 31.9 1.0
CD2 A:HIS83 4.5 21.5 0.4
CE1 A:HIS210 4.6 37.9 1.0
CG A:HIS83 4.6 21.6 0.4
OD1 A:ASP82 4.6 22.2 1.0
CA A:GLY211 4.8 40.4 1.0
O A:HOH506 4.9 39.0 1.0
NE2 A:HIS210 4.9 36.9 1.0
CB A:ASN253 5.0 15.2 1.0

Zinc binding site 3 out of 4 in 5ud1

Go back to Zinc Binding Sites List in 5ud1
Zinc binding site 3 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori


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 H180Q Variant of Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:35.3
occ:0.46
 ZN B:ZN403 2.0 37.3 0.5
OE2 B:GLU134 2.5 35.5 1.0
OE1 B:GLU134 2.6 33.2 1.0
NE2 B:HIS83 2.7 24.7 1.0
ND1 B:HIS210 2.8 33.6 1.0
O B:HOH617 2.8 50.5 1.0
CD B:GLU134 2.9 32.0 1.0
CE1 B:HIS83 3.5 26.9 1.0
CE1 B:HIS210 3.6 33.7 1.0
CG B:HIS210 3.7 32.4 1.0
CD2 B:HIS83 3.8 25.5 1.0
CB B:HIS210 4.0 27.9 1.0
OD2 B:ASP104 4.3 32.4 1.0
CG B:GLU134 4.4 24.0 1.0
O B:HOH621 4.4 34.4 1.0
O B:HOH606 4.7 34.7 1.0
ND1 B:HIS83 4.7 25.7 1.0
NE2 B:HIS210 4.8 32.2 1.0
CD2 B:HIS210 4.9 32.6 1.0
CG B:HIS83 4.9 26.4 1.0
CG B:ASP104 4.9 30.4 1.0
CE B:MET102 4.9 31.8 1.0

Zinc binding site 4 out of 4 in 5ud1

Go back to Zinc Binding Sites List in 5ud1
Zinc binding site 4 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori


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 H180Q Variant of Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:37.3
occ:0.54
 ZN B:ZN402 2.0 35.3 0.5
OD2 B:ASP104 2.5 32.4 1.0
OE1 B:GLU134 2.7 33.2 1.0
NE2 B:HIS83 2.9 24.7 1.0
OE2 B:GLU134 3.1 35.5 1.0
CD B:GLU134 3.2 32.0 1.0
CD2 B:HIS83 3.2 25.5 1.0
CG B:ASP104 3.3 30.4 1.0
OD1 B:ASP104 3.7 28.9 1.0
CE1 B:HIS83 4.2 26.9 1.0
O B:HOH617 4.2 50.5 1.0
O B:HOH589 4.2 27.8 1.0
O B:HOH560 4.3 39.1 1.0
OG B:SER106 4.5 27.6 1.0
ND1 B:HIS210 4.5 33.6 1.0
CB B:ASP104 4.5 25.1 1.0
CG B:HIS83 4.6 26.4 1.0
CG B:GLU134 4.6 24.0 1.0
CE B:MET102 4.9 31.8 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: Thu Aug 21 09:23:13 2025

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