Atomistry » Magnesium » PDB 7ctv-7d82 » 7cvh
Atomistry »
  Magnesium »
    PDB 7ctv-7d82 »
      7cvh »

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

Go back to Magnesium Binding Sites List in 7cvh
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

Go back to Magnesium Binding Sites List in 7cvh
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

Go back to Magnesium Binding Sites List in 7cvh
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

Go back to Magnesium Binding Sites List in 7cvh
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

Go back to Magnesium Binding Sites List in 7cvh
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

Go back to Magnesium Binding Sites List in 7cvh
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

Go back to Magnesium Binding Sites List in 7cvh
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

Go back to Magnesium Binding Sites List in 7cvh
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy