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Magnesium in PDB 7cvh: Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate

Enzymatic activity of Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate

All present enzymatic activity of Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate:
3.1.3.11;

Protein crystallography data

The structure of Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate, PDB code: 7cvh was solved by Y.Chen, J.Zhang, C.Li, Y.Cao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.25 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.392, 83.426, 277.355, 90, 90, 90
R / Rfree (%) 17.8 / 21.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate (pdb code 7cvh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate, PDB code: 7cvh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7cvh

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Magnesium binding site 1 out of 8 in the Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:11.3
occ:1.00
 OD2 A:ASP119 2.1 20.1 1.0
OE2 A:GLU281 2.1 19.1 1.0
OD1 A:ASP122 2.2 17.1 1.0
O1 A:FBP401 2.4 19.8 1.0
O2P A:FBP401 2.6 22.9 1.0
P1 A:FBP401 3.0 17.6 1.0
CG A:ASP122 3.2 13.3 1.0
CD A:GLU281 3.2 14.8 1.0
CG A:ASP119 3.4 12.0 1.0
CB A:ASP122 3.5 11.8 1.0
C1 A:FBP401 3.5 15.0 1.0
CA A:ASP122 3.7 13.1 1.0
CG A:GLU281 3.7 11.3 1.0
MG A:MG403 3.8 6.1 1.0
NH2 A:ARG277 3.8 19.7 1.0
O3P A:FBP401 4.0 19.2 1.0
O3 A:FBP401 4.1 12.0 1.0
O1P A:FBP401 4.2 21.2 1.0
OD1 A:ASP119 4.2 14.9 1.0
CB A:ASP119 4.3 10.9 1.0
OD2 A:ASP122 4.3 16.6 1.0
OE1 A:GLU281 4.3 16.0 1.0
N A:GLY123 4.3 13.7 1.0
C3 A:FBP401 4.5 11.7 1.0
C2 A:FBP401 4.6 14.8 1.0
C A:ASP122 4.6 11.4 1.0
N A:ASP122 4.7 11.6 1.0
OE1 A:GLU98 4.7 27.1 1.0
CD1 A:ILE136 4.8 11.2 1.0
O A:LEU121 4.9 12.3 1.0

Magnesium binding site 2 out of 8 in 7cvh

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Magnesium binding site 2 out of 8 in the Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:6.1
occ:1.00
 O2P A:FBP401 2.1 22.9 1.0
OE1 A:GLU98 2.3 27.1 1.0
O A:HOH662 2.3 20.6 1.0
OD1 A:ASP119 2.4 14.9 1.0
O A:LEU121 2.5 12.3 1.0
OD2 A:ASP119 2.8 20.1 1.0
CG A:ASP119 2.9 12.0 1.0
C A:LEU121 3.4 9.4 1.0
CD A:GLU98 3.4 25.6 1.0
P1 A:FBP401 3.6 17.6 1.0
MG A:MG402 3.8 11.3 1.0
CA A:ASP122 4.0 13.1 1.0
O3P A:FBP401 4.0 19.2 1.0
N A:ASP122 4.1 11.6 1.0
CG A:GLU98 4.3 21.1 1.0
OE2 A:GLU98 4.3 30.6 1.0
O1P A:FBP401 4.3 21.2 1.0
N A:LEU121 4.4 8.9 1.0
CB A:ASP119 4.4 10.9 1.0
CA A:LEU121 4.4 10.6 1.0
CB A:GLU98 4.5 11.0 1.0
OD1 A:ASP75 4.5 45.0 1.0
O1 A:FBP401 4.6 19.8 1.0
OE2 A:GLU99 4.6 35.1 1.0
O A:HOH563 4.9 32.4 1.0
O A:HOH502 4.9 26.3 1.0
C A:ASP122 4.9 11.4 1.0
CB A:LEU121 5.0 11.7 1.0
N A:GLY123 5.0 13.7 1.0
CB A:ASP122 5.0 11.8 1.0

Magnesium binding site 3 out of 8 in 7cvh

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Magnesium binding site 3 out of 8 in the Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:15.1
occ:1.00
 OE2 C:GLU281 2.0 32.8 1.0
OD2 C:ASP119 2.1 24.3 1.0
OD1 C:ASP122 2.1 20.5 1.0
O1 C:FBP401 2.5 33.9 1.0
O2P C:FBP401 2.6 34.8 1.0
P1 C:FBP401 3.0 33.8 1.0
CG C:ASP122 3.1 22.0 1.0
CD C:GLU281 3.2 18.9 1.0
OE2 C:GLU98 3.2 46.4 1.0
CG C:ASP119 3.3 15.8 1.0
MG C:MG403 3.5 18.2 1.0
CB C:ASP122 3.6 16.8 1.0
C1 C:FBP401 3.7 21.3 1.0
CA C:ASP122 3.7 17.8 1.0
O1P C:FBP401 3.8 41.8 1.0
CG C:GLU281 4.0 16.2 1.0
OD1 C:ASP119 4.1 19.0 1.0
OE1 C:GLU281 4.1 15.9 1.0
CD C:GLU98 4.1 36.3 1.0
N C:GLY123 4.2 18.9 1.0
OD2 C:ASP122 4.3 24.2 1.0
O3 C:FBP401 4.3 16.8 1.0
CB C:ASP119 4.3 13.9 1.0
O3P C:FBP401 4.3 26.9 1.0
C C:ASP122 4.5 20.9 1.0
C3 C:FBP401 4.6 17.9 1.0
OE1 C:GLU98 4.6 44.8 1.0
C2 C:FBP401 4.7 25.0 1.0
N C:ASP122 4.8 16.2 1.0
O C:LEU121 5.0 15.4 1.0

