Zinc in PDB 5gk5: Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution

Enzymatic activity of Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution

All present enzymatic activity of Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution:
4.1.2.13;

Protein crystallography data

The structure of Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution, PDB code: 5gk5 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) 22.06 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 72.834, 90.535, 113.733, 90.07, 90.01, 90.21
R / Rfree (%) 17.2 / 20.7

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution (pdb code 5gk5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution, PDB code: 5gk5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 5gk5

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Zinc binding site 1 out of 14 in the Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:26.4
occ:0.67
 OE1 A:GLU174 2.1 25.4 1.0
NE2 A:HIS226 2.2 31.5 1.0
CE1 A:HIS110 2.2 25.5 1.0
OE2 A:GLU174 2.3 29.0 1.0
O A:HOH573 2.4 28.6 1.0
ND1 A:HIS264 2.4 32.2 1.0
CD A:GLU174 2.5 26.4 1.0
NE2 A:HIS110 3.1 24.6 1.0
CD2 A:HIS226 3.1 31.1 1.0
CE1 A:HIS264 3.2 25.7 1.0
CE1 A:HIS226 3.2 31.0 1.0
ND1 A:HIS110 3.3 28.0 1.0
CG A:HIS264 3.5 27.5 1.0
ZN A:ZN403 3.8 34.5 0.5
CB A:HIS264 3.9 25.0 1.0
CG A:GLU174 4.0 24.7 1.0
O A:HOH520 4.2 27.2 1.0
OD2 A:ASP144 4.2 26.5 1.0
CG A:HIS226 4.3 38.1 1.0
ND1 A:HIS226 4.3 36.0 1.0
CD2 A:HIS110 4.3 19.7 1.0
NE2 A:HIS264 4.4 21.0 1.0
CG A:HIS110 4.4 27.0 1.0
CD2 A:HIS264 4.6 21.9 1.0
CG A:ASP144 4.7 25.5 1.0
CB A:GLU174 4.7 20.2 1.0

Zinc binding site 2 out of 14 in 5gk5

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Zinc binding site 2 out of 14 in the Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:34.5
occ:0.49
 NE2 A:HIS110 2.0 24.6 1.0
O A:HOH617 2.1 28.9 1.0
O A:HOH576 2.4 27.5 1.0
O A:HOH631 2.6 41.9 1.0
CD2 A:HIS110 3.0 19.7 1.0
CE1 A:HIS110 3.0 25.5 1.0
CD2 A:HIS226 3.1 31.1 1.0
ND1 A:HIS264 3.3 32.2 1.0
CG A:HIS264 3.3 27.5 1.0
CB A:HIS264 3.4 25.0 1.0
NE2 A:HIS226 3.5 31.5 1.0
ZN A:ZN402 3.8 26.4 0.7
CE1 A:HIS264 4.1 25.7 1.0
ND1 A:HIS110 4.1 28.0 1.0
CG A:HIS226 4.1 38.1 1.0
CG A:HIS110 4.1 27.0 1.0
CD2 A:HIS264 4.1 21.9 1.0
ND2 A:ASN286 4.2 22.7 1.0
CA A:HIS264 4.3 24.2 1.0
OD2 A:ASP109 4.5 20.7 1.0
NE2 A:HIS264 4.5 21.0 1.0
N A:GLY265 4.5 27.4 1.0
OD1 A:ASP109 4.5 22.1 1.0
CE1 A:HIS226 4.6 31.0 1.0
CB A:HIS226 4.9 39.1 1.0
C A:HIS264 4.9 26.1 1.0
ND1 A:HIS226 4.9 36.0 1.0
CG A:ASP109 5.0 22.6 1.0

