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Magnesium in PDB 1aa1: Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate

Enzymatic activity of Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate

All present enzymatic activity of Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate:
4.1.1.39;

Protein crystallography data

The structure of Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate, PDB code: 1aa1 was solved by T.C.Taylor, I.Andersson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 157.600, 158.700, 203.300, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 22.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate (pdb code 1aa1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate, PDB code: 1aa1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1aa1

Go back to Magnesium Binding Sites List in 1aa1
Magnesium binding site 1 out of 4 in the Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg476

b:29.0
occ:1.00
OE1 L:GLU204 2.4 17.0 1.0
OQ2 L:KCX201 2.4 35.7 1.0
O3 L:3PG477 2.4 35.7 1.0
O2 L:3PG477 2.4 43.4 1.0
OD1 L:ASP203 2.5 19.9 1.0
O L:HOH614 2.7 37.8 1.0
OQ1 L:KCX201 2.9 29.8 1.0
C1 L:3PG477 3.0 43.0 1.0
CX L:KCX201 3.0 28.3 1.0
C2 L:3PG477 3.2 41.2 1.0
CD L:GLU204 3.4 18.2 1.0
CG L:ASP203 3.5 14.8 1.0
OE2 L:GLU204 3.7 20.1 1.0
NE2 L:HIS294 3.8 10.4 1.0
O1 L:3PG477 4.0 46.1 1.0
OD2 L:ASP203 4.1 16.0 1.0
NZ L:KCX201 4.2 27.2 1.0
N L:GLU204 4.2 10.1 1.0
CA L:ASP203 4.3 8.3 1.0
CG2 L:THR173 4.3 19.3 1.0
C3 L:3PG477 4.4 38.4 1.0
CB L:ASP203 4.4 10.9 1.0
NZ L:LYS177 4.6 20.2 1.0
CE1 L:HIS294 4.6 8.3 1.0
CD2 L:HIS294 4.7 10.8 1.0
O L:HOH608 4.7 45.5 1.0
CG L:GLU204 4.7 13.8 1.0
C L:ASP203 4.8 11.0 1.0
OG1 L:THR173 4.9 27.1 1.0

Magnesium binding site 2 out of 4 in 1aa1

Go back to Magnesium Binding Sites List in 1aa1
Magnesium binding site 2 out of 4 in the Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg476

b:29.0
occ:1.00
OE1 B:GLU204 2.4 17.0 1.0
OQ2 B:KCX201 2.4 35.7 1.0
O3 B:3PG477 2.4 35.7 1.0
O2 B:3PG477 2.4 43.4 1.0
OD1 B:ASP203 2.5 19.9 1.0
O B:HOH623 2.7 37.8 1.0
OQ1 B:KCX201 2.9 29.8 1.0
C1 B:3PG477 3.0 43.0 1.0
CX B:KCX201 3.0 28.3 1.0
C2 B:3PG477 3.2 41.2 1.0
CD B:GLU204 3.4 18.2 1.0
CG B:ASP203 3.5 14.8 1.0
OE2 B:GLU204 3.7 20.1 1.0
NE2 B:HIS294 3.8 10.4 1.0
O1 B:3PG477 4.0 46.1 1.0
OD2 B:ASP203 4.1 16.0 1.0
NZ B:KCX201 4.2 27.2 1.0
N B:GLU204 4.2 10.1 1.0
CA B:ASP203 4.3 8.3 1.0
CG2 B:THR173 4.3 19.3 1.0
C3 B:3PG477 4.4 38.4 1.0
CB B:ASP203 4.4 10.9 1.0
NZ B:LYS177 4.6 20.2 1.0
CE1 B:HIS294 4.6 8.3 1.0
CD2 B:HIS294 4.7 10.8 1.0
O B:HOH616 4.7 45.5 1.0
CG B:GLU204 4.7 13.8 1.0
C B:ASP203 4.8 11.0 1.0
OG1 B:THR173 4.9 27.1 1.0

