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

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

All present enzymatic activity of D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 in Complex with Fructose-1,6- Bisphosphate:
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 in Complex with Fructose-1,6- Bisphosphate, PDB code: 3rpl 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) 25.72 / 2.40
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 145.222, 145.222, 169.104, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 20.7

Other elements in 3rpl:

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

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

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 in Complex with Fructose-1,6- Bisphosphate (pdb code 3rpl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 in Complex with Fructose-1,6- Bisphosphate, PDB code: 3rpl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 3rpl

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Magnesium binding site 1 out of 12 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 in Complex with Fructose-1,6- Bisphosphate


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 in Complex with Fructose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg346

b:46.4
occ:1.00
 O6P A:FBP350 2.7 32.2 1.0
OD2 A:ASP198 3.2 24.6 1.0
O5 A:FBP350 3.2 22.4 1.0
O1 A:FBP350 3.2 26.2 1.0
O A:HOH668 3.5 45.4 1.0
O A:HOH449 3.5 44.2 1.0
O6 A:FBP350 3.6 32.5 1.0
P2 A:FBP350 3.6 23.7 1.0
C2 A:FBP350 4.0 26.6 1.0
O2P A:FBP350 4.0 26.0 1.0
P1 A:FBP350 4.0 27.4 1.0
O2 A:FBP350 4.0 20.4 1.0
O3P A:FBP350 4.1 27.4 1.0
C1 A:FBP350 4.1 26.2 1.0
O5P A:FBP350 4.1 26.7 1.0
CG A:ASP198 4.2 24.5 1.0
C6 A:FBP350 4.2 24.2 1.0
NH2 A:ARG176 4.2 16.4 1.0
C5 A:FBP350 4.3 23.2 1.0
OD1 A:ASP198 4.6 23.6 1.0
O A:HOH500 4.7 24.6 1.0
O4P A:FBP350 5.0 23.6 1.0

Magnesium binding site 2 out of 12 in 3rpl

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Magnesium binding site 2 out of 12 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 in Complex with Fructose-1,6- Bisphosphate


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 in Complex with Fructose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg347

b:29.4
occ:1.00
 OE1 A:GLU225 2.6 22.2 1.0
OD1 A:ASP97 2.6 24.0 1.0
OE2 A:GLU100 2.8 20.8 1.0
O A:HOH422 2.8 27.7 1.0
C1 A:FBP350 3.2 26.2 1.0
O1P A:FBP350 3.3 21.8 1.0
CD A:GLU225 3.4 26.9 1.0
OD2 A:ASP97 3.4 22.7 1.0
CG A:ASP97 3.4 22.5 1.0
O A:HOH523 3.4 36.7 1.0
CA A:GLU100 3.5 16.6 1.0
CG A:GLU225 3.6 20.5 1.0
CB A:GLU100 3.6 18.6 1.0
CD A:GLU100 3.8 23.7 1.0
P1 A:FBP350 4.0 27.4 1.0
O3P A:FBP350 4.0 27.4 1.0
N A:GLY101 4.1 17.2 1.0
O1 A:FBP350 4.1 26.2 1.0
C3 A:FBP350 4.1 23.1 1.0
C2 A:FBP350 4.2 26.6 1.0
C A:GLU100 4.3 18.9 1.0
CG A:GLU100 4.3 21.1 1.0
O A:CYS99 4.3 20.4 1.0
OE2 A:GLU225 4.5 24.2 1.0
N A:GLU100 4.6 19.4 1.0
O3 A:FBP350 4.6 24.2 1.0
OE1 A:GLU100 4.8 24.2 1.0
CB A:ASP97 4.8 20.2 1.0
C A:CYS99 4.9 21.4 1.0
O5 A:FBP350 5.0 22.4 1.0

Magnesium binding site 3 out of 12 in 3rpl

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Magnesium binding site 3 out of 12 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 in Complex with Fructose-1,6- Bisphosphate


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 in Complex with Fructose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg348

b:37.9
occ:1.00
 OD1 A:ASP33 2.7 27.1 1.0
O A:HOH468 3.0 30.3 1.0
O A:HOH422 3.1 27.7 1.0
OE2 A:GLU57 3.2 29.7 1.0
OD2 A:ASP97 3.3 22.7 1.0
O A:HOH489 3.3 30.1 1.0
O A:CYS99 3.5 20.4 1.0
N A:CYS99 3.6 19.6 1.0
CG A:ASP33 3.6 24.2 1.0
OD2 A:ASP33 3.6 26.0 1.0
CD A:PRO98 3.7 17.0 1.0
OE1 A:GLU57 3.8 30.6 1.0
CD A:GLU57 3.9 32.6 1.0
N A:PRO98 4.0 19.2 1.0
C A:CYS99 4.0 21.4 1.0
CA A:CYS99 4.1 17.7 1.0
O A:HOH523 4.2 36.7 1.0
CB A:CYS99 4.4 15.7 1.0
C A:ASP97 4.4 21.0 1.0
CG A:ASP97 4.4 22.5 1.0
O A:HOH381 4.5 26.1 1.0
CA A:ASP97 4.5 19.2 1.0
C A:PRO98 4.6 19.0 1.0
CG A:PRO98 4.6 18.5 1.0
CB A:PRO98 4.6 15.6 1.0
CA A:PRO98 4.7 18.1 1.0
CG2 A:VAL37 4.8 16.4 1.0
CG2 A:THR102 4.9 19.2 1.0
N A:GLU100 4.9 19.4 1.0
CB A:ASP33 5.0 20.7 1.0

Magnesium binding site 4 out of 12 in 3rpl

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Magnesium binding site 4 out of 12 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 in Complex with Fructose-1,6- Bisphosphate


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 in Complex with Fructose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg346

b:43.9
occ:1.00
 O4P B:FBP350 2.8 20.8 1.0
OD2 B:ASP198 2.8 22.2 1.0
O1 B:FBP350 3.4 31.2 1.0
O5 B:FBP350 3.7 22.7 1.0
O1P B:FBP350 3.7 36.0 1.0
CG B:ASP198 3.8 27.2 1.0
NH2 B:ARG176 3.9 16.6 1.0
P2 B:FBP350 4.0 26.3 1.0
OD1 B:ASP198 4.1 22.9 1.0
O2 B:FBP350 4.2 20.4 1.0
P1 B:FBP350 4.2 27.9 1.0
C2 B:FBP350 4.3 24.4 1.0
O6 B:FBP350 4.3 26.4 1.0
C1 B:FBP350 4.4 26.5 1.0
O B:HOH495 4.5 23.3 1.0
O6P B:FBP350 4.5 25.8 1.0
C6 B:FBP350 4.6 21.8 1.0
O2P B:FBP350 4.6 35.6 1.0
C5 B:FBP350 4.7 23.3 1.0

Magnesium binding site 5 out of 12 in 3rpl

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Magnesium binding site 5 out of 12 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 in Complex with Fructose-1,6- Bisphosphate


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 in Complex with Fructose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg347

b:31.4
occ:1.00
 OD1 B:ASP97 2.6 19.4 1.0
OE1 B:GLU225 2.7 21.9 1.0
O B:HOH391 3.0 25.5 1.0
OE2 B:GLU100 3.1 21.2 1.0
C1 B:FBP350 3.2 26.5 1.0
O3P B:FBP350 3.3 28.0 1.0
OD2 B:ASP97 3.3 19.9 1.0
CG B:ASP97 3.4 21.4 1.0
CA B:GLU100 3.4 20.0 1.0
CB B:GLU100 3.5 21.0 1.0
CD B:GLU225 3.5 22.9 1.0
CG B:GLU225 3.8 21.1 1.0
N B:GLY101 3.9 20.9 1.0
P1 B:FBP350 3.9 27.9 1.0
O2P B:FBP350 4.0 35.6 1.0
O1 B:FBP350 4.0 31.2 1.0
CD B:GLU100 4.0 26.4 1.0
C B:GLU100 4.1 18.9 1.0
O B:CYS99 4.1 21.2 1.0
C3 B:FBP350 4.1 25.4 1.0
C2 B:FBP350 4.3 24.4 1.0
CG B:GLU100 4.3 28.2 1.0
N B:GLU100 4.4 22.5 1.0
O3 B:FBP350 4.5 23.7 1.0
OE2 B:GLU225 4.6 29.9 1.0
C B:CYS99 4.7 23.8 1.0
CB B:ASP97 4.8 15.8 1.0
O5 B:FBP350 5.0 22.7 1.0

Magnesium binding site 6 out of 12 in 3rpl

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Magnesium binding site 6 out of 12 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 in Complex with Fructose-1,6- Bisphosphate


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 in Complex with Fructose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg348

b:35.0
occ:1.00
 OD1 B:ASP33 2.8 23.5 1.0
O B:HOH391 3.0 25.5 1.0
OD2 B:ASP97 3.2 19.9 1.0
N B:CYS99 3.3 19.3 1.0
OE2 B:GLU57 3.4 27.3 1.0
O B:HOH426 3.4 20.6 1.0
O B:CYS99 3.4 21.2 1.0
CD B:PRO98 3.6 21.2 1.0
CG B:ASP33 3.6 24.8 1.0
OE1 B:GLU57 3.7 28.0 1.0
OD2 B:ASP33 3.8 24.6 1.0
C B:CYS99 3.8 23.8 1.0
N B:PRO98 3.9 21.6 1.0
CA B:CYS99 3.9 18.5 1.0
CD B:GLU57 3.9 32.4 1.0
CB B:CYS99 4.1 20.8 1.0
C B:ASP97 4.2 18.4 1.0
CG B:ASP97 4.3 21.4 1.0
C B:PRO98 4.4 16.8 1.0
CA B:ASP97 4.4 17.2 1.0
CG B:PRO98 4.4 19.0 1.0
CB B:PRO98 4.5 14.4 1.0
CA B:PRO98 4.5 17.3 1.0
CG2 B:VAL37 4.7 18.3 1.0
CG2 B:THR102 4.8 24.4 1.0
N B:GLU100 4.8 22.5 1.0
O B:ASP97 4.9 16.3 1.0
CB B:ASP33 5.0 16.9 1.0

Magnesium binding site 7 out of 12 in 3rpl

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Magnesium binding site 7 out of 12 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 in Complex with Fructose-1,6- Bisphosphate


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 in Complex with Fructose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg346

b:48.7
occ:1.00
 O4P C:FBP350 2.9 26.0 1.0
OD2 C:ASP198 3.1 20.6 1.0
O1 C:FBP350 3.2 34.4 1.0
O5 C:FBP350 3.4 29.8 1.0
O3P C:FBP350 3.5 25.8 1.0
P1 C:FBP350 3.8 33.5 1.0
O1P C:FBP350 3.9 26.1 1.0
C2 C:FBP350 4.1 28.6 1.0
O2 C:FBP350 4.1 25.1 1.0
P2 C:FBP350 4.1 22.7 1.0
O C:HOH625 4.1 32.5 1.0
C1 C:FBP350 4.1 26.9 1.0
CG C:ASP198 4.2 24.1 1.0
O C:HOH496 4.3 24.1 1.0
O6 C:FBP350 4.3 27.4 1.0
NH2 C:ARG176 4.4 21.7 1.0
C5 C:FBP350 4.5 26.9 1.0
C6 C:FBP350 4.5 25.5 1.0
O6P C:FBP350 4.5 26.6 1.0
OD1 C:ASP198 4.6 19.2 1.0

Magnesium binding site 8 out of 12 in 3rpl

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Magnesium binding site 8 out of 12 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 in Complex with Fructose-1,6- Bisphosphate


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 in Complex with Fructose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg347

b:34.3
occ:1.00
 OD1 C:ASP97 2.7 29.1 1.0
OE1 C:GLU225 2.8 26.0 1.0
OE2 C:GLU100 2.9 27.3 1.0
C1 C:FBP350 3.2 26.9 1.0
CG C:GLU100 3.3 24.4 1.0
O C:HOH391 3.3 28.7 1.0
O2P C:FBP350 3.4 26.0 1.0
CG C:ASP97 3.4 26.8 1.0
OD2 C:ASP97 3.5 27.1 1.0
CD C:GLU100 3.5 22.6 1.0
CD C:GLU225 3.5 28.2 1.0
CA C:GLU100 3.6 19.7 1.0
CG C:GLU225 3.6 20.8 1.0
O C:HOH624 3.7 35.5 1.0
CB C:GLU100 4.0 17.2 1.0
O1P C:FBP350 4.0 26.1 1.0
C3 C:FBP350 4.0 22.8 1.0
P1 C:FBP350 4.1 33.5 1.0
N C:GLY101 4.1 16.0 1.0
O1 C:FBP350 4.1 34.4 1.0
C2 C:FBP350 4.2 28.6 1.0
C C:GLU100 4.3 17.9 1.0
O C:CYS99 4.3 22.7 1.0
O3 C:FBP350 4.4 20.3 1.0
N C:GLU100 4.5 17.4 1.0
OE2 C:GLU225 4.6 24.8 1.0
OE1 C:GLU100 4.8 25.6 1.0
C C:CYS99 4.8 22.2 1.0
CB C:ASP97 4.9 20.4 1.0
O5 C:FBP350 5.0 29.8 1.0

Magnesium binding site 9 out of 12 in 3rpl

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Magnesium binding site 9 out of 12 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 in Complex with Fructose-1,6- Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 in Complex with Fructose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg348

b:40.0
occ:1.00
 O C:HOH391 2.8 28.7 1.0
OD1 C:ASP33 2.8 34.4 1.0
OE1 C:GLU57 2.9 28.4 1.0
OD2 C:ASP97 3.1 27.1 1.0
O C:HOH611 3.2 34.9 1.0
N C:CYS99 3.4 23.6 1.0
O C:CYS99 3.6 22.7 1.0
CD C:PRO98 3.6 21.8 1.0
CD C:GLU57 3.7 30.9 1.0
N C:PRO98 3.8 22.4 1.0
CG C:ASP33 3.8 30.8 1.0
OE2 C:GLU57 3.9 30.7 1.0
C C:CYS99 4.0 22.2 1.0
CA C:CYS99 4.0 19.2 1.0
OD2 C:ASP33 4.1 37.1 1.0
CB C:CYS99 4.2 21.6 1.0
C C:ASP97 4.2 19.4 1.0
CG C:ASP97 4.3 26.8 1.0
CA C:ASP97 4.4 21.1 1.0
O C:HOH624 4.4 35.5 1.0
C C:PRO98 4.4 21.0 1.0
CG C:PRO98 4.5 20.7 1.0
CB C:PRO98 4.5 18.6 1.0
CA C:PRO98 4.5 21.1 1.0
O C:HOH757 4.6 33.0 1.0
CG2 C:VAL37 4.8 23.0 1.0
CG2 C:THR102 4.9 24.3 1.0
N C:GLU100 4.9 17.4 1.0
O C:ASP97 4.9 20.6 1.0
CB C:ASP97 5.0 20.4 1.0

Magnesium binding site 10 out of 12 in 3rpl

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Magnesium binding site 10 out of 12 in the D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 in Complex with Fructose-1,6- Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of D-Fructose 1,6-Bisphosphatase Class 2/Sedoheptulose 1,7-Bisphosphatase of Synechocystis Sp. Pcc 6803 in Complex with Fructose-1,6- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg346

b:39.4
occ:1.00
 O4P D:FBP350 2.7 19.4 1.0
OD1 D:ASP198 3.1 25.7 1.0
O1 D:FBP350 3.2 30.1 1.0
O D:HOH590 3.2 33.2 1.0
O5 D:FBP350 3.3 27.1 1.0
O1P D:FBP350 3.7 31.4 1.0
O2P D:FBP350 3.8 25.7 1.0
P1 D:FBP350 3.8 28.4 1.0
CG D:ASP198 3.9 23.6 1.0
OD2 D:ASP198 3.9 17.1 1.0
P2 D:FBP350 3.9 25.2 1.0
C2 D:FBP350 4.0 27.4 1.0
O2 D:FBP350 4.1 25.1 1.0
O D:HOH619 4.1 36.1 1.0
O6 D:FBP350 4.1 23.5 1.0
C1 D:FBP350 4.2 27.4 1.0
NH2 D:ARG176 4.3 20.1 1.0
C6 D:FBP350 4.3 24.4 1.0
C5 D:FBP350 4.3 25.1 1.0
O D:HOH497 4.5 22.8 1.0
O6P D:FBP350 4.5 30.3 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 10:32:57 2024

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