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Zinc in PDB 5ud2: Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Dhap

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

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

Protein crystallography data

The structure of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Dhap, PDB code: 5ud2 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) 35.79 / 1.78
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.407, 63.089, 64.789, 82.51, 75.96, 74.39
R / Rfree (%) 19.3 / 21.6

Other elements in 5ud2:

The structure of Class II Fructose-1,6-Bisphosphate Aldolase H180Q 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 H180Q Variant of Helicobacter Pylori with Dhap (pdb code 5ud2). 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 with Dhap, PDB code: 5ud2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5ud2

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Zinc binding site 1 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q 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 H180Q Variant of Helicobacter Pylori with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:37.2
occ:0.70
 HE1 A:HIS83 1.8 30.7 0.3
O A:HOH512 2.1 34.6 1.0
O A:HOH598 2.4 27.3 1.0
NE2 A:HIS83 2.5 25.7 0.7
ND1 A:HIS210 2.6 15.1 0.7
CE1 A:HIS83 2.7 25.6 0.3
OE2 A:GLU134 2.7 27.2 1.0
OE1 A:GLU134 2.8 27.0 1.0
CD A:GLU134 3.1 25.8 1.0
HE1 A:HIS83 3.2 30.1 0.7
CE1 A:HIS83 3.2 25.0 0.7
ND1 A:HIS210 3.4 17.2 0.3
CE1 A:HIS210 3.4 15.6 0.7
NE2 A:HIS83 3.4 26.0 0.3
HE1 A:HIS210 3.4 18.7 0.7
CD2 A:HIS83 3.6 25.6 0.7
CG A:HIS210 3.7 16.1 0.7
HB3 A:HIS210 3.7 20.3 0.7
ND1 A:HIS83 3.7 25.4 0.3
HB3 A:HIS210 3.7 20.2 0.3
ZN A:ZN403 3.8 24.2 0.3
CG A:HIS210 3.8 16.7 0.3
HD2 A:HIS83 3.9 30.8 0.7
HD1 A:HIS83 3.9 30.5 0.3
CE1 A:HIS210 3.9 16.6 0.3
HE1 A:MET102 4.0 23.2 1.0
OD2 A:ASP104 4.0 30.2 1.0
HB2 A:HIS210 4.0 20.2 0.3
HB2 A:HIS210 4.0 20.3 0.7
CB A:HIS210 4.1 16.9 0.7
CB A:HIS210 4.1 16.9 0.3
HE1 A:HIS210 4.2 19.9 0.3
ND1 A:HIS83 4.4 24.3 0.7
CD2 A:HIS210 4.4 17.1 0.3
NE2 A:HIS210 4.5 16.7 0.3
CG A:GLU134 4.6 20.3 1.0
O A:HOH510 4.6 37.0 1.0
NE2 A:HIS210 4.6 17.4 0.7
CG A:HIS83 4.7 24.1 0.7
CD2 A:HIS83 4.7 25.2 0.3
CD2 A:HIS210 4.8 16.9 0.7
O A:HOH597 4.8 22.3 1.0
CG A:ASP104 4.8 29.0 1.0
HG3 A:GLU134 4.8 24.4 1.0
CG A:HIS83 4.8 24.2 0.3
CE A:MET102 4.9 19.3 1.0
HB2 A:GLU134 5.0 19.0 1.0