Magnesium binding site 3 out of 4 in 1aa1

Go back to Magnesium Binding Sites List in 1aa1
Magnesium binding site 3 out of 4 in the Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg476

b:29.0
occ:1.00
OE1 E:GLU204 2.4 17.0 1.0
OQ2 E:KCX201 2.4 35.7 1.0
O3 E:3PG477 2.4 35.7 1.0
O2 E:3PG477 2.4 43.4 1.0
OD1 E:ASP203 2.5 19.9 1.0
O E:HOH622 2.7 37.8 1.0
OQ1 E:KCX201 2.9 29.8 1.0
C1 E:3PG477 3.0 43.0 1.0
CX E:KCX201 3.0 28.3 1.0
C2 E:3PG477 3.2 41.2 1.0
CD E:GLU204 3.4 18.2 1.0
CG E:ASP203 3.5 14.8 1.0
OE2 E:GLU204 3.7 20.1 1.0
NE2 E:HIS294 3.8 10.4 1.0
O1 E:3PG477 4.0 46.1 1.0
OD2 E:ASP203 4.1 16.0 1.0
NZ E:KCX201 4.2 27.2 1.0
N E:GLU204 4.2 10.1 1.0
CA E:ASP203 4.3 8.3 1.0
CG2 E:THR173 4.3 19.3 1.0
C3 E:3PG477 4.4 38.4 1.0
CB E:ASP203 4.4 10.9 1.0
NZ E:LYS177 4.6 20.2 1.0
CE1 E:HIS294 4.6 8.3 1.0
CD2 E:HIS294 4.7 10.8 1.0
O E:HOH616 4.7 45.5 1.0
CG E:GLU204 4.7 13.8 1.0
C E:ASP203 4.8 11.0 1.0
OG1 E:THR173 4.9 27.1 1.0

Magnesium binding site 4 out of 4 in 1aa1

Go back to Magnesium Binding Sites List in 1aa1
Magnesium binding site 4 out of 4 in the Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg476

b:29.0
occ:1.00
OE1 H:GLU204 2.4 17.0 1.0
OQ2 H:KCX201 2.4 35.7 1.0
O3 H:3PG477 2.4 35.7 1.0
O2 H:3PG477 2.4 43.4 1.0
OD1 H:ASP203 2.5 19.9 1.0
O H:HOH625 2.7 37.8 1.0
OQ1 H:KCX201 2.9 29.8 1.0
C1 H:3PG477 3.0 43.0 1.0
CX H:KCX201 3.0 28.3 1.0
C2 H:3PG477 3.2 41.2 1.0
CD H:GLU204 3.4 18.2 1.0
CG H:ASP203 3.5 14.8 1.0
OE2 H:GLU204 3.7 20.1 1.0
NE2 H:HIS294 3.8 10.4 1.0
O1 H:3PG477 4.0 46.1 1.0
OD2 H:ASP203 4.1 16.0 1.0
NZ H:KCX201 4.2 27.2 1.0
N H:GLU204 4.2 10.1 1.0
CA H:ASP203 4.3 8.3 1.0
CG2 H:THR173 4.3 19.3 1.0
C3 H:3PG477 4.4 38.4 1.0
CB H:ASP203 4.4 10.9 1.0
NZ H:LYS177 4.6 20.2 1.0
CE1 H:HIS294 4.6 8.3 1.0
CD2 H:HIS294 4.7 10.8 1.0
O H:HOH619 4.7 45.5 1.0
CG H:GLU204 4.7 13.8 1.0
C H:ASP203 4.8 11.0 1.0
OG1 H:THR173 4.9 27.1 1.0

Reference:

T.C.Taylor, I.Andersson. Structure of A Product Complex of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase. Biochemistry V. 36 4041 1997.
ISSN: ISSN 0006-2960
PubMed: 9092835
DOI: 10.1021/BI962818W
Page generated: Mon Dec 14 03:30:01 2020

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