Magnesium binding site 4 out of 8 in 7cvh

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Magnesium binding site 4 out of 8 in the Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:18.2
occ:1.00
 O2P C:FBP401 2.1 34.8 1.0
OD1 C:ASP119 2.5 19.0 1.0
O C:LEU121 2.5 15.4 1.0
O C:HOH515 2.5 24.7 1.0
O C:HOH633 2.6 32.5 1.0
OE1 C:GLU98 2.8 44.8 1.0
OD2 C:ASP119 2.9 24.3 1.0
CG C:ASP119 3.1 15.8 1.0
C C:LEU121 3.4 18.6 1.0
CD C:GLU98 3.4 36.3 1.0
OE2 C:GLU98 3.5 46.4 1.0
P1 C:FBP401 3.5 33.8 1.0
MG C:MG402 3.5 15.1 1.0
OG C:SER124 3.7 31.3 1.0
CA C:ASP122 3.7 17.8 1.0
O1P C:FBP401 3.8 41.8 1.0
N C:ASP122 3.9 16.2 1.0
O3P C:FBP401 4.4 26.9 1.0
N C:LEU121 4.4 15.3 1.0
CA C:LEU121 4.5 15.5 1.0
OE2 C:GLU99 4.5 41.6 1.0
O1 C:FBP401 4.5 33.9 1.0
CB C:ASP119 4.6 13.9 1.0
N C:GLY123 4.6 18.9 1.0
C C:ASP122 4.6 20.9 1.0
CG C:GLU98 4.6 26.5 1.0
OD1 C:ASP75 4.7 36.5 1.0
CB C:GLU98 4.7 18.3 1.0
CB C:ASP122 4.7 16.8 1.0
OD1 C:ASP122 4.8 20.5 1.0
N C:SER124 5.0 26.7 1.0
CB C:SER124 5.0 27.2 1.0

Magnesium binding site 5 out of 8 in 7cvh

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Magnesium binding site 5 out of 8 in the Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:14.0
occ:1.00
 OE2 B:GLU281 2.0 28.9 1.0
OD2 B:ASP119 2.1 25.1 1.0
OD1 B:ASP122 2.1 17.3 1.0
O1 B:FBP401 2.4 24.1 1.0
O1P B:FBP401 2.5 24.2 1.0
P1 B:FBP401 3.0 25.1 1.0
OE2 B:GLU98 3.0 38.2 1.0
CG B:ASP122 3.1 19.8 1.0
CD B:GLU281 3.2 19.1 1.0
CG B:ASP119 3.3 18.1 1.0
CB B:ASP122 3.5 17.2 1.0
C1 B:FBP401 3.6 19.6 1.0
CA B:ASP122 3.6 15.2 1.0
MG B:MG403 3.8 14.5 1.0
O3P B:FBP401 3.9 29.6 1.0
CG B:GLU281 3.9 17.8 1.0
OD1 B:ASP119 4.1 21.4 1.0
OE1 B:GLU281 4.1 16.9 1.0
O2P B:FBP401 4.1 25.4 1.0
CD B:GLU98 4.2 31.1 1.0
OD2 B:ASP122 4.3 19.1 1.0
CB B:ASP119 4.3 17.2 1.0
N B:GLY123 4.3 20.2 1.0
O3 B:FBP401 4.3 15.3 1.0
C B:ASP122 4.5 16.9 1.0
C2 B:FBP401 4.6 21.0 1.0
C3 B:FBP401 4.6 19.0 1.0
N B:ASP122 4.7 15.5 1.0
OE1 B:GLU98 4.8 37.9 1.0
O B:LEU121 4.9 16.1 1.0
CD1 B:ILE136 4.9 15.8 1.0

Magnesium binding site 6 out of 8 in 7cvh

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Magnesium binding site 6 out of 8 in the Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:14.5
occ:1.00
 O1P B:FBP401 2.3 24.2 1.0
O B:LEU121 2.4 16.1 1.0
O B:HOH513 2.4 28.9 1.0
OD1 B:ASP119 2.5 21.4 1.0
OE1 B:GLU98 2.7 37.9 1.0
OD2 B:ASP119 3.0 25.1 1.0
OE2 B:GLU98 3.1 38.2 1.0
CG B:ASP119 3.1 18.1 1.0
CD B:GLU98 3.1 31.1 1.0
C B:LEU121 3.3 14.8 1.0
O B:HOH598 3.6 32.2 1.0
P1 B:FBP401 3.7 25.1 1.0
MG B:MG402 3.8 14.0 1.0
CA B:ASP122 3.9 15.2 1.0
N B:ASP122 3.9 15.5 1.0
O3P B:FBP401 4.1 29.6 1.0
N B:LEU121 4.3 15.3 1.0
CA B:LEU121 4.4 15.8 1.0
CG B:GLU98 4.4 26.1 1.0
OE2 B:GLU99 4.4 36.2 1.0
O2P B:FBP401 4.5 25.4 1.0
OD1 B:ASP75 4.5 42.4 1.0
CB B:GLU98 4.6 24.5 1.0
CB B:ASP119 4.6 17.2 1.0
C B:ASP122 4.7 16.9 1.0
O B:HOH701 4.8 43.3 1.0
O1 B:FBP401 4.8 24.1 1.0
N B:GLY123 4.8 20.2 1.0
CB B:ASP122 4.9 17.2 1.0
CB B:LEU121 4.9 13.9 1.0

Magnesium binding site 7 out of 8 in 7cvh

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Magnesium binding site 7 out of 8 in the Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:18.3
occ:1.00
 OE2 D:GLU281 2.0 25.0 1.0
OD2 D:ASP119 2.1 24.8 1.0
OD1 D:ASP122 2.1 17.5 1.0
O2P D:FBP602 2.4 28.8 1.0
O1 D:FBP602 2.4 26.6 1.0
P1 D:FBP602 2.9 29.1 1.0
CG D:ASP122 3.1 20.5 1.0
CD D:GLU281 3.2 18.3 1.0
CG D:ASP119 3.3 19.9 1.0
CB D:ASP122 3.4 18.1 1.0
CA D:ASP122 3.6 18.8 1.0
C1 D:FBP602 3.7 23.9 1.0
MG D:MG604 3.7 21.0 1.0
CG D:GLU281 3.8 16.6 1.0
O3P D:FBP602 3.9 31.6 1.0
OD1 D:ASP119 3.9 17.1 1.0
OE1 D:GLU98 4.0 36.8 1.0
OE2 D:GLU98 4.1 49.0 1.0
O1P D:FBP602 4.1 27.7 1.0
N D:GLY123 4.2 16.6 1.0
OE1 D:GLU281 4.2 19.9 1.0
OD2 D:ASP122 4.2 23.8 1.0
CB D:ASP119 4.3 18.7 1.0
O3 D:FBP602 4.3 16.2 1.0
CD D:GLU98 4.4 33.0 1.0
C D:ASP122 4.4 18.9 1.0
C3 D:FBP602 4.6 16.0 1.0
N D:ASP122 4.6 14.9 1.0
C2 D:FBP602 4.7 22.6 1.0
CD1 D:ILE136 4.9 14.2 1.0
O D:LEU121 4.9 18.2 1.0

Magnesium binding site 8 out of 8 in 7cvh

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Magnesium binding site 8 out of 8 in the Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human Fructose-1,6-Bisphosphatase 1 in Complex with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg604

b:21.0
occ:1.00
 O2P D:FBP602 2.2 28.8 1.0
OE1 D:GLU98 2.3 36.8 1.0
OD1 D:ASP119 2.4 17.1 1.0
O D:LEU121 2.5 18.2 1.0
O D:HOH711 2.7 38.0 1.0
CG D:ASP119 3.2 19.9 1.0
OD2 D:ASP119 3.2 24.8 1.0
C D:LEU121 3.4 18.8 1.0
CD D:GLU98 3.4 33.0 1.0
P1 D:FBP602 3.6 29.1 1.0
MG D:MG603 3.7 18.3 1.0
CA D:ASP122 3.9 18.8 1.0
OE2 D:GLU98 4.0 49.0 1.0
N D:ASP122 4.0 14.9 1.0
O3P D:FBP602 4.1 31.6 1.0
O1P D:FBP602 4.2 27.7 1.0
N D:LEU121 4.4 13.1 1.0
CA D:LEU121 4.5 15.1 1.0
CB D:ASP119 4.6 18.7 1.0
CG D:GLU98 4.6 32.3 1.0
OE2 D:GLU99 4.6 52.5 1.0
O1 D:FBP602 4.7 26.6 1.0
CB D:GLU98 4.7 24.5 1.0
C D:ASP122 4.8 18.9 1.0
N D:GLY123 4.8 16.6 1.0
CB D:ASP122 4.8 18.1 1.0

Reference:

Y.Chen, J.Zhang, C.Li, Y.Cao. The Structural Basis For Ggpp Activation on the Enzymatic Activities FBP1 To Be Published.
Page generated: Wed Oct 2 14:39:59 2024

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