Phosphorus 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

Phosphorus Binding Sites:

The binding sites of Phosphorus 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 Phosphorus atom.
In total 8 binding sites of Phosphorus where determined in the Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate, PDB code: 1aa1:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Phosphorus binding site 1 out of 8 in 1aa1

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Phosphorus binding site 1 out of 8 in the Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P 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:P477

b:36.4
occ:1.00
 P L:3PG477 0.0 36.4 1.0
O4P L:3PG477 1.5 38.9 1.0
O2P L:3PG477 1.5 37.1 1.0
O3P L:3PG477 1.5 40.0 1.0
O1P L:3PG477 1.7 38.1 1.0
C3 L:3PG477 2.8 38.4 1.0
O L:HOH513 3.6 17.6 1.0
O L:HOH617 3.7 23.1 1.0
N L:GLY404 3.8 27.4 1.0
N L:GLY403 3.9 22.0 1.0
CA L:GLY403 3.9 24.0 1.0
N L:GLY381 4.0 28.7 1.0
O L:HOH630 4.1 29.3 1.0
C2 L:3PG477 4.1 41.2 1.0
NZ L:LYS175 4.3 45.3 1.0
C L:GLY403 4.4 27.3 1.0
O L:HOH662 4.7 53.5 1.0
CA L:GLY381 4.7 28.6 1.0
CA L:GLY380 4.7 29.7 1.0
O3 L:3PG477 4.7 35.7 1.0
N L:GLY380 4.7 30.2 1.0
C L:GLY380 4.8 30.2 1.0
CA L:GLY404 4.9 26.5 1.0

Phosphorus binding site 2 out of 8 in 1aa1

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Phosphorus binding site 2 out of 8 in the Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P 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
L:P478

b:44.0
occ:1.00
 P L:3PG478 0.0 44.0 1.0
O2P L:3PG478 1.5 45.2 1.0
O3P L:3PG478 1.5 46.0 1.0
O4P L:3PG478 1.5 43.4 1.0
O1P L:3PG478 1.7 42.0 1.0
C3 L:3PG478 2.6 42.3 1.0
NH2 L:ARG295 3.7 10.2 1.0
NE L:ARG295 3.7 10.1 1.0
NE2 L:HIS298 3.8 3.9 1.0
O L:HOH666 3.8 43.1 1.0
C2 L:3PG478 3.9 44.2 1.0
O L:HOH628 3.9 26.3 1.0
CZ L:ARG295 4.1 12.8 1.0
O L:HOH619 4.5 22.2 1.0
CD2 L:HIS298 4.6 4.8 1.0
CE1 L:HIS298 4.6 3.8 1.0
O3 L:3PG478 4.6 41.3 1.0
C1 L:3PG478 4.7 47.2 1.0
CG L:ARG295 4.8 9.2 1.0
CD L:ARG295 4.8 9.3 1.0

Phosphorus binding site 3 out of 8 in 1aa1

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Phosphorus binding site 3 out of 8 in the Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P 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
B:P477

b:36.4
occ:1.00
 P B:3PG477 0.0 36.4 1.0
O4P B:3PG477 1.5 38.9 1.0
O2P B:3PG477 1.5 37.1 1.0
O3P B:3PG477 1.5 40.0 1.0
O1P B:3PG477 1.7 38.1 1.0
C3 B:3PG477 2.8 38.4 1.0
O B:HOH521 3.6 17.6 1.0
O B:HOH626 3.7 23.1 1.0
N B:GLY404 3.8 27.4 1.0
N B:GLY403 3.9 22.0 1.0
CA B:GLY403 3.9 24.0 1.0
N B:GLY381 4.0 28.7 1.0
O B:HOH639 4.1 29.3 1.0
C2 B:3PG477 4.1 41.2 1.0
NZ B:LYS175 4.3 45.3 1.0
C B:GLY403 4.4 27.3 1.0
O B:HOH671 4.7 53.5 1.0
CA B:GLY381 4.7 28.6 1.0
CA B:GLY380 4.7 29.7 1.0
O3 B:3PG477 4.7 35.7 1.0
N B:GLY380 4.7 30.2 1.0
C B:GLY380 4.8 30.2 1.0
CA B:GLY404 4.9 26.5 1.0

Phosphorus binding site 4 out of 8 in 1aa1

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Phosphorus binding site 4 out of 8 in the Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P 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
B:P478

b:44.0
occ:1.00
 P B:3PG478 0.0 44.0 1.0
O2P B:3PG478 1.5 45.2 1.0
O3P B:3PG478 1.5 46.0 1.0
O4P B:3PG478 1.5 43.4 1.0
O1P B:3PG478 1.7 42.0 1.0
C3 B:3PG478 2.6 42.3 1.0
NH2 B:ARG295 3.7 10.2 1.0
NE B:ARG295 3.7 10.1 1.0
NE2 B:HIS298 3.8 3.9 1.0
O B:HOH675 3.8 43.1 1.0
C2 B:3PG478 3.9 44.2 1.0
O B:HOH637 3.9 26.3 1.0
CZ B:ARG295 4.1 12.8 1.0
O B:HOH628 4.5 22.2 1.0
CD2 B:HIS298 4.6 4.8 1.0
CE1 B:HIS298 4.6 3.8 1.0
O3 B:3PG478 4.6 41.3 1.0
C1 B:3PG478 4.7 47.2 1.0
CG B:ARG295 4.8 9.2 1.0
CD B:ARG295 4.8 9.3 1.0

Phosphorus binding site 5 out of 8 in 1aa1

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Phosphorus binding site 5 out of 8 in the Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:P477

b:36.4
occ:1.00
 P E:3PG477 0.0 36.4 1.0
O4P E:3PG477 1.5 38.9 1.0
O2P E:3PG477 1.5 37.1 1.0
O3P E:3PG477 1.5 40.0 1.0
O1P E:3PG477 1.7 38.1 1.0
C3 E:3PG477 2.8 38.4 1.0
O E:HOH520 3.6 17.6 1.0
O E:HOH625 3.7 23.1 1.0
N E:GLY404 3.8 27.4 1.0
N E:GLY403 