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Zinc in PDB 1dos: Structure of Fructose-Bisphosphate Aldolase

Enzymatic activity of Structure of Fructose-Bisphosphate Aldolase

All present enzymatic activity of Structure of Fructose-Bisphosphate Aldolase:
4.1.2.13;

Protein crystallography data

The structure of Structure of Fructose-Bisphosphate Aldolase, PDB code: 1dos was solved by N.Blom, S.Tetreault, R.Coulombe, J.Sygusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.530, 73.380, 57.800, 90.00, 106.60, 90.00
R / Rfree (%) 17.1 / 20.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Fructose-Bisphosphate Aldolase (pdb code 1dos). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Fructose-Bisphosphate Aldolase, PDB code: 1dos:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1dos

Go back to Zinc Binding Sites List in 1dos
Zinc binding site 1 out of 4 in the Structure of Fructose-Bisphosphate Aldolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Fructose-Bisphosphate Aldolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1005

b:16.9
occ:0.60
ZN A:ZN1005 0.0 16.9 0.6
NE2 A:HIS110 2.1 13.5 0.6
NE2 A:HIS226 2.1 18.8 0.6
OE1 A:GLU174 2.1 11.8 0.4
ND1 A:HIS264 2.2 12.6 0.6
CE1 A:HIS110 2.2 22.2 0.4
CE1 A:HIS226 2.3 44.5 0.4
ND1 A:HIS264 2.4 31.2 0.4
OE1 A:GLU174 2.4 20.4 0.6
OE2 A:GLU174 2.4 14.7 0.4
CD A:GLU174 2.6 14.0 0.4
OE2 A:GLU174 2.8 25.7 0.6
CD A:GLU174 2.8 22.6 0.6
O A:HOH1122 2.9 41.5 1.0
CE1 A:HIS264 3.0 9.8 0.6
CD2 A:HIS226 3.0 22.4 0.6
NE2 A:HIS110 3.0 26.2 0.4
CE1 A:HIS110 3.0 14.6 0.6
NE2 A:HIS226 3.1 43.9 0.4
CD2 A:HIS110 3.1 12.3 0.6
CE1 A:HIS264 3.1 33.3 0.4
CE1 A:HIS226 3.1 18.7 0.6
ND1 A:HIS110 3.2 20.5 0.4
CG A:HIS264 3.2 10.2 0.6
HE2 A:HIS226 3.2 42.9 0.4
ND1 A:HIS226 3.3 45.4 0.4
ZN A:ZN1005 3.3 32.4 0.4
CG A:HIS264 3.3 29.9 0.4
HD1 A:HIS110 3.4 20.6 0.4
HD1 A:HIS226 3.6 44.0 0.4
CB A:HIS264 3.7 9.3 0.6
CB A:HIS264 3.8 24.5 0.4
CG A:GLU174 4.1 13.2 0.4
O A:HOH1148 4.1 25.2 1.0
NE2 A:HIS264 4.2 5.5 0.6
CG A:GLU174 4.2 19.9 0.6
NE2 A:HIS264 4.2 32.9 0.4
CG A:HIS226 4.2 23.0 0.6
ND1 A:HIS110 4.2 16.0 0.6
ND1 A:HIS226 4.2 19.5 0.6
CD2 A:HIS110 4.2 23.7 0.4
CG A:HIS110 4.2 14.2 0.6
CD2 A:HIS226 4.3 44.0 0.4
CD2 A:HIS264 4.3 11.0 0.6
CD2 A:HIS264 4.3 32.8 0.4
CG A:HIS110 4.3 20.7 0.4
O A:HOH1373 4.3 70.7 1.0
CG A:HIS226 4.4 45.1 0.4
OD2 A:ASP144 4.5 16.5 0.6
OD2 A:ASP144 4.5 22.3 0.4
O A:HOH1227 4.6 49.9 1.0
O A:HOH1376 4.7 97.1 1.0
CE A:MET142 4.8 14.9 1.0
CB A:GLU174 4.8 15.6 0.4
O A:HOH1291 4.8 31.4 1.0
CB A:GLU174 5.0 17.9 0.6
HE2 A:HIS264 5.0 0.0 0.4
HE2 A:HIS264 5.0 0.0 0.6

Zinc binding site 2 out of 4 in 1dos

Go back to Zinc Binding Sites List in 1dos
Zinc binding site 2 out of 4 in the Structure of Fructose-Bisphosphate Aldolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Fructose-Bisphosphate Aldolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1005

b:32.4
occ:0.40
ZN A:ZN1005 0.0 32.4 0.4
CE1 A:HIS110 1.9 14.6 0.6
NE2 A:HIS110 2.0 26.2 0.4
O A:HOH1433 2.2 28.0 1.0
ND1 A:HIS264 2.3 31.2 0.4
O A:HOH1291 2.3 31.4 1.0
NE2 A:HIS110 2.7 13.5 0.6
O A:HOH1116 2.7 31.6 1.0
CE1 A:HIS110 2.8 22.2 0.4
HD1 A:HIS226 3.0 44.0 0.4
ND1 A:HIS110 3.0 16.0 0.6
CE1 A:HIS264 3.0 33.3 0.4
CG A:HIS264 3.1 29.9 0.4
CD2 A:HIS110 3.1 23.7 0.4
CD2 A:HIS226 3.1 22.4 0.6
HD1 A:HIS110 3.2 15.9 0.6
ND1 A:HIS226 3.3 45.4 0.4
ZN A:ZN1005 3.3 16.9 0.6
CG A:HIS264 3.4 10.2 0.6
CB A:HIS264 3.4 9.3 0.6
ND1 A:HIS264 3.5 12.6 0.6
CE1 A:HIS226 3.5 44.5 0.4
CB A:HIS264 3.5 24.5 0.4
NE2 A:HIS226 3.6 18.8 0.6
H A:GLY265 3.7 17.2 0.6
CD2 A:HIS110 3.9 12.3 0.6
H A:GLY265 4.0 22.8 0.4
ND1 A:HIS110 4.0 20.5 0.4
NE2 A:HIS264 4.0 32.9 0.4
CD2 A:HIS264 4.0 32.8 0.4
CG A:HIS110 4.1 14.2 0.6
CD2 A:HIS264 4.1 11.0 0.6
CG A:HIS226 4.1 23.0 0.6
CE1 A:HIS264 4.1 9.8 0.6
CG A:HIS110 4.2 20.7 0.4
O A:HOH1233 4.2 55.0 1.0
CG A:HIS226 4.2 45.1 0.4
CA A:HIS264 4.3 12.1 0.6
CA A:HIS264 4.4 21.2 0.4
OD1 A:ASN286 4.4 13.5 1.0
N A:GLY265 4.5 17.1 0.6
NE2 A:HIS226 4.5 43.9 0.4
NE2 A:HIS264 4.5 5.5 0.6
N A:GLY265 4.5 22.7 0.4
CE1 A:HIS226 4.6 18.7 0.6
OD1 A:ASP109 4.7 8.2 0.6
CB A:HIS226 4.8 28.9 0.6
O A:HOH1537 4.8 53.7 1.0
C A:HIS264 4.8 15.4 0.6
HE2 A:HIS264 4.8 0.0 0.4
HD1 A:HIS110 4.8 20.6 0.4
OD1 A:ASP109 4.8 11.9 0.4
C A:HIS264 4.8 22.3 0.4
OD2 A:ASP109 4.8 11.1 0.6
CD2 A:HIS226 4.8 44.0 0.4
CB A:HIS226 4.9 45.8 0.4
ND1 A:HIS226 4.9 19.5 0.6
O A:HOH1227 4.9 49.9 1.0

Zinc binding site 3 out of 4 in 1dos

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Zinc binding site 3 out of 4 in the Structure of Fructose-Bisphosphate Aldolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Fructose-Bisphosphate Aldolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1323

b:28.3
occ:0.40
ZN B:ZN1323 0.0 28.3 0.4
CE1 B:HIS226 2.1 66.4 0.6
NE2 B:HIS110 2.1 25.1 0.4
NE2 B:HIS226 2.1 34.4 0.4
ND1 B:HIS264 2.2 24.1 0.4
OE1 B:GLU174 2.2 28.9 0.4
CE1 B:HIS110 2.3 23.4 0.6
OE1 B:GLU174 2.3 24.7 0.6
ND1 B:HIS264 2.5 27.0 0.6
OE2 B:GLU174 2.7 24.5 0.6
CD B:GLU174 2.7 21.6 0.6
CD B:GLU174 2.8 27.7 0.4
NE2 B:HIS110 2.8 26.0 0.6
HE2 B:HIS226 2.9 67.5 0.6
CE1 B:HIS264 2.9 21.8 0.4
NE2 B:HIS226 2.9 67.3 0.6
CE1 B:HIS264 3.0 25.5 0.6
CE1 B:HIS226 3.0 39.3 0.4
CE1 B:HIS110 3.1 22.9 0.4
CD2 B:HIS226 3.1 39.8 0.4
CG B:HIS264 3.1 21.8 0.4
OE2 B:GLU174 3.1 29.5 0.4
CD2 B:HIS110 3.1 22.5 0.4
ND1 B:HIS226 3.2 66.2 0.6
ZN B:ZN1323 3.2 32.5 0.6
CG B:HIS264 3.3 23.9 0.6
ND1 B:HIS110 3.4 21.2 0.6
O B:HOH1668 3.6 49.9 1.0
HD1 B:HIS226 3.6 65.6 0.6
CB B:HIS264 3.7 19.2 0.4
CB B:HIS264 3.8 20.6 0.6
HD1 B:HIS110 3.8 21.8 0.6
NE2 B:HIS264 3.9 20.2 0.4
NE2 B:HIS264 3.9 22.6 0.6
CG B:GLU174 3.9 24.4 0.4
CD2 B:HIS264 4.0 20.8 0.4
CD2 B:HIS264 4.1 23.3 0.6
CG B:GLU174 4.1 16.2 0.6
CD2 B:HIS226 4.1 67.4 0.6
ND1 B:HIS226 4.1 42.5 0.4
CD2 B:HIS110 4.1 25.4 0.6
CG B:HIS226 4.2 44.3 0.4
ND1 B:HIS110 4.2 22.3 0.4
CG B:HIS226 4.3 66.5 0.6
CE B:MET142 4.3 20.8 1.0
CG B:HIS110 4.3 21.2 0.4
CG B:HIS110 4.4 21.8 0.6
O B:HOH1793 4.5 31.9 1.0
HE2 B:HIS264 4.6 22.9 0.6
O B:HOH1675 4.6 31.8 1.0
OD2 B:ASP144 4.7 18.3 0.4
HE2 B:HIS264 4.8 20.8 0.4
CB B:GLU174 4.8 20.4 0.4
CB B:GLU174 4.8 14.9 0.6
O B:HOH1524 4.9 48.9 1.0
O B:HOH1783 4.9 29.3 1.0
HD1 B:HIS226 5.0 43.9 0.4

