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Zinc in PDB 1fj9: Fructose-1,6-Bisphosphatase (Mutant Y57W) Products/Zn/Amp Complex (T- State)

Enzymatic activity of Fructose-1,6-Bisphosphatase (Mutant Y57W) Products/Zn/Amp Complex (T- State)

All present enzymatic activity of Fructose-1,6-Bisphosphatase (Mutant Y57W) Products/Zn/Amp Complex (T- State):
3.1.3.11;

Protein crystallography data

The structure of Fructose-1,6-Bisphosphatase (Mutant Y57W) Products/Zn/Amp Complex (T- State), PDB code: 1fj9 was solved by C.V.Iancu, J.Y.Choe, R.B.Honzatko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 5.00 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 59.820, 165.480, 79.290, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Fructose-1,6-Bisphosphatase (Mutant Y57W) Products/Zn/Amp Complex (T- State) (pdb code 1fj9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Fructose-1,6-Bisphosphatase (Mutant Y57W) Products/Zn/Amp Complex (T- State), PDB code: 1fj9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1fj9

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Zinc binding site 1 out of 4 in the Fructose-1,6-Bisphosphatase (Mutant Y57W) Products/Zn/Amp Complex (T- State)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Fructose-1,6-Bisphosphatase (Mutant Y57W) Products/Zn/Amp Complex (T- State) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:16.6
occ:1.00
OD2 A:ASP118 1.9 11.1 1.0
O3 A:PO4402 2.0 23.7 1.0
OE2 A:GLU280 2.2 9.3 1.0
OD2 A:ASP121 2.3 11.7 1.0
O1 A:F6P400 2.8 20.4 1.0
CG A:ASP118 2.9 8.9 1.0
CG A:ASP121 3.1 10.2 1.0
P A:PO4402 3.2 22.3 1.0
CB A:ASP121 3.3 10.0 1.0
CD A:GLU280 3.3 16.2 1.0
OD1 A:ASP118 3.3 9.2 1.0
CA A:ASP121 3.4 7.9 1.0
O4 A:PO4402 3.5 22.6 1.0
OE1 A:GLU97 3.7 20.5 1.0
O2 A:PO4402 3.7 25.3 1.0
CG A:GLU280 3.7 16.1 1.0
ZN A:ZN404 3.8 58.1 1.0
C1 A:F6P400 4.2 15.5 1.0
CB A:ASP118 4.2 10.2 1.0
O3 A:F6P400 4.2 9.2 1.0
OD1 A:ASP121 4.3 10.1 1.0
N A:GLY122 4.3 5.2 1.0
OE1 A:GLU280 4.3 17.6 1.0
O1 A:PO4402 4.3 27.1 1.0
C A:ASP121 4.4 8.2 1.0
N A:ASP121 4.4 9.9 1.0
CD1 A:ILE135 4.7 5.0 1.0
CD A:GLU97 4.7 21.2 1.0
C3 A:F6P400 4.8 12.6 1.0
O A:LEU120 4.8 10.2 1.0
C2 A:F6P400 4.9 13.9 1.0
C A:LEU120 5.0 9.7 1.0

Zinc binding site 2 out of 4 in 1fj9

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Zinc binding site 2 out of 4 in the Fructose-1,6-Bisphosphatase (Mutant Y57W) Products/Zn/Amp Complex (T- State)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Fructose-1,6-Bisphosphatase (Mutant Y57W) Products/Zn/Amp Complex (T- State) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:58.1
occ:1.00
OD1 A:ASP118 2.4 9.2 1.0
O3 A:PO4402 2.5 23.7 1.0
O A:LEU120 2.6 10.2 1.0
OE1 A:GLU97 2.6 20.5 1.0
O1 A:PO4402 3.0 27.1 1.0
P A:PO4402 3.3 22.3 1.0
C A:LEU120 3.3 9.7 1.0
CD A:GLU97 3.3 21.2 1.0
CG A:ASP118 3.4 8.9 1.0
OE2 A:GLU97 3.6 22.4 1.0
OD2 A:ASP118 3.7 11.1 1.0
ZN A:ZN403 3.8 16.6 1.0
N A:ASP121 3.9 9.9 1.0
CA A:ASP121 4.0 7.9 1.0
N A:LEU120 4.0 8.7 1.0
CA A:LEU120 4.2 7.7 1.0
O4 A:PO4402 4.3 22.6 1.0
O2 A:PO4402 4.3 25.3 1.0
OE2 A:GLU98 4.3 27.5 1.0
CG A:GLU97 4.5 20.4 1.0
CB A:GLU97 4.6 19.0 1.0
CB A:ASP118 4.6 10.2 1.0
CD A:PRO119 4.7 7.7 1.0
CA A:ASP118 4.8 9.2 1.0
CB A:LEU120 4.8 8.3 1.0
N A:PRO119 4.9 9.1 1.0
C A:ASP118 4.9 10.5 1.0
CG A:PRO119 4.9 8.1 1.0
CB A:ASP121 4.9 10.0 1.0
C A:ASP121 4.9 8.2 1.0