Zinc binding site 2 out of 4 in 5ud2

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Zinc binding site 2 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q 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 H180Q Variant of Helicobacter Pylori with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:24.2
occ:0.30
 HE1 A:HIS83 1.7 30.1 0.7
O A:HOH598 2.1 27.3 1.0
NE2 A:HIS83 2.1 26.0 0.3
O A:HOH501 2.2 31.5 1.0
ND1 A:HIS210 2.3 17.2 0.3
CE1 A:HIS83 2.4 25.0 0.7
O2 A:13P404 2.5 31.5 1.0
O3 A:13P404 2.7 28.3 1.0
HB3 A:HIS210 2.8 20.3 0.7
HB3 A:HIS210 2.9 20.2 0.3
CE1 A:HIS83 3.1 25.6 0.3
NE2 A:HIS83 3.1 25.7 0.7
CD2 A:HIS83 3.1 25.2 0.3
HE1 A:HIS83 3.2 30.7 0.3
CE1 A:HIS210 3.2 16.6 0.3
CG A:HIS210 3.2 16.7 0.3
ND1 A:HIS83 3.3 24.3 0.7
C2 A:13P404 3.3 31.4 1.0
HD2 A:HIS83 3.3 30.3 0.3
HE1 A:HIS210 3.4 19.9 0.3
HO3 A:13P404 3.4 34.0 1.0
C3 A:13P404 3.5 29.7 1.0
HD1 A:HIS83 3.5 29.2 0.7
CG A:HIS210 3.5 16.1 0.7
CB A:HIS210 3.5 16.9 0.3
HD22 A:ASN253 3.5 13.4 1.0
CB A:HIS210 3.5 16.9 0.7
ND1 A:HIS210 3.6 15.1 0.7
H A:GLY211 3.6 26.8 1.0
ZN A:ZN402 3.8 37.2 0.7
H31 A:13P404 3.8 35.6 1.0
HA A:HIS210 4.0 21.2 0.7
HA A:HIS210 4.1 20.8 0.3
CD2 A:HIS210 4.1 16.9 0.7
ND1 A:HIS83 4.2 25.4 0.3
CD2 A:HIS83 4.2 25.6 0.7
CG A:HIS83 4.2 24.2 0.3
CE1 A:HIS210 4.2 15.6 0.7
N A:GLY211 4.3 22.4 1.0
HB2 A:HIS210 4.3 20.2 0.3
HB2 A:HIS210 4.3 20.3 0.7
CG A:HIS83 4.3 24.1 0.7
CA A:HIS210 4.3 17.7 0.7
CA A:HIS210 4.3 17.3 0.3
ND2 A:ASN253 4.3 11.1 1.0
NE2 A:HIS210 4.4 16.7 0.3
CD2 A:HIS210 4.4 17.1 0.3
H32 A:13P404 4.5 35.6 1.0
OD1 A:ASP82 4.5 19.4 1.0
NE2 A:HIS210 4.5 17.4 0.7
HD2 A:HIS210 4.6 20.2 0.7
C1 A:13P404 4.6 31.3 1.0
HB3 A:ASN253 4.6 11.8 1.0
CB A:GLN180 4.7 99.8 1.0
HD21 A:ASN253 4.7 13.4 1.0
HE1 A:HIS210 4.7 18.7 0.7
HB2 A:ASN253 4.7 11.8 1.0
C A:HIS210 4.8 19.4 0.3
C A:HIS210 4.8 19.3 0.7
H12 A:13P404 4.9 37.6 1.0
O A:HOH590 4.9 31.1 1.0
HD1 A:HIS83 5.0 30.5 0.3
HD2 A:HIS83 5.0 30.8 0.7
OD2 A:ASP82 5.0 20.2 1.0

Zinc binding site 3 out of 4 in 5ud2

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Zinc binding site 3 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q 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 H180Q Variant of Helicobacter Pylori with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:32.3
occ:0.50
 HE1 B:HIS83 1.6 26.1 0.5
O B:HOH536 2.1 27.2 1.0
NE2 B:HIS83 2.5 21.8 0.5
CE1 B:HIS83 2.5 21.7 0.5
ND1 B:HIS210 2.6 17.3 0.5
OE1 B:GLU134 2.7 26.3 1.0
OE2 B:GLU134 2.9 26.2 1.0
CD B:GLU134 3.2 24.8 1.0
HE1 B:HIS83 3.2 21.2 0.5
CE1 B:HIS83 3.2 17.7 0.5
NE2 B:HIS83 3.2 21.9 0.5
ND1 B:HIS210 3.2 17.9 0.5
CE1 B:HIS210 3.4 18.4 0.5
HB3 B:HIS210 3.5 21.6 0.5
HE1 B:HIS210 3.5 22.1 0.5
HB3 B:HIS210 3.5 21.6 0.5
ZN B:ZN403 3.6 25.0 0.5
CG B:HIS210 3.6 17.9 0.5
CD2 B:HIS83 3.6 20.9 0.5
CG B:HIS210 3.6 17.8 0.5
ND1 B:HIS83 3.6 21.2 0.5
HB2 B:HIS210 3.8 21.6 0.5
HB2 B:HIS210 3.8 21.6 0.5
CE1 B:HIS210 3.8 17.3 0.5
HD1 B:HIS83 3.9 25.4 0.5
CB B:HIS210 3.9 18.0 0.5
HD2 B:HIS83 3.9 25.1 0.5
CB B:HIS210 3.9 18.0 0.5
O B:HOH506 4.0 23.1 1.0
HE1 B:MET102 4.1 22.9 1.0
HE1 B:HIS210 4.1 20.7 0.5
OD2 B:ASP104 4.3 21.9 1.0
O B:HOH548 4.3 32.7 1.0
CD2 B:HIS210 4.4 17.6 0.5
ND1 B:HIS83 4.4 20.8 0.5
CD2 B:HIS83 4.5 20.9 0.5
NE2 B:HIS210 4.5 18.3 0.5
NE2 B:HIS210 4.6 18.3 0.5
CG B:HIS83 4.6 19.7 0.5
O B:HOH525 4.6 21.1 1.0
CG B:GLU134 4.7 19.2 1.0
CG B:HIS83 4.7 20.1 0.5
CD2 B:HIS210 4.7 18.2 0.5
CG B:ASP104 4.9 20.6 1.0
CE B:MET102 4.9 19.1 1.0
HE3 B:MET102 5.0 22.9 1.0

Zinc binding site 4 out of 4 in 5ud2

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Zinc binding site 4 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q 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 H180Q Variant of Helicobacter Pylori with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:25.0
occ:0.50
 HE1 B:HIS83 1.6 21.2 0.5
NE2 B:HIS83 2.0 21.9 0.5
CE1 B:HIS83 2.2 17.7 0.5
O B:HOH548 2.3 32.7 1.0
ND1 B:HIS210 2.4 17.9 0.5
O3 B:13P404 2.5 29.8 1.0
O2 B:13P404 2.5 31.2 1.0
HB3 B:HIS210 2.8 21.6 0.5
HB3 B:HIS210 2.9 21.6 0.5
NE2 B:HIS83 2.9 21.8 0.5
CD2 B:HIS83 3.0 20.9 0.5
CE1 B:HIS83 3.0 21.7 0.5
HO3 B:13P404 3.1 35.7 1.0
HD2 B:HIS83 3.1 25.1 0.5
ND1 B:HIS83 3.2 20.8 0.5
C2 B:13P404 3.3 31.4 1.0
C3 B:13P404 3.3 30.7 1.0
HE1 B:HIS83 3.3 26.1 0.5
CG B:HIS210 3.3 17.8 0.5
CE1 B:HIS210 3.4 17.3 0.5
HD1 B:HIS83 3.5 25.0 0.5
H32 B:13P404 3.5 36.9 1.0
HE1 B:HIS210 3.5 20.7 0.5
CB B:HIS210 3.5 18.0 0.5
CG B:HIS210 3.5 17.9 0.5
ND1 B:HIS210 3.6 17.3 0.5
ZN B:ZN402 3.6 32.3 0.5
HD22 B:ASN253 3.6 15.1 1.0
CB B:HIS210 3.6 18.0 0.5
H B:GLY211 3.7 24.6 1.0
CD2 B:HIS83 4.0 20.9 0.5
CG B:HIS83 4.1 20.1 0.5
ND1 B:HIS83 4.1 21.2 0.5
HA B:HIS210 4.1 21.2 0.5
HA B:HIS210 4.2 21.3 0.5
CG B:HIS83 4.2 19.7 0.5
CE1 B:HIS210 4.3 18.4 0.5
CD2 B:HIS210 4.3 18.2 0.5
HB2 B:HIS210 4.3 21.6 0.5
HB2 B:HIS210 4.3 21.6 0.5
H31 B:13P404 4.3 36.9 1.0
ND2 B:ASN253 4.4 12.6 1.0
N B:GLY211 4.4 20.5 1.0
CA B:HIS210 4.4 17.7 0.5
CA B:HIS210 4.4 17.7 0.5
OD1 B:ASP82 4.4 14.2 1.0
NE2 B:HIS210 4.5 18.3 0.5
CD2 B:HIS210 4.5 17.6 0.5
O B:HOH558 4.6 32.6 1.0
NE2 B:HIS210 4.6 18.3 0.5
C1 B:13P404 4.7 31.6 1.0
HB3 B:ASN253 4.7 14.4 1.0
HE1 B:HIS210 4.7 22.1 0.5
HD2 B:HIS210 4.7 21.8 0.5
HD21 B:ASN253 4.8 15.1 1.0
HB2 B:ASN253 4.8 14.4 1.0
HD2 B:HIS83 4.8 25.1 0.5
C B:HIS210 4.9 18.7 0.5
C B:HIS210 4.9 18.7 0.5
HD1 B:HIS83 4.9 25.4 0.5
CB B:GLN180 5.0 80.4 1.0
OD2 B:ASP82 5.0 13.6 1.0
O1 B:13P404 5.0 29.7 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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