Zinc binding site 3 out of 14 in 5gk5

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Zinc binding site 3 out of 14 in the Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:22.4
occ:0.75
 NE2 B:HIS226 2.1 24.7 1.0
CE1 B:HIS110 2.2 14.6 1.0
OE1 B:GLU174 2.2 20.1 1.0
ND1 B:HIS264 2.4 23.5 1.0
OE2 B:GLU174 2.4 20.1 1.0
O B:HOH578 2.4 20.8 1.0
CD B:GLU174 2.6 20.9 1.0
NE2 B:HIS110 3.1 22.5 1.0
CD2 B:HIS226 3.1 26.3 1.0
CE1 B:HIS226 3.2 25.2 1.0
ND1 B:HIS110 3.2 22.2 1.0
CE1 B:HIS264 3.2 22.5 1.0
CG B:HIS264 3.5 21.7 1.0
O B:HOH501 3.6 21.3 1.0
CB B:HIS264 3.8 20.4 1.0
CG B:GLU174 4.1 16.7 1.0
CG B:HIS226 4.2 33.7 1.0
ND1 B:HIS226 4.2 32.3 1.0
CD2 B:HIS110 4.3 15.0 1.0
OD2 B:ASP144 4.3 20.7 1.0
CG B:HIS110 4.3 21.3 1.0
NE2 B:HIS264 4.4 15.8 1.0
CD2 B:HIS264 4.5 18.7 1.0
CG B:ASP144 4.8 20.9 1.0
CB B:GLU174 4.8 16.2 1.0

Zinc binding site 4 out of 14 in 5gk5

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Zinc binding site 4 out of 14 in the Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:27.7
occ:0.64
 OE2 C:GLU174 1.6 28.1 1.0
CE1 C:HIS110 2.2 23.1 1.0
NE2 C:HIS226 2.3 32.7 1.0
CD C:GLU174 2.4 26.4 1.0
OE1 C:GLU174 2.4 30.6 1.0
ND1 C:HIS264 2.5 32.8 1.0
O C:HOH1223 2.5 28.4 1.0
CE1 C:HIS226 3.1 30.3 1.0
NE2 C:HIS110 3.1 29.0 1.0
CE1 C:HIS264 3.3 31.9 1.0
ND1 C:HIS110 3.3 24.6 1.0
CD2 C:HIS226 3.4 32.0 1.0
CG C:HIS264 3.5 26.0 1.0
CG C:GLU174 3.9 25.8 1.0
CB C:HIS264 3.9 24.5 1.0
ZN C:ZN404 4.0 33.6 0.5
OD2 C:ASP144 4.2 26.1 1.0
CE C:MET142 4.2 36.8 1.0
ND1 C:HIS226 4.2 36.0 1.0
CD2 C:HIS110 4.3 23.9 1.0
CG C:HIS110 4.4 23.9 1.0
CG C:HIS226 4.4 34.0 1.0
NE2 C:HIS264 4.5 22.6 1.0
CD2 C:HIS264 4.6 26.3 1.0
CB C:GLU174 4.6 20.6 1.0
CG C:ASP144 4.7 26.6 1.0

Zinc binding site 5 out of 14 in 5gk5

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Zinc binding site 5 out of 14 in the Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn404

b:33.6
occ:0.51
 O C:HOH1308 2.1 31.3 1.0
NE2 C:HIS110 2.2 29.0 1.0
O C:HOH1227 2.4 29.8 1.0
O C:HOH1322 2.5 38.9 1.0
CD2 C:HIS110 3.1 23.9 1.0
CD2 C:HIS226 3.1 32.0 1.0
CE1 C:HIS110 3.3 23.1 1.0
NE2 C:HIS226 3.4 32.7 1.0
CB C:HIS264 3.5 24.5 1.0
ND1 C:HIS264 3.5 32.8 1.0
CG C:HIS264 3.5 26.0 1.0
ZN C:ZN403 4.0 27.7 0.6
CG C:HIS226 4.2 34.0 1.0
CG C:HIS110 4.3 23.9 1.0
CE1 C:HIS264 4.3 31.9 1.0
ND2 C:ASN286 4.3 22.6 1.0
ND1 C:HIS110 4.3 24.6 1.0
CA C:HIS264 4.3 25.8 1.0
CD2 C:HIS264 4.3 26.3 1.0
OD2 C:ASP109 4.4 20.1 1.0
N C:GLY265 4.5 28.9 1.0
CE1 C:HIS226 4.5 30.3 1.0
OD1 C:ASP109 4.6 23.0 1.0
NE2 C:HIS264 4.7 22.6 1.0
C C:HIS264 4.9 26.8 1.0
ND1 C:HIS226 4.9 36.0 1.0
CG C:ASP109 4.9 25.3 1.0
CB C:ASN286 5.0 21.5 1.0
CB C:HIS226 5.0 37.1 1.0