Zinc binding site 3 out of 4 in 1fj9

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Zinc binding site 3 out of 4 in the Fructose-1,6-Bisphosphatase (Mutant Y57W) Products/Zn/Amp Complex (T- State)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Fructose-1,6-Bisphosphatase (Mutant Y57W) Products/Zn/Amp Complex (T- State) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn413

b:10.5
occ:1.00
O1 B:PO4412 1.9 19.5 1.0
OD2 B:ASP118 1.9 14.2 1.0
OD2 B:ASP121 1.9 8.2 1.0
OE1 B:GLU280 2.0 5.0 1.0
CG B:ASP121 2.9 7.2 1.0
CG B:ASP118 2.9 11.7 1.0
CD B:GLU280 3.0 6.1 1.0
P B:PO4412 3.2 20.5 1.0
CB B:ASP121 3.2 7.3 1.0
OD1 B:ASP118 3.4 11.5 1.0
CG B:GLU280 3.4 6.3 1.0
OE1 B:GLU97 3.5 28.5 1.0
O3 B:PO4412 3.5 21.0 1.0
ZN B:ZN414 3.6 48.9 1.0
CA B:ASP121 3.6 7.7 1.0
C1 B:F6P410 3.9 15.6 1.0
O4 B:PO4412 4.0 21.6 1.0
OD1 B:ASP121 4.0 9.8 1.0
OE2 B:GLU280 4.1 6.7 1.0
O2 B:PO4412 4.2 22.6 1.0
CB B:ASP118 4.2 10.8 1.0
N B:GLY122 4.4 7.4 1.0
NH2 B:ARG276 4.4 27.0 1.0
C B:ASP121 4.5 8.4 1.0
O3 B:F6P410 4.5 8.8 1.0
CD B:GLU97 4.6 24.7 1.0
N B:ASP121 4.6 8.6 1.0
CD1 B:ILE135 4.7 7.9 1.0
O1 B:F6P410 4.8 20.0 1.0
OE2 B:GLU97 4.9 25.0 1.0
C2 B:F6P410 4.9 13.9 1.0
CB B:GLU280 4.9 7.3 1.0
C3 B:F6P410 5.0 12.5 1.0

Zinc binding site 4 out of 4 in 1fj9

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Zinc binding site 4 out of 4 in the Fructose-1,6-Bisphosphatase (Mutant Y57W) Products/Zn/Amp Complex (T- State)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Fructose-1,6-Bisphosphatase (Mutant Y57W) Products/Zn/Amp Complex (T- State) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn414

b:48.9
occ:1.00
OD1 B:ASP118 2.3 11.5 1.0
O1 B:PO4412 2.7 19.5 1.0
O2 B:PO4412 2.7 22.6 1.0
OE1 B:GLU97 2.7 28.5 1.0
O B:HOH669 2.7 26.5 1.0
O B:LEU120 2.8 11.3 1.0
P B:PO4412 3.2 20.5 1.0
CG B:ASP118 3.3 11.7 1.0
CD B:GLU97 3.3 24.7 1.0
C B:LEU120 3.4 9.0 1.0
OE2 B:GLU97 3.4 25.0 1.0
ZN B:ZN413 3.6 10.5 1.0
OD2 B:ASP118 3.6 14.2 1.0
CA B:ASP121 3.7 7.7 1.0
N B:ASP121 3.8 8.6 1.0
O3 B:PO4412 4.0 21.0 1.0
N B:LEU120 4.1 7.2 1.0
CA B:LEU120 4.3 9.3 1.0
O4 B:PO4412 4.5 21.6 1.0
CG B:GLU97 4.5 23.8 1.0
CB B:ASP121 4.5 7.3 1.0
CB B:ASP118 4.6 10.8 1.0
CB B:GLU97 4.6 19.8 1.0
OE1 B:GLU98 4.7 29.7 1.0
OD2 B:ASP121 4.8 8.2 1.0
C B:ASP118 4.8 9.6 1.0
C B:ASP121 4.8 8.4 1.0
CA B:ASP118 4.8 9.9 1.0
N B:GLY122 4.8 7.4 1.0
OE1 B:GLU280 5.0 5.0 1.0

Reference:

S.W.Nelson, C.V.Iancu, J.Y.Choe, R.B.Honzatko, H.J.Fromm. Tryptophan Fluorescence Reveals the Conformational State of A Dynamic Loop in Recombinant Porcine Fructose-1,6-Bisphosphatase. Biochemistry V. 39 11100 2000.
ISSN: ISSN 0006-2960
PubMed: 10998248
DOI: 10.1021/BI000609C
Page generated: Wed Dec 16 02:49:13 2020

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