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Zinc in PDB 5ud4: Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Tbp

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

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

Protein crystallography data

The structure of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Tbp, PDB code: 5ud4 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) 45.14 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.391, 62.590, 64.817, 81.98, 75.74, 74.23
R / Rfree (%) 13.4 / 17.7

Other elements in 5ud4:

The structure of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Tbp 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 Tbp (pdb code 5ud4). 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 Tbp, PDB code: 5ud4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5ud4

Go back to Zinc Binding Sites List in 5ud4
Zinc binding site 1 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Tbp


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 Tbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:24.4
occ:0.70
 HE1 A:HIS83 1.8 17.4 0.3
O A:HOH582 2.1 13.6 1.0
O A:HOH564 2.3 30.0 1.0
O A:HOH737 2.4 29.8 1.0
OE2 A:GLU134 2.4 20.5 1.0
ND1 A:HIS210 2.5 13.3 1.0
NE2 A:HIS83 2.6 11.4 0.7
OE1 A:GLU134 2.6 15.9 1.0
CE1 A:HIS83 2.7 14.5 0.3
CD A:GLU134 2.8 16.9 1.0
CE1 A:HIS210 3.3 13.1 1.0
HE1 A:HIS210 3.3 15.8 1.0
CE1 A:HIS83 3.3 11.4 0.7
HE1 A:HIS83 3.4 13.7 0.7
NE2 A:HIS83 3.4 14.3 0.3
CG A:HIS210 3.6 11.6 1.0
CD2 A:HIS83 3.7 11.5 0.7
HB3 A:HIS210 3.7 13.3 1.0
ZN A:ZN403 3.7 24.4 0.2
ND1 A:HIS83 3.8 14.2 0.3
O A:HOH503 3.8 23.7 1.0
HB2 A:HIS210 3.9 13.3 1.0
HD2 A:HIS83 3.9 13.8 0.7
CB A:HIS210 4.0 11.1 1.0
HE1 A:MET102 4.0 17.9 1.0
HD1 A:HIS83 4.0 17.1 0.3
CG A:GLU134 4.4 12.4 1.0
O A:HOH647 4.4 21.6 1.0
NE2 A:HIS210 4.4 12.2 1.0
O A:HOH550 4.5 23.3 1.0
OD2 A:ASP104 4.5 18.0 1.0
ND1 A:HIS83 4.6 10.3 0.7
CD2 A:HIS210 4.6 12.5 1.0
HG3 A:GLU134 4.6 14.9 1.0
CD2 A:HIS83 4.7 14.0 0.3
O A:HOH761 4.7 30.0 1.0
CG A:HIS83 4.7 10.4 0.7
HG2 A:GLU134 4.8 14.9 1.0
HB2 A:GLU134 4.8 12.6 1.0
CG A:HIS83 4.9 13.4 0.3
CE A:MET102 4.9 15.0 1.0
HG A:SER106 5.0 17.3 1.0

Zinc binding site 2 out of 4 in 5ud4

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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 Tbp


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 Tbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:24.4
occ:0.20
 HE1 A:HIS83 1.9 13.7 0.7
HO3 A:P6T404 2.0 22.6 1.0
NE2 A:HIS83 2.2 14.3 0.3
O A:HOH737 2.4 29.8 1.0
CE1 A:HIS83 2.5 11.4 0.7
O2 A:P6T404 2.5 20.4 1.0
HB3 A:HIS210 2.7 13.3 1.0
O3 A:P6T404 2.9 18.9 1.0
CD2 A:HIS83 3.1 14.0 0.3
H4 A:P6T404 3.1 23.8 1.0
CE1 A:HIS83 3.2 14.5 0.3
NE2 A:HIS83 3.2 11.4 0.7
C2 A:P6T404 3.2 20.2 1.0
HD2 A:HIS83 3.3 16.8 0.3
C3 A:P6T404 3.3 19.3 1.0
HE1 A:HIS83 3.4 17.4 0.3
ND1 A:HIS83 3.4 10.3 0.7
O4 A:P6T404 3.4 22.9 1.0
CG A:HIS210 3.4 11.6 1.0
CB A:HIS210 3.4 11.1 1.0
C4 A:P6T404 3.4 19.8 1.0
HD21 A:ASN253 3.5 11.7 1.0
ND1 A:HIS210 3.6 13.3 1.0
HD1 A:HIS83 3.6 12.3 0.7
H A:GLY211 3.7 14.3 1.0
ZN A:ZN402 3.7 24.4 0.7
HB3 A:GLN180 3.9 40.4 1.0
HA A:HIS210 4.0 12.2 1.0
HO4 A:P6T404 4.0 27.5 1.0
CD2 A:HIS210 4.1 12.5 1.0
HB2 A:HIS210 4.1 13.3 1.0
CE1 A:HIS210 4.2 13.1 1.0
CA A:HIS210 4.2 10.2 1.0
ND1 A:HIS83 4.2 14.2 0.3
CD2 A:HIS83 4.3 11.5 0.7
CG A:HIS83 4.3 13.4 0.3
ND2 A:ASN253 4.3 9.8 1.0
N A:GLY211 4.3 11.9 1.0
CG A:HIS83 4.4 10.4 0.7
H3 A:P6T404 4.4 23.2 1.0
HD2 A:HIS210 4.5 15.0 1.0
NE2 A:HIS210 4.5 12.2 1.0
OE1 A:GLN180 4.5 44.8 1.0
OD1 A:ASP82 4.6 10.5 1.0
HD22 A:ASN253 4.6 11.7 1.0
C1 A:P6T404 4.6 19.8 1.0
O A:HOH564 4.7 30.0 1.0
HB3 A:ASN253 4.7 10.0 1.0
HB2 A:GLN180 4.7 40.4 1.0
CB A:GLN180 4.7 33.6 1.0
HB2 A:ASN253 4.7 10.0 1.0
C A:HIS210 4.8 11.2 1.0
HE1 A:HIS210 4.8 15.8 1.0
C5 A:P6T404 4.9 17.4 1.0
O1 A:P6T404 5.0 19.4 1.0

Zinc binding site 3 out of 4 in 5ud4

Go back to Zinc Binding Sites List in 5ud4
Zinc binding site 3 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Tbp


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 Tbp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:21.7
occ:0.70
 HE1 B:HIS83 1.8 15.6 0.3
O B:HOH762 2.1 14.3 1.0
O B:HOH776 2.1 28.8 1.0
OE2 B:GLU134 2.4 19.7 1.0
ND1 B:HIS210 2.5 12.6 1.0
OE1 B:GLU134 2.5 16.3 1.0
NE2 B:HIS83 2.5 10.9 0.7
O B:HOH969 2.5 33.2 1.0
CE1 B:HIS83 2.6 13.0 0.3
CD B:GLU134 2.8 17.2 1.0
CE1 B:HIS210 3.2 12.7 1.0
HE1 B:HIS210 3.3 15.2 1.0
CE1 B:HIS83 3.3 10.5 0.7
HE1 B:HIS83 3.4 12.6 0.7
NE2 B:HIS83 3.4 13.2 0.3
CG B:HIS210 3.6 10.7 1.0
CD2 B:HIS83 3.6 11.2 0.7
ND1 B:HIS83 3.8 12.6 0.3
HB3 B:HIS210 3.8 12.1 1.0
ZN B:ZN403 3.8 21.7 0.2
O B:HOH702 3.8 33.2 1.0
HD2 B:HIS83 3.8 13.4 0.7
HB2 B:HIS210 3.9 12.1 1.0
HE1 B:MET102 3.9 18.9 1.0
HD1 B:HIS83 4.0 15.1 0.3
CB B:HIS210 4.0 10.1 1.0
CG B:GLU134 4.3 12.9 1.0
OD2 B:ASP104 4.4 17.0 1.0
NE2 B:HIS210 4.4 11.0 1.0
O B:HOH908 4.4 19.8 1.0
O B:HOH737 4.5 20.9 1.0
ND1 B:HIS83 4.5 10.4 0.7
HG3 B:GLU134 4.6 15.5 1.0
CD2 B:HIS210 4.6 11.8 1.0
CD2 B:HIS83 4.7 12.3 0.3
O B:HOH706 4.7 35.5 1.0
CG B:HIS83 4.7 10.6 0.7
HG2 B:GLU134 4.7 15.5 1.0
HB2 B:GLU134 4.7 12.9 1.0
O B:HOH990 4.8 33.3 1.0
CG B:HIS83 4.8 11.9 0.3
O B:HOH957 4.9 31.8 1.0
CE B:MET102 4.9 15.7 1.0
CG B:ASP104 4.9 14.8 1.0

Zinc binding site 4 out of 4 in 5ud4

Go back to Zinc Binding Sites List in 5ud4
Zinc binding site 4 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Tbp


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 Tbp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:21.7
occ:0.20
 HO3 B:P6T404 1.9 17.5 1.0
HE1 B:HIS83 2.1 12.6 0.7
NE2 B:HIS83 2.1 13.2 0.3
O B:HOH969 2.4 33.2 1.0
CE1 B:HIS83 2.5 10.5 0.7
O2 B:P6T404 2.6 16.6 1.0
HB3 B:HIS210 2.7 12.1 1.0
O3 B:P6T404 2.9 14.6 1.0
CD2 B:HIS83 3.1 12.3 0.3
O B:HOH706 3.1 35.5 1.0
CE1 B:HIS83 3.1 13.0 0.3
H4 B:P6T404 3.1 20.2 1.0
NE2 B:HIS83 3.1 10.9 0.7
HD2 B:HIS83 3.2 14.8 0.3
O4 B:P6T404 3.2 19.9 1.0
C2 B:P6T404 3.3 16.9 1.0
HE1 B:HIS83 3.3 15.6 0.3
ND1 B:HIS83 3.4 10.4 0.7
C3 B:P6T404 3.4 15.6 1.0
C4 B:P6T404 3.4 16.8 1.0
CB B:HIS210 3.5 10.1 1.0
CG B:HIS210 3.5 10.7 1.0
HD1 B:HIS83 3.6 12.5 0.7
HD22 B:ASN253 3.7 10.4 1.0
ND1 B:HIS210 3.7 12.6 1.0
HO4 B:P6T404 3.7 23.8 1.0
H B:GLY211 3.7 14.1 1.0
ZN B:ZN402 3.8 21.7 0.7
HB3 B:GLN180 3.8 30.0 1.0
HA B:HIS210 4.1 12.7 1.0
HB2 B:HIS210 4.2 12.1 1.0
CD2 B:HIS210 4.2 11.8 1.0
CD2 B:HIS83 4.2 11.2 0.7
CG B:HIS83 4.2 11.9 0.3
ND1 B:HIS83 4.2 12.6 0.3
CG B:HIS83 4.3 10.6 0.7
N B:GLY211 4.3 11.7 1.0
CE1 B:HIS210 4.4 12.7 1.0
CA B:HIS210 4.4 10.6 1.0
ND2 B:ASN253 4.4 8.7 1.0
H3 B:P6T404 4.4 18.7 1.0
O B:HOH776 4.5 28.8 1.0
OE1 B:GLN180 4.6 35.6 1.0
HD2 B:HIS210 4.6 14.1 1.0
NE2 B:HIS210 4.6 11.0 1.0
OD1 B:ASP82 4.7 9.7 1.0
C1 B:P6T404 4.7 17.8 1.0
CB B:GLN180 4.7 25.0 1.0
HD21 B:ASN253 4.7 10.4 1.0
HB3 B:ASN253 4.8 8.7 1.0
C B:HIS210 4.8 11.4 1.0
HB2 B:ASN253 4.9 8.7 1.0
HB2 B:GLN180 4.9 30.0 1.0
HE1 B:HIS210 4.9 15.2 1.0
HD2 B:HIS83 4.9 13.4 0.7
C5 B:P6T404 4.9 14.7 1.0
HD1 B:HIS83 5.0 15.1 0.3

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 09:24:08 2025

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