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Magnesium in PDB 4kxp: Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant I10D in T-State

Enzymatic activity of Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant I10D in T-State

All present enzymatic activity of Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant I10D in T-State:
3.1.3.11;

Protein crystallography data

The structure of Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant I10D in T-State, PDB code: 4kxp was solved by C.V.Iancu, S.Mukund, J.-Y.Choe, H.J.Fromm, R.B.Honzatko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.66 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 59.544, 166.382, 78.946, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 25.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant I10D in T-State (pdb code 4kxp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant I10D in T-State, PDB code: 4kxp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4kxp

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Magnesium binding site 1 out of 4 in the Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant I10D in T-State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant I10D in T-State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:2.0
occ:1.00
 OD2 A:ASP121 1.8 19.1 1.0
OD2 A:ASP118 1.8 19.9 1.0
OE2 A:GLU280 1.8 23.3 1.0
O2 A:PO4402 1.9 30.2 1.0
CG A:ASP121 2.8 22.0 1.0
CG A:ASP118 2.9 22.4 1.0
CD A:GLU280 3.0 21.4 1.0
O1 A:PO4402 3.0 27.6 1.0
P A:PO4402 3.0 29.7 1.0
CB A:ASP121 3.3 21.2 1.0
OD1 A:ASP118 3.3 23.7 1.0
CG A:GLU280 3.5 23.6 1.0
CA A:ASP121 3.6 21.4 1.0
O3 A:PO4402 3.7 22.5 1.0
NH2 A:ARG276 3.8 37.8 1.0
OD1 A:ASP121 3.9 24.2 1.0
OE1 A:GLU280 4.0 22.8 1.0
O3 A:F6P401 4.1 12.6 1.0
CB A:ASP118 4.2 22.0 1.0
O4 A:PO4402 4.2 29.8 1.0
OE2 A:GLU97 4.3 21.4 1.0
C1 A:F6P401 4.5 17.5 1.0
N A:GLY122 4.5 21.4 1.0
MG A:MG404 4.6 61.4 1.0
C A:ASP121 4.6 21.5 1.0
O1 A:F6P401 4.6 19.3 1.0
N A:ASP121 4.7 20.3 1.0
CD1 A:ILE135 4.7 17.8 1.0
C3 A:F6P401 4.9 15.8 1.0
CZ A:ARG276 4.9 37.4 1.0
O A:LEU120 4.9 20.0 1.0
CE A:MET248 4.9 16.1 1.0
CB A:GLU280 5.0 23.9 1.0
CD A:GLU97 5.0 23.8 1.0

Magnesium binding site 2 out of 4 in 4kxp

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Magnesium binding site 2 out of 4 in the Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant I10D in T-State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant I10D in T-State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:61.4
occ:1.00
 OD1 A:ASP118 2.3 23.7 1.0
OE2 A:GLU97 2.4 21.4 1.0
O A:LEU120 2.6 20.0 1.0
O1 A:PO4402 2.7 27.6 1.0
C A:LEU120 3.2 19.8 1.0
N A:LEU120 3.2 19.9 1.0
CG A:ASP118 3.4 22.4 1.0
CD A:PRO119 3.5 20.7 1.0
CD A:GLU97 3.6 23.8 1.0
CA A:LEU120 3.8 20.1 1.0
N A:PRO119 3.9 21.8 1.0
C A:ASP118 3.9 21.7 1.0
N A:ASP121 4.0 20.3 1.0
OE2 A:GLU98 4.0 35.5 1.0
OD2 A:ASP118 4.1 19.9 1.0
P A:PO4402 4.2 29.7 1.0
C A:PRO119 4.3 19.8 1.0
CA A:ASP121 4.3 21.4 1.0
O A:ASP118 4.3 20.5 1.0
CA A:ASP118 4.3 21.7 1.0
CB A:LEU120 4.4 20.1 1.0
CB A:GLU97 4.4 25.0 1.0
CG A:PRO119 4.4 21.1 1.0
CA A:PRO119 4.5 20.6 1.0
CB A:ASP118 4.5 22.0 1.0
OE1 A:GLU97 4.5 24.9 1.0
CB A:PRO119 4.5 20.1 1.0
CG A:GLU97 4.5 23.8 1.0
MG A:MG403 4.6 2.0 1.0
OD1 A:ASP74 4.6 49.8 1.0
CG A:GLU98 4.8 31.8 1.0
O2 A:PO4402 4.8 30.2 1.0
O4 A:PO4402 4.8 29.8 1.0
CD A:GLU98 4.8 34.3 1.0
O A:HOH512 4.9 35.7 1.0
O3 A:PO4402 5.0 22.5 1.0

