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Zinc in PDB 5vjd: Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with Dhap

Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with Dhap

All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with Dhap:
4.1.2.13;

Protein crystallography data

The structure of Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with Dhap, PDB code: 5vjd was solved by J.Sygusch, M.Coincon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.87 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.174, 71.454, 88.185, 90.00, 108.94, 90.00
R / Rfree (%) 14.8 / 17.3

Other elements in 5vjd:

The structure of Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with Dhap also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with Dhap (pdb code 5vjd). 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 of Escherichia Coli with Dhap, PDB code: 5vjd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5vjd

Go back to Zinc Binding Sites List in 5vjd
Zinc binding site 1 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli 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 of Escherichia Coli with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:18.9
occ:0.50
 ZN A:ZN402 0.0 18.9 0.5
HE1 A:HIS110 0.9 23.1 0.5
CE1 A:HIS110 1.8 19.2 0.5
NE2 A:HIS110 1.9 18.9 0.5
NE2 A:HIS226 2.0 38.4 0.4
O3 A:13P404 2.1 23.3 1.0
ND1 A:HIS264 2.1 15.8 0.5
HO3 A:13P404 2.5 28.0 1.0
O2 A:13P404 2.7 21.7 1.0
NE2 A:HIS110 2.7 19.1 0.5
CE1 A:HIS226 2.8 37.7 0.4
CD2 A:HIS110 2.8 18.3 0.5
HB3 A:HIS264 2.8 17.6 0.5
HE1 A:HIS226 2.8 45.3 0.4
HB3 A:HIS264 2.9 17.5 0.5
ND1 A:HIS110 2.9 18.4 0.5
CE1 A:HIS110 2.9 18.9 0.5
O A:HOH814 3.0 32.4 0.5
HD2 A:HIS110 3.0 22.0 0.5
C3 A:13P404 3.0 21.6 1.0
CE1 A:HIS264 3.0 15.2 0.5
ND1 A:HIS264 3.1 14.9 0.5
CG A:HIS264 3.1 15.2 0.5
HD1 A:HIS110 3.1 22.1 0.5
CD2 A:HIS226 3.2 38.4 0.4
C2 A:13P404 3.2 22.1 1.0
HE1 A:HIS110 3.2 22.7 0.5
HE1 A:HIS264 3.2 18.3 0.5
H32 A:13P404 3.2 25.9 1.0
CG A:HIS264 3.3 14.2 0.5
HD22 A:ASN286 3.5 17.7 1.0
CB A:HIS264 3.5 14.6 0.5
ZN A:ZN402 3.5 17.6 0.5
HD2 A:HIS226 3.5 46.1 0.4
CB A:HIS264 3.5 14.6 0.5
CE1 A:HIS264 3.7 13.0 0.5
HG23 A:THR178 3.8 43.3 0.5
CD2 A:HIS110 3.9 17.5 0.5
H31 A:13P404 4.0 25.9 1.0
ND1 A:HIS226 4.0 38.6 0.4
CG A:HIS110 4.0 18.0 0.5
CG A:HIS110 4.0 18.1 0.5
ND1 A:HIS110 4.0 18.7 0.5
H A:GLY265 4.1 20.7 1.0
CD2 A:HIS264 4.1 14.4 0.5
HA A:HIS264 4.1 17.4 0.5
HE1 A:HIS264 4.1 15.7 0.5
HB2 A:HIS264 4.2 17.5 0.5
NE2 A:HIS264 4.2 15.2 0.5
HA A:HIS264 4.2 17.4 0.5
ND2 A:ASN286 4.2 14.8 1.0
CG A:HIS226 4.2 41.7 0.4
HB2 A:HIS264 4.2 17.6 0.5
CD2 A:HIS264 4.2 15.4 0.5
NE2 A:HIS264 4.3 14.7 0.5
OD2 A:ASP109 4.3 14.9 1.0
OD1 A:ASP109 4.4 15.8 1.0
CA A:HIS264 4.4 14.5 0.5
CA A:HIS264 4.4 14.5 0.5
HD21 A:ASN286 4.5 17.7 1.0
C1 A:13P404 4.6 21.6 1.0
HB2 A:ASN286 4.6 16.6 1.0
HD2 A:HIS264 4.7 17.3 0.5
O A:HOH843 4.7 54.0 1.0
N A:GLY265 4.7 17.2 1.0
HB3 A:ASN286 4.7 16.6 1.0
HD2 A:HIS110 4.7 21.0 0.5
HD1 A:HIS226 4.7 46.3 0.4
HB A:THR178 4.7 43.9 0.5
CG2 A:THR178 4.7 36.1 0.5
CG A:ASP109 4.7 14.7 1.0
O A:HOH851 4.8 33.1 0.5
OG1 A:THR178 4.8 35.7 0.5
HD1 A:HIS110 4.8 22.5 0.5
H11 A:13P404 4.9 25.9 1.0
HE2 A:HIS264 4.9 17.6 0.5
HE2 A:HIS264 4.9 18.3 0.5
CB A:ASN286 5.0 13.9 1.0

Zinc binding site 2 out of 4 in 5vjd

Go back to Zinc Binding Sites List in 5vjd
Zinc binding site 2 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli 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 of Escherichia Coli with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:17.6
occ:0.50
 ZN A:ZN402 0.0 17.6 0.5
HE1 A:HIS110 1.1 22.7 0.5
CE1 A:HIS110 2.0 18.9 0.5
NE2 A:HIS110 2.0 19.1 0.5
OE1 A:GLU174 2.1 21.2 0.5
OE2 A:GLU174 2.2 20.5 0.5
O A:HOH814 2.3 32.4 0.5
OE1 A:GLU174 2.3 20.4 0.5
ND1 A:HIS264 2.3 14.9 0.5
OG1 A:THR178 2.3 35.7 0.5
O A:HOH541 2.4 29.8 1.0
CD A:GLU174 2.6 19.9 0.5
CD A:GLU174 2.8 20.2 0.5
NE2 A:HIS110 2.8 18.9 0.5
OE2 A:GLU174 3.0 20.8 0.5
HB A:THR178 3.0 43.9 0.5
CD2 A:HIS110 3.0 17.5 0.5
CE1 A:HIS264 3.0 13.0 0.5
HE1 A:HIS264 3.1 15.7 0.5
CE1 A:HIS110 3.1 19.2 0.5
ND1 A:HIS110 3.1 18.7 0.5
HD2 A:HIS110 3.1 21.0 0.5
HE1 A:HIS226 3.2 45.3 0.4
CB A:THR178 3.2 36.6 0.5
ND1 A:HIS264 3.2 15.8 0.5
HE1 A:HIS110 3.3 23.1 0.5
HD1 A:HIS110 3.3 22.5 0.5
CG A:HIS264 3.4 14.2 0.5
ZN A:ZN402 3.5 18.9 0.5
CG A:HIS264 3.5 15.2 0.5
HB3 A:HIS264 3.6 17.6 0.5
HB3 A:HIS264 3.6 17.5 0.5
HG23 A:THR178 3.7 43.3 0.5
HE3 A:MET142 3.7 29.7 1.0
CE1 A:HIS264 3.7 15.2 0.5
HB2 A:HIS264 3.8 17.5 0.5
CE1 A:HIS226 3.8 37.7 0.4
HB2 A:HIS264 3.8 17.6 0.5
CB A:HIS264 3.9 14.6 0.5
CB A:HIS264 3.9 14.6 0.5
H A:THR178 3.9 50.7 0.5
O A:HOH851 3.9 33.1 0.5
CG2 A:THR178 4.0 36.1 0.5
HE1 A:HIS264 4.0 18.3 0.5
CG A:GLU174 4.1 19.1 0.5
CD2 A:HIS110 4.1 18.3 0.5
CD2 A:HIS264 4.1 15.4 0.5
O A:HOH551 4.1 27.7 1.0
CG A:HIS110 4.1 18.1 0.5
ND1 A:HIS110 4.2 18.4 0.5
OD1 A:ASP144 4.2 21.7 1.0
CG A:HIS110 4.2 18.0 0.5
O A:HOH838 4.2 37.5 1.0
NE2 A:HIS226 4.2 38.4 0.4
NE2 A:HIS264 4.2 15.2 0.5
CG A:GLU174 4.2 19.0 0.5
NE2 A:HIS264 4.3 14.7 0.5
HG3 A:GLU174 4.4 22.9 0.5
CA A:THR178 4.4 40.8 0.5
HG3 A:GLU174 4.4 23.0 0.5
HB2 A:GLU174 4.4 21.1 0.5
CD2 A:HIS264 4.5 14.4 0.5
N A:THR178 4.5 42.3 0.5
HG22 A:THR178 4.5 43.3 0.5
HB2 A:GLU174 4.5 21.2 0.5
HG2 A:GLU174 4.5 23.0 0.5
CE A:MET142 4.6 24.7 1.0
HE2 A:MET142 4.7 29.7 1.0
HD2 A:HIS264 4.7 18.5 0.5
HB1 A:ALA219 4.7 17.5 1.0
HG21 A:THR178 4.7 43.3 0.5
HE2 A:HIS264 4.8 18.3 0.5
CG A:ASP144 4.8 21.0 1.0
HG2 A:GLU174 4.9 22.9 0.5
ND1 A:HIS226 4.9 38.6 0.4
CB A:GLU174 4.9 17.7 0.5
CB A:GLU174 4.9 17.6 0.5
HD2 A:HIS110 4.9 22.0 0.5
HA A:THR178 4.9 49.0 0.5
HD1 A:HIS110 4.9 22.1 0.5
HE2 A:HIS264 5.0 17.6 0.5