Zinc binding site 6 out of 14 in 5gk5

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Zinc binding site 6 out of 14 in the Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn403

b:26.1
occ:0.68
 OE1 D:GLU174 2.1 23.6 1.0
CE1 D:HIS110 2.1 23.0 1.0
NE2 D:HIS226 2.2 30.5 1.0
OE2 D:GLU174 2.2 26.2 1.0
ND1 D:HIS264 2.4 30.9 1.0
CD D:GLU174 2.5 22.5 1.0
O D:HOH572 2.5 29.8 1.0
NE2 D:HIS110 3.0 24.6 1.0
CE1 D:HIS226 3.1 32.4 1.0
ND1 D:HIS110 3.2 21.8 1.0
CE1 D:HIS264 3.2 23.5 1.0
CD2 D:HIS226 3.3 36.1 1.0
CG D:HIS264 3.5 24.0 1.0
ZN D:ZN404 3.7 35.2 0.5
CB D:HIS264 3.9 20.0 1.0
CG D:GLU174 4.0 21.9 1.0
OD2 D:ASP144 4.2 21.9 1.0
CD2 D:HIS110 4.2 17.6 1.0
ND1 D:HIS226 4.3 40.1 1.0
O D:HOH555 4.3 27.2 1.0
CG D:HIS110 4.3 22.4 1.0
CG D:HIS226 4.4 41.7 1.0
NE2 D:HIS264 4.4 19.5 1.0
CD2 D:HIS264 4.6 18.9 1.0
CB D:GLU174 4.7 17.8 1.0
CG D:ASP144 4.7 22.6 1.0
CE D:MET142 5.0 36.0 1.0

Zinc binding site 7 out of 14 in 5gk5

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Zinc binding site 7 out of 14 in the Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn404

b:35.2
occ:0.45
 NE2 D:HIS110 2.0 24.6 1.0
O D:HOH636 2.3 28.6 1.0
O D:HOH556 2.4 26.9 1.0
O D:HOH644 2.5 34.5 1.0
CD2 D:HIS110 2.9 17.6 1.0
CE1 D:HIS110 3.0 23.0 1.0
CD2 D:HIS226 3.3 36.1 1.0
ND1 D:HIS264 3.3 30.9 1.0
CG D:HIS264 3.4 24.0 1.0
CB D:HIS264 3.5 20.0 1.0
NE2 D:HIS226 3.6 30.5 1.0
ZN D:ZN403 3.7 26.1 0.7
CE1 D:HIS264 4.0 23.5 1.0
CG D:HIS110 4.1 22.4 1.0
ND1 D:HIS110 4.1 21.8 1.0
ND2 D:ASN286 4.2 17.1 1.0
CD2 D:HIS264 4.2 18.9 1.0
CG D:HIS226 4.3 41.7 1.0
CA D:HIS264 4.4 22.3 1.0
NE2 D:HIS264 4.5 19.5 1.0
OD2 D:ASP109 4.5 23.4 1.0
OD1 D:ASP109 4.5 20.8 1.0
CE1 D:HIS226 4.6 32.4 1.0
N D:GLY265 4.7 29.7 1.0
CG D:ASP109 4.9 21.9 1.0
ND1 D:HIS226 5.0 40.1 1.0

Zinc binding site 8 out of 14 in 5gk5

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Zinc binding site 8 out of 14 in the Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn403