Zinc binding site 4 out of 4 in 1dos

Go back to Zinc Binding Sites List in 1dos
Zinc binding site 4 out of 4 in the Structure of Fructose-Bisphosphate Aldolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Fructose-Bisphosphate Aldolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1323

b:32.5
occ:0.60
ZN B:ZN1323 0.0 32.5 0.6
CE1 B:HIS110 1.8 22.9 0.4
NE2 B:HIS110 2.1 26.0 0.6
ND1 B:HIS264 2.2 27.0 0.6
O B:HOH1793 2.2 31.9 1.0
O B:HOH1783 2.2 29.3 1.0
NE2 B:HIS110 2.6 25.1 0.4
O B:HOH1782 2.7 20.8 1.0
HD1 B:HIS226 2.8 65.6 0.6
ND1 B:HIS110 2.9 22.3 0.4
CD2 B:HIS110 3.0 25.4 0.6
CE1 B:HIS264 3.0 25.5 0.6
CE1 B:HIS110 3.1 23.4 0.6
CG B:HIS264 3.2 23.9 0.6
HD1 B:HIS110 3.2 22.6 0.4
ZN B:ZN1323 3.2 28.3 0.4
CG B:HIS264 3.2 21.8 0.4
ND1 B:HIS226 3.3 66.2 0.6
CE1 B:HIS226 3.5 66.4 0.6
CD2 B:HIS226 3.5 39.8 0.4
CB B:HIS264 3.5 19.2 0.4
HD22 B:ASN286 3.5 14.3 1.0
CD2 B:HIS264 3.5 20.8 0.4
ND1 B:HIS264 3.6 24.1 0.4
CB B:HIS264 3.6 20.6 0.6
NE2 B:HIS226 3.8 34.4 0.4
CD2 B:HIS110 3.8 22.5 0.4
CE1 B:HIS264 4.0 21.8 0.4
NE2 B:HIS264 4.0 20.2 0.4
CG B:HIS110 4.0 21.2 0.4
ND1 B:HIS110 4.1 21.2 0.6
CG B:HIS110 4.1 21.8 0.6
NE2 B:HIS264 4.2 22.6 0.6
ND2 B:ASN286 4.2 14.2 1.0
CD2 B:HIS264 4.2 23.3 0.6
H B:GLY265 4.2 28.0 0.4
O B:HOH1748 4.3 93.9 1.0
O B:HOH1722 4.3 45.4 1.0
OD1 B:ASP109 4.3 14.2 0.6
OD1 B:ASP109 4.4 9.7 0.4
CA B:HIS264 4.4 20.0 0.4
CG B:HIS226 4.4 44.3 0.4
H B:GLY265 4.4 29.8 0.6
CG B:HIS226 4.5 66.5 0.6
CA B:HIS264 4.5 21.1 0.6
HD21 B:ASN286 4.6 13.8 1.0
OD2 B:ASP109 4.6 17.0 0.6
OD2 B:ASP109 4.6 12.1 0.4
NE2 B:HIS226 4.7 67.3 0.6
HE2 B:HIS264 4.7 20.8 0.4
CE1 B:HIS226 4.8 39.3 0.4
CG B:ASP109 4.9 15.3 0.6
CG B:ASP109 4.9 11.4 0.4
N B:GLY265 5.0 27.9 0.4

Reference:

N.S.Blom, S.Tetreault, R.Coulombe, J.Sygusch. Novel Active Site in Escherichia Coli Fructose 1,6-Bisphosphate Aldolase. Nat.Struct.Biol. V. 3 856 1996.
ISSN: ISSN 1072-8368
PubMed: 8836102
DOI: 10.1038/NSB1096-856
Page generated: Wed Dec 16 02:47:26 2020

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