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Zinc in PDB 5gk4: Native Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 2.0 Angstrom Resolution

Enzymatic activity of Native Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 2.0 Angstrom Resolution

All present enzymatic activity of Native Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 2.0 Angstrom Resolution:
4.1.2.13;

Protein crystallography data

The structure of Native Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 2.0 Angstrom Resolution, PDB code: 5gk4 was solved by T.H.Tran, K.H.Huynh, T.H.Ho, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.126, 72.893, 72.455, 90.00, 103.20, 90.00
R / Rfree (%) 15.3 / 20

Zinc Binding Sites:

The binding sites of Zinc atom in the Native Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 2.0 Angstrom Resolution (pdb code 5gk4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Native Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 2.0 Angstrom Resolution, PDB code: 5gk4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5gk4

Go back to Zinc Binding Sites List in 5gk4
Zinc binding site 1 out of 4 in the Native Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Native Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:28.8
occ:0.40
 OE1 A:GLU174 1.7 29.4 1.0
CE1 A:HIS110 2.3 23.0 0.6
O A:HOH629 2.3 36.2 1.0
NE2 A:HIS110 2.4 23.0 0.4
CD A:GLU174 2.4 29.6 1.0
OE2 A:GLU174 2.5 29.9 1.0
ND1 A:HIS264 2.5 25.8 0.4
O A:HOH534 2.8 30.8 1.0
CD2 A:HIS110 3.1 23.4 0.4
NE2 A:HIS110 3.1 22.9 0.6
CE1 A:HIS264 3.2 24.8 0.4
O A:HOH658 3.2 26.5 1.0
ND1 A:HIS110 3.2 25.1 0.6
ND1 A:HIS264 3.4 20.0 0.6
CE1 A:HIS110 3.5 22.9 0.4
CG A:HIS264 3.6 23.0 0.4
CG A:HIS264 3.6 19.5 0.6
ZN A:ZN404 3.7 21.0 0.6
CE1 A:HIS264 3.8 21.7 0.6
CG A:GLU174 3.9 24.1 1.0
CB A:HIS264 4.1 20.2 0.6
CB A:HIS264 4.1 22.5 0.4
CE A:MET142 4.1 29.9 1.0
CD2 A:HIS264 4.1 19.6 0.6
O A:HOH531 4.1 38.0 1.0
OD2 A:ASP144 4.1 25.6 1.0
NE2 A:HIS264 4.2 19.2 0.6
CD2 A:HIS110 4.3 22.1 0.6
CG A:HIS110 4.3 22.6 0.4
NE2 A:HIS264 4.4 23.1 0.4
CG A:HIS110 4.4 23.1 0.6
ND1 A:HIS110 4.5 22.4 0.4
CD2 A:HIS264 4.6 22.8 0.4
CB A:GLU174 4.6 21.8 1.0
CG A:ASP144 4.7 24.3 1.0
O A:HOH671 4.9 40.8 1.0

Zinc binding site 2 out of 4 in 5gk4

Go back to Zinc Binding Sites List in 5gk4
Zinc binding site 2 out of 4 in the Native Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Native Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:21.0
occ:0.60
 CE1 A:HIS110 2.1 22.9 0.4
O A:HOH652 2.1 25.6 1.0
NE2 A:HIS110 2.1 22.9 0.6
O A:HOH656 2.2 33.1 1.0
O A:HOH560 2.2 25.4 1.0
ND1 A:HIS264 2.2 20.0 0.6
O A:HOH658 2.4 26.5 1.0
NE2 A:HIS110 2.7 23.0 0.4
ND1 A:HIS264 2.9 25.8 0.4
CE1 A:HIS110 3.1 23.0 0.6
CD2 A:HIS110 3.1 22.1 0.6
CE1 A:HIS264 3.2 21.7 0.6
CG A:HIS264 3.3 19.5 0.6
ND1 A:HIS110 3.3 22.4 0.4
CG A:HIS264 3.3 23.0 0.4
CB A:HIS264 3.6 20.2 0.6
CE1 A:HIS264 3.6 24.8 0.4
CB A:HIS264 3.6 22.5 0.4
ZN A:ZN403 3.7 28.8 0.4
CD2 A:HIS110 4.0 23.4 0.4
O A:HOH629 4.1 36.2 1.0
O A:HOH671 4.1 40.8 1.0
CD2 A:HIS264 4.2 22.8 0.4
ND2 A:ASN286 4.2 19.7 1.0
ND1 A:HIS110 4.2 25.1 0.6
CG A:HIS110 4.3 23.1 0.6
NE2 A:HIS264 4.3 23.1 0.4
CG A:HIS110 4.3 22.6 0.4
NE2 A:HIS264 4.3 19.2 0.6
CD2 A:HIS264 4.4 19.6 0.6
OD1 A:ASP109 4.4 18.6 1.0
CA A:HIS264 4.4 19.9 0.6
CA A:HIS264 4.4 21.5 0.4
OD2 A:ASP109 4.5 18.3 1.0
N A:GLY265 4.8 25.2 1.0
CG A:ASP109 4.9 18.9 1.0