b:26.8
occ:0.68
 OE1 E:GLU174 2.1 26.7 1.0
CE1 E:HIS110 2.2 25.3 1.0
OE2 E:GLU174 2.3 30.8 1.0
NE2 E:HIS226 2.3 34.0 1.0
ND1 E:HIS264 2.4 29.1 1.0
O E:HOH559 2.4 28.0 1.0
CD E:GLU174 2.5 28.1 1.0
NE2 E:HIS110 3.0 26.5 1.0
CE1 E:HIS264 3.2 26.9 1.0
CD2 E:HIS226 3.2 35.1 1.0
ND1 E:HIS110 3.3 27.4 1.0
CE1 E:HIS226 3.3 32.4 1.0
CG E:HIS264 3.5 29.1 1.0
ZN E:ZN404 3.8 33.9 0.5
CB E:HIS264 3.9 26.8 1.0
CG E:GLU174 4.0 26.8 1.0
OD2 E:ASP144 4.1 25.9 1.0
CD2 E:HIS110 4.2 22.8 1.0
O E:HOH539 4.2 31.9 1.0
CE E:MET142 4.3 39.0 1.0
CG E:HIS110 4.4 26.1 1.0
NE2 E:HIS264 4.4 22.1 1.0
ND1 E:HIS226 4.4 39.4 1.0
CG E:HIS226 4.4 40.2 1.0
CD2 E:HIS264 4.6 25.7 1.0
CG E:ASP144 4.7 26.9 1.0
CB E:GLU174 4.7 23.5 1.0

Zinc binding site 9 out of 14 in 5gk5

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Zinc binding site 9 out of 14 in the Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn404

b:33.9
occ:0.48
 NE2 E:HIS110 2.1 26.5 1.0
O E:HOH619 2.1 27.9 1.0
O E:HOH535 2.3 28.8 1.0
O E:HOH626 2.7 40.1 1.0
CD2 E:HIS110 3.0 22.8 1.0
CE1 E:HIS110 3.2 25.3 1.0
CD2 E:HIS226 3.2 35.1 1.0
ND1 E:HIS264 3.3 29.1 1.0
CG E:HIS264 3.3 29.1 1.0
CB E:HIS264 3.4 26.8 1.0
NE2 E:HIS226 3.7 34.0 1.0
ZN E:ZN403 3.8 26.8 0.7
CE1 E:HIS264 4.1 26.9 1.0
CD2 E:HIS264 4.1 25.7 1.0
CG E:HIS110 4.2 26.1 1.0
CG E:HIS226 4.2 40.2 1.0
ND2 E:ASN286 4.2 21.3 1.0
ND1 E:HIS110 4.2 27.4 1.0
CA E:HIS264 4.3 25.1 1.0
OD2 E:ASP109 4.5 21.2 1.0
NE2 E:HIS264 4.5 22.1 1.0
OD1 E:ASP109 4.5 22.4 1.0
N E:GLY265 4.6 28.8 1.0
CE1 E:HIS226 4.7 32.4 1.0
CB E:HIS226 4.9 40.8 1.0
C E:HIS264 4.9 25.6 1.0
ND1 E:HIS226 4.9 39.4 1.0
CG E:ASP109 4.9 23.2 1.0

Zinc binding site 10 out of 14 in 5gk5

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Zinc binding site 10 out of 14 in the Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Apo Structure of Fructose 1,6-Bisphosphate Aldolase From Escherichia Coli at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:22.4
occ:0.75
 NE2 F:HIS226 2.1 22.8 1.0
CE1 F:HIS110 2.2 15.0 1.0
OE1 F:GLU174 2.2 18.8 1.0
O F:HOH573 2.3 21.7 1.0
OE2 F:GLU174 2.4 18.1 1.0
ND1 F:HIS264 2.4 23.4 1.0
CD F:GLU174 2.6 21.6 1.0
CD2 F:HIS226 3.0 27.3 1.0
CE1 F:HIS226 3.1 24.3 1.0
NE2 F:HIS110 3.1 25.0 1.0
ND1 F:HIS110 3.2 25.0 1.0
CE1 F:HIS264 3.2 22.8 1.0
CG F:HIS264 3.5 22.6 1.0
O F:HOH501 3.7 25.6 1.0
CB F:HIS264 3.9 20.8 1.0
CG F:GLU174 4.1 15.6 1.0
ND1 F:HIS226 4.2 29.7 1.0
CG F:HIS226 4.2 29.6 1.0
OD2 F:ASP144 4.2 22.2 1.0
CD2 F:HIS110 4.3 14.9 1.0
CG F:HIS110 4.3 19.1 1.0
NE2 F:HIS264 4.4 17.2 1.0
CD2 F:HIS264 4.6 16.2 1.0
CG F:ASP144 4.7 19.3 1.0
CB F:GLU174 4.8 17.1 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 1.9 Angstrom Resolution To Be Published.
Page generated: Wed Dec 16 06:19:27 2020

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