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Magnesium in PDB 3roj: D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803

Enzymatic activity of D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803

All present enzymatic activity of D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803:
3.1.3.11; 3.1.3.37;

Protein crystallography data

The structure of D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803, PDB code: 3roj was solved by X.Hu, D.Hui, F.Lingling, W.Jian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.54 / 2.30
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 144.282, 144.282, 168.795, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 20.4

Other elements in 3roj:

The structure of D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 also contains other interesting chemical elements:

Chlorine (Cl) 23 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 (pdb code 3roj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803, PDB code: 3roj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3roj

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Magnesium binding site 1 out of 8 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg346

b:52.8
occ:1.00
 OE1 A:GLU100 2.9 33.1 1.0
OE1 A:GLU225 3.0 40.1 1.0
O A:HOH495 3.1 27.4 1.0
CL A:CL361 3.2 55.4 1.0
OD1 A:ASP97 3.4 36.1 1.0
OD2 A:ASP97 3.6 27.9 1.0
CD A:GLU225 3.8 33.5 1.0
CG A:ASP97 3.9 27.3 1.0
CG A:GLU225 3.9 32.5 1.0
CD A:GLU100 4.1 31.1 1.0
O A:HOH577 4.2 34.2 1.0
CA A:GLU100 4.2 24.2 1.0
N A:GLY101 4.3 22.9 1.0
O A:CYS99 4.5 23.9 1.0
C A:GLU100 4.8 23.5 1.0
CB A:GLU100 4.8 25.9 1.0
OE2 A:GLU100 4.8 30.3 1.0
OE2 A:GLU225 4.9 35.0 1.0
O A:HOH812 5.0 42.5 1.0

Magnesium binding site 2 out of 8 in 3roj

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Magnesium binding site 2 out of 8 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg347

b:36.5
occ:1.00
 OD1 A:ASP33 2.7 25.6 1.0
O A:HOH495 2.9 27.4 1.0
OE2 A:GLU57 3.1 29.7 1.0
OE1 A:GLU57 3.4 30.9 1.0
N A:CYS99 3.5 20.4 1.0
CD A:PRO98 3.5 20.5 1.0
CG A:ASP33 3.5 24.7 1.0
O A:HOH563 3.5 40.8 1.0
CD A:GLU57 3.6 28.3 1.0
OD2 A:ASP97 3.6 27.9 1.0
OD2 A:ASP33 3.7 30.5 1.0
O A:CYS99 3.9 23.9 1.0
N A:PRO98 3.9 22.0 1.0
CA A:CYS99 4.2 20.7 1.0
C A:CYS99 4.2 22.1 1.0
CG A:PRO98 4.3 19.9 1.0
CB A:CYS99 4.3 19.0 1.0
CB A:PRO98 4.3 19.6 1.0
C A:ASP97 4.4 21.8 1.0
CG2 A:VAL37 4.4 19.7 1.0
C A:PRO98 4.5 20.0 1.0
CA A:PRO98 4.5 19.4 1.0
CA A:ASP97 4.6 22.3 1.0
CG A:ASP97 4.8 27.3 1.0
CB A:ASP33 4.9 22.6 1.0
CG2 A:THR102 5.0 22.2 1.0

Magnesium binding site 3 out of 8 in 3roj

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Magnesium binding site 3 out of 8 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg346

b:48.5
occ:1.00
 OE1 B:GLU225 2.8 31.5 1.0
OD1 B:ASP97 2.9 27.9 1.0
OE1 B:GLU100 3.0 32.7 1.0
O B:HOH409 3.6 29.2 1.0
OD2 B:ASP97 3.7 22.9 1.0
CG B:ASP97 3.7 24.2 1.0
CD B:GLU225 3.7 33.5 1.0
CG B:GLU225 3.8 31.5 1.0
CL B:CL354 3.8 53.7 1.0
CA B:GLU100 4.1 22.6 1.0
CD B:GLU100 4.1 32.4 1.0
CB B:GLU100 4.4 24.1 1.0
N B:GLY101 4.5 21.1 1.0
O B:CYS99 4.7 21.7 1.0
CG B:GLU100 4.8 33.7 1.0
C B:GLU100 4.8 21.5 1.0
OE2 B:GLU225 4.9 31.5 1.0

Magnesium binding site 4 out of 8 in 3roj

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Magnesium binding site 4 out of 8 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg347

b:36.8
occ:1.00
 OD1 B:ASP33 2.7 25.9 1.0
O B:HOH409 2.9 29.2 1.0
OE1 B:GLU57 3.2 32.1 1.0
N B:CYS99 3.3 19.0 1.0
O B:HOH426 3.3 40.5 1.0
OE2 B:GLU57 3.3 30.4 1.0
CD B:PRO98 3.4 18.6 1.0
OD2 B:ASP97 3.5 22.9 1.0
O B:CYS99 3.5 21.7 1.0
CG B:ASP33 3.6 27.4 1.0
CD B:GLU57 3.6 30.4 1.0
OD2 B:ASP33 3.7 30.9 1.0
N B:PRO98 3.8 19.6 1.0
CA B:CYS99 4.0 19.1 1.0
C B:CYS99 4.0 20.3 1.0
CG B:PRO98 4.1 19.4 1.0
CB B:CYS99 4.1 19.2 1.0
CB B:PRO98 4.2 18.2 1.0
C B:ASP97 4.2 20.3 1.0
C B:PRO98 4.2 18.4 1.0
CA B:PRO98 4.3 19.4 1.0
CG2 B:VAL37 4.3 20.4 1.0
CA B:ASP97 4.5 19.9 1.0
CG B:ASP97 4.7 24.2 1.0
CB B:ASP33 4.9 23.1 1.0
O B:ASP97 4.9 20.1 1.0

Magnesium binding site 5 out of 8 in 3roj

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Magnesium binding site 5 out of 8 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg346

b:42.5
occ:1.00
 OD1 C:ASP97 2.8 32.7 1.0
OE1 C:GLU225 2.8 34.4 1.0
OE1 C:GLU100 2.9 40.7 1.0
O C:HOH408 3.0 30.8 1.0
O2 C:SO4352 3.1 60.6 1.0
OD2 C:ASP97 3.4 28.6 1.0
O C:HOH582 3.4 46.1 1.0
CG C:ASP97 3.4 27.8 1.0
O4 C:SO4352 3.5 44.6 1.0
S C:SO4352 3.6 54.7 1.0
O3 C:SO4352 3.6 51.1 1.0
CG C:GLU100 3.6 29.1 1.0
CD C:GLU225 3.6 35.0 1.0
CD C:GLU100 3.6 32.4 1.0
CA C:GLU100 3.7 25.9 1.0
CG C:GLU225 3.8 27.4 1.0
N C:GLY101 4.0 26.9 1.0
CB C:GLU100 4.2 25.6 1.0
O C:CYS99 4.3 24.4 1.0
O C:HOH587 4.3 30.7 1.0
C C:GLU100 4.4 24.3 1.0
O C:HOH571 4.4 43.2 1.0
N C:GLU100 4.6 25.2 1.0
OE2 C:GLU225 4.8 30.1 1.0
C C:CYS99 4.8 25.2 1.0
OE2 C:GLU100 4.8 31.2 1.0
CB C:ASP97 4.9 23.9 1.0
O1 C:SO4352 5.0 45.3 1.0

Magnesium binding site 6 out of 8 in 3roj

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Magnesium binding site 6 out of 8 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg347

b:39.4
occ:1.00
 OD1 C:ASP33 2.7 32.2 1.0
OE2 C:GLU57 2.9 29.4 1.0
O C:HOH408 3.0 30.8 1.0
OD2 C:ASP97 3.3 28.6 1.0
O C:HOH601 3.3 36.8 1.0
N C:CYS99 3.3 22.0 1.0
CD C:PRO98 3.4 22.6 1.0
N C:PRO98 3.6 22.6 1.0
CD C:GLU57 3.6 33.2 1.0
OE1 C:GLU57 3.7 35.1 1.0
CG C:ASP33 3.7 29.5 1.0
O C:CYS99 3.7 24.4 1.0
CA C:CYS99 4.0 24.0 1.0
C C:CYS99 4.0 25.2 1.0
C C:ASP97 4.1 22.4 1.0
OD2 C:ASP33 4.1 33.8 1.0
CG C:PRO98 4.1 22.3 1.0
CB C:PRO98 4.2 20.7 1.0
CB C:CYS99 4.2 22.8 1.0
C C:PRO98 4.2 21.0 1.0
CA C:PRO98 4.3 22.5 1.0
CA C:ASP97 4.3 23.8 1.0
CG C:ASP97 4.4 27.8 1.0
CG2 C:VAL37 4.6 23.3 1.0
O C:ASP97 4.8 21.2 1.0
O C:HOH582 4.8 46.1 1.0
N C:GLU100 5.0 25.2 1.0
CB C:ASP33 5.0 26.2 1.0