Zinc binding site 3 out of 4 in 5gk4

Go back to Zinc Binding Sites List in 5gk4
Zinc binding site 3 out of 4 in the Native Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Native Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:24.6
occ:0.50
 OE1 B:GLU174 2.1 25.5 1.0
O B:HOH606 2.1 36.6 1.0
CE1 B:HIS110 2.2 17.3 0.5
NE2 B:HIS110 2.3 17.3 0.5
OE2 B:GLU174 2.4 27.3 1.0
ND1 B:HIS264 2.5 23.0 0.5
CD B:GLU174 2.6 26.4 1.0
O B:HOH534 2.7 31.8 1.0
CD2 B:HIS110 3.1 19.1 0.5
O B:HOH682 3.1 35.8 1.0
NE2 B:HIS110 3.1 18.1 0.5
CE1 B:HIS264 3.2 21.6 0.5
ND1 B:HIS110 3.2 19.0 0.5
CE1 B:HIS110 3.4 17.9 0.5
ND1 B:HIS264 3.4 19.2 0.5
CG B:HIS264 3.6 19.6 0.5
CG B:HIS264 3.6 21.2 0.5
ZN B:ZN402 3.7 20.0 0.5
CE1 B:HIS264 3.9 19.4 0.5
CB B:HIS264 3.9 18.8 0.5
CB B:HIS264 4.0 19.8 0.5
CG B:GLU174 4.1 21.0 1.0
CD2 B:HIS264 4.1 20.0 0.5
OD2 B:ASP144 4.2 21.8 1.0
NE2 B:HIS264 4.2 18.0 0.5
O B:HOH602 4.3 32.7 1.0
CD2 B:HIS110 4.3 18.1 0.5
CG B:HIS110 4.3 19.5 0.5
CG B:HIS110 4.4 19.3 0.5
NE2 B:HIS264 4.4 19.9 0.5
ND1 B:HIS110 4.5 18.3 0.5
CE B:MET142 4.5 34.2 1.0
CD2 B:HIS264 4.6 19.7 0.5
CB B:GLU174 4.8 18.5 1.0
CG B:ASP144 4.8 21.4 1.0

Zinc binding site 4 out of 4 in 5gk4

Go back to Zinc Binding Sites List in 5gk4
Zinc binding site 4 out of 4 in the Native Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Native Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 2.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:20.0
occ:0.50
 CE1 B:HIS110 2.0 17.9 0.5
NE2 B:HIS110 2.0 18.1 0.5
O B:HOH674 2.1 22.8 1.0
ND1 B:HIS264 2.1 19.2 0.5
O B:HOH673 2.2 27.8 1.0
O B:HOH550 2.3 23.1 1.0
O B:HOH682 2.6 35.8 1.0
NE2 B:HIS110 2.7 17.3 0.5
CE1 B:HIS110 3.0 17.3 0.5
CD2 B:HIS110 3.0 18.1 0.5
ND1 B:HIS264 3.0 23.0 0.5
CE1 B:HIS264 3.1 19.4 0.5
ND1 B:HIS110 3.1 18.3 0.5
CG B:HIS264 3.2 19.6 0.5
CG B:HIS264 3.3 21.2 0.5
O B:HOH697 3.4 40.3 1.0
CB B:HIS264 3.5 18.8 0.5
CB B:HIS264 3.5 19.8 0.5
ZN B:ZN401 3.7 24.6 0.5
CE1 B:HIS264 3.7 21.6 0.5
CD2 B:HIS110 3.9 19.1 0.5
ND1 B:HIS110 4.1 19.0 0.5
CD2 B:HIS264 4.1 19.7 0.5
CG B:HIS110 4.1 19.3 0.5
O B:HOH606 4.1 36.6 1.0
CG B:HIS110 4.2 19.5 0.5
NE2 B:HIS264 4.2 18.0 0.5
ND2 B:ASN286 4.2 16.4 1.0
CD2 B:HIS264 4.3 20.0 0.5
OD1 B:ASP109 4.3 16.2 1.0
NE2 B:HIS264 4.3 19.9 0.5
CA B:HIS264 4.4 19.2 0.5
CA B:HIS264 4.5 19.9 0.5
OD2 B:ASP109 4.6 18.4 1.0
CG B:ASP109 4.9 19.2 1.0
N B:GLY265 5.0 23.6 1.0

Reference:

T.H.Tran, K.H.Huynh, T.H.Ho, L.W.Kang. Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 2.0 Angstrom Resolution To Be Published.
Page generated: Sun Oct 27 17:02:09 2024

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