Zinc binding site 3 out of 4 in 5vjd

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

b:18.1
occ:0.65
 ZN B:ZN402 0.0 18.1 0.7
HE1 B:HIS110 1.1 24.2 0.5
CE1 B:HIS110 2.0 20.2 0.5
NE2 B:HIS110 2.0 19.7 0.5
NE2 B:HIS226 2.0 43.8 1.0
O3 B:13P404 2.1 23.1 1.0
ND1 B:HIS264 2.1 18.6 1.0
HO3 B:13P404 2.6 27.8 1.0
O2 B:13P404 2.6 20.0 1.0
CE1 B:HIS226 2.8 46.0 1.0
NE2 B:HIS110 2.8 20.1 0.5
HB3 B:HIS264 2.9 21.5 1.0
HE1 B:HIS226 2.9 55.2 1.0
O B:HOH790 2.9 18.5 0.5
CD2 B:HIS110 3.0 19.0 0.5
CE1 B:HIS110 3.0 20.8 0.5
C3 B:13P404 3.0 20.8 1.0
ND1 B:HIS110 3.1 20.2 0.5
CE1 B:HIS264 3.1 19.7 1.0
HD2 B:HIS110 3.2 22.8 0.5
CG B:HIS264 3.2 19.2 1.0
HE1 B:HIS110 3.2 25.0 0.5
CD2 B:HIS226 3.2 45.6 1.0
C2 B:13P404 3.2 20.6 1.0
H32 B:13P404 3.2 25.0 1.0
HE1 B:HIS264 3.2 23.6 1.0
HD1 B:HIS110 3.3 24.3 0.5
ZN B:ZN402 3.4 17.7 0.3
CB B:HIS264 3.5 17.9 1.0
HD2 B:HIS226 3.5 54.7 1.0
HG22 B:THR178 3.6 26.2 0.5
HD22 B:ASN286 3.6 16.3 1.0
HG1 B:THR178 4.0 28.7 0.5
H31 B:13P404 4.0 25.0 1.0
ND1 B:HIS226 4.0 45.5 1.0
H B:GLY265 4.0 19.9 1.0
CD2 B:HIS110 4.1 15.7 0.5
ND1 B:HIS110 4.1 18.1 0.5
CG B:HIS110 4.1 17.6 0.5
CG B:HIS110 4.2 18.3 0.5
HB2 B:HIS264 4.2 21.5 1.0
HA B:HIS264 4.2 19.7 1.0
CG B:HIS226 4.2 42.9 1.0
NE2 B:HIS264 4.2 19.0 1.0
CD2 B:HIS264 4.3 18.6 1.0
ND2 B:ASN286 4.3 13.6 1.0
OD1 B:ASP109 4.4 15.4 1.0
OD2 B:ASP109 4.4 15.7 1.0
CA B:HIS264 4.4 16.4 1.0
CG2 B:THR178 4.5 21.8 0.5
C1 B:13P404 4.6 22.1 1.0
HB B:THR178 4.6 27.3 0.5
HB2 B:ASN286 4.6 15.5 1.0
N B:GLY265 4.6 16.6 1.0
HD21 B:ASN286 4.7 16.3 1.0
HB3 B:ASN286 4.7 15.5 1.0
OG1 B:THR178 4.7 23.9 0.5
HD1 B:HIS226 4.7 54.6 1.0
CG B:ASP109 4.9 15.7 1.0
HD2 B:HIS110 4.9 18.8 0.5
HD1 B:HIS110 4.9 21.7 0.5
CB B:THR178 4.9 22.8 0.5
H11 B:13P404 4.9 26.5 1.0
O B:HOH835 5.0 31.4 1.0
HG23 B:THR178 5.0 26.2 0.5
HE2 B:HIS264 5.0 22.9 1.0

Zinc binding site 4 out of 4 in 5vjd

Go back to Zinc Binding Sites List in 5vjd
Zinc binding site 4 out of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli 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 of Escherichia Coli with Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:17.7
occ:0.35
 ZN B:ZN402 0.0 17.7 0.3
HE1 B:HIS110 1.2 25.0 0.5
HG1 B:THR178 1.8 28.7 0.5
CE1 B:HIS110 2.1 20.8 0.5
NE2 B:HIS110 2.1 20.1 0.5
O B:HOH790 2.1 18.5 0.5
OE1 B:GLU174 2.1 29.2 1.0
OG1 B:THR178 2.4 23.9 0.5
CD B:GLU174 2.8 27.3 1.0
O B:HOH671 2.8 33.4 1.0
OE2 B:GLU174 2.8 29.7 1.0
NE2 B:HIS110 2.9 19.7 0.5
HB B:THR178 3.0 27.3 0.5
CE1 B:HIS110 3.1 20.2 0.5
CD2 B:HIS110 3.1 15.7 0.5
ND1 B:HIS110 3.1 18.1 0.5
ND1 B:HIS264 3.1 18.6 1.0
CB B:THR178 3.2 22.8 0.5
HE1 B:HIS110 3.2 24.2 0.5
HE1 B:MET142 3.3 22.8 1.0
HD2 B:HIS110 3.3 18.8 0.5
HD1 B:HIS110 3.4 21.7 0.5
ZN B:ZN402 3.4 18.1 0.7
CG B:HIS264 3.5 19.2 1.0
HE1 B:HIS226 3.6 55.2 1.0
HG22 B:THR178 3.6 26.2 0.5
CE1 B:HIS264 3.6 19.7 1.0
HB3 B:HIS264 3.7 21.5 1.0
HB2 B:HIS264 3.9 21.5 1.0
HE1 B:HIS264 3.9 23.6 1.0
CB B:HIS264 4.0 17.9 1.0
CG2 B:THR178 4.0 21.8 0.5
CD2 B:HIS110 4.1 19.0 0.5
CE1 B:HIS226 4.2 46.0 1.0
H B:THR178 4.2 27.6 0.5
CD2 B:HIS264 4.2 18.6 1.0
ND1 B:HIS110 4.2 20.2 0.5
O B:HOH788 4.2 36.1 1.0
NE2 B:HIS264 4.2 19.0 1.0
OD2 B:ASP144 4.2 19.5 1.0
CG B:GLU174 4.2 21.7 1.0
CG B:HIS110 4.2 18.3 0.5
CE B:MET142 4.2 19.0 1.0
CG B:HIS110 4.2 17.6 0.5
O B:HOH835 4.2 31.4 1.0
NE2 B:HIS226 4.4 43.8 1.0
HB2 B:GLU174 4.5 21.5 1.0
HG3 B:GLU174 4.5 26.0 1.0
HG21 B:THR178 4.5 26.2 0.5
CA B:THR178 4.5 23.0 0.5
HE2 B:MET142 4.6 22.8 1.0
N B:THR178 4.6 23.0 0.5
HE3 B:MET142 4.7 22.8 1.0
HB1 B:ALA219 4.7 16.2 1.0
HG23 B:THR178 4.7 26.2 0.5
HE2 B:HIS264 4.8 22.9 1.0
HD2 B:HIS264 4.8 22.4 1.0
HG2 B:GLU174 4.8 26.0 1.0
CG B:ASP144 4.9 18.7 1.0
CB B:GLU174 4.9 17.9 1.0
HD2 B:HIS110 4.9 22.8 0.5
HD1 B:HIS110 5.0 24.3 0.5
HA B:THR178 5.0 27.6 0.5

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 12:58:42 2024

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