Magnesium binding site 7 out of 8 in 3roj

Go back to Magnesium Binding Sites List in 3roj
Magnesium binding site 7 out of 8 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg346

b:44.7
occ:1.00
 OD1 D:ASP97 2.8 30.2 1.0
OE1 D:GLU225 2.9 35.9 1.0
OE2 D:GLU100 2.9 34.3 1.0
O2 D:SO4350 3.1 37.4 1.0
O4 D:SO4350 3.4 49.0 1.0
O D:HOH395 3.4 34.6 1.0
CG D:ASP97 3.6 27.6 1.0
OD2 D:ASP97 3.6 27.6 1.0
CG D:GLU225 3.6 28.9 1.0
CD D:GLU225 3.7 33.8 1.0
CD D:GLU100 3.7 30.6 1.0
CG D:GLU100 3.7 31.8 1.0
CA D:GLU100 3.8 26.3 1.0
S D:SO4350 3.9 52.3 1.0
O D:HOH804 3.9 38.7 1.0
N D:GLY101 4.0 24.3 1.0
O D:HOH722 4.3 40.9 1.0
C D:GLU100 4.3 25.5 1.0
CB D:GLU100 4.3 28.9 1.0
O D:CYS99 4.4 23.8 1.0
O1 D:SO4350 4.7 54.1 1.0
OE1 D:GLU100 4.8 32.0 1.0
OE2 D:GLU225 4.8 32.2 1.0
N D:GLU100 4.8 25.5 1.0
O3 D:SO4350 5.0 44.5 1.0

Magnesium binding site 8 out of 8 in 3roj

Go back to Magnesium Binding Sites List in 3roj
Magnesium binding site 8 out of 8 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg347

b:36.6
occ:1.00
 OD1 D:ASP33 2.8 27.8 1.0
O D:HOH395 3.0 34.6 1.0
N D:CYS99 3.2 20.8 1.0
OE2 D:GLU57 3.2 33.8 1.0
OE1 D:GLU57 3.3 29.6 1.0
OD2 D:ASP97 3.4 27.6 1.0
CD D:PRO98 3.4 24.1 1.0
O D:HOH823 3.4 45.1 1.0
O D:CYS99 3.6 23.8 1.0
N D:PRO98 3.6 23.0 1.0
CD D:GLU57 3.6 33.7 1.0
CG D:ASP33 3.8 29.6 1.0
CA D:CYS99 3.9 23.6 1.0
CB D:PRO98 4.0 21.6 1.0
O D:HOH412 4.0 41.2 1.0
C D:CYS99 4.0 24.0 1.0
CG D:PRO98 4.0 23.5 1.0
CB D:CYS99 4.0 21.9 1.0
C D:ASP97 4.1 24.2 1.0
C D:PRO98 4.1 21.7 1.0
CA D:PRO98 4.2 23.1 1.0
OD2 D:ASP33 4.2 36.8 1.0
CG2 D:VAL37 4.3 22.9 1.0
CA D:ASP97 4.4 25.1 1.0
CG D:ASP97 4.5 27.6 1.0
O D:ASP97 4.8 22.6 1.0

Reference:

X.Hu, F.Lingling. New Insights Into the Structural and Interactional Basis For A Promising Route Towards Fructose-1,6-/Sedoheptulose-1,7-Bisphosphatases Controlling To Be Published.
Page generated: Thu Aug 15 10:32:52 2024

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