Magnesium binding site 3 out of 4 in 4kxp

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Magnesium binding site 3 out of 4 in the Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant I10D in T-State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant I10D in T-State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:2.0
occ:1.00
 OD2 B:ASP118 1.8 23.5 1.0
OD2 B:ASP121 1.9 9.6 1.0
O3 B:PO4402 1.9 29.3 1.0
OE1 B:GLU280 2.0 23.1 1.0
CG B:ASP121 2.6 16.5 1.0
CG B:ASP118 2.8 19.8 1.0
P B:PO4402 3.1 28.6 1.0
CB B:ASP121 3.1 15.2 1.0
CD B:GLU280 3.1 21.9 1.0
OD1 B:ASP118 3.2 24.4 1.0
O4 B:PO4402 3.4 28.0 1.0
CA B:ASP121 3.5 16.0 1.0
OD1 B:ASP121 3.6 17.6 1.0
CG B:GLU280 3.6 18.8 1.0
O2 B:PO4402 3.7 27.5 1.0
CB B:ASP118 4.2 17.6 1.0
OE2 B:GLU280 4.2 22.1 1.0
OE1 B:GLU97 4.3 36.1 1.0
O1 B:PO4402 4.3 33.3 1.0
O3 B:F6P401 4.4 16.4 1.0
C1 B:F6P401 4.4 17.9 1.0
N B:ASP121 4.5 15.8 1.0
N B:GLY122 4.5 17.9 1.0
C B:ASP121 4.5 16.9 1.0
NH1 B:ARG276 4.5 31.0 1.0
O1 B:F6P401 4.6 16.7 1.0
O B:LEU120 4.6 17.6 1.0
O2 B:F6P401 4.8 17.1 1.0
C B:LEU120 4.9 16.8 1.0
C3 B:F6P401 5.0 16.7 1.0
CD B:GLU97 5.0 33.7 1.0
C2 B:F6P401 5.0 16.6 1.0

Magnesium binding site 4 out of 4 in 4kxp

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Magnesium binding site 4 out of 4 in the Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant I10D in T-State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant I10D in T-State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:35.5
occ:1.00
 OD2 B:ASP74 2.6 46.8 1.0
O B:LEU120 2.8 17.6 1.0
OE1 B:GLU97 3.1 36.1 1.0
N B:LEU120 3.1 16.6 1.0
OD1 B:ASP118 3.2 24.4 1.0
CG B:PRO119 3.3 18.5 1.0
O4 B:PO4402 3.4 28.0 1.0
OE1 B:GLU98 3.5 30.3 1.0
C B:LEU120 3.5 16.8 1.0
CD B:PRO119 3.7 17.6 1.0
CA B:LEU120 3.7 17.0 1.0
CG B:ASP74 3.7 43.0 1.0
O B:HOH547 4.0 39.4 1.0
CB B:LEU120 4.0 17.8 1.0
N B:PRO119 4.0 17.0 1.0
CD B:GLU98 4.1 29.5 1.0
CG B:GLU98 4.1 30.4 1.0
C B:PRO119 4.2 17.0 1.0
OD1 B:ASP74 4.2 42.4 1.0
CD B:GLU97 4.2 33.7 1.0
CB B:PRO119 4.2 17.1 1.0
CA B:PRO119 4.4 17.1 1.0
CG B:ASP118 4.4 19.8 1.0
N B:ASP121 4.5 15.8 1.0
C B:ASP118 4.5 18.1 1.0
P B:PO4402 4.8 28.6 1.0
CB B:GLU97 4.9 28.9 1.0
CB B:ASP74 4.9 40.6 1.0
OE2 B:GLU97 4.9 34.4 1.0
CA B:ASP118 4.9 17.6 1.0

Reference:

Y.Gao, C.V.Iancu, S.Mukind, J.Y.Choe, R.B.Honzatko. Mechanism of Displacement of A Catalytically Essential Loop From the Active Site of Mammalian Fructose-1,6-Bisphosphatase. Biochemistry V. 52 5206 2013.
ISSN: ISSN 0006-2960
PubMed: 23844654
DOI: 10.1021/BI400532N
Page generated: Sat Aug 17 04:23:53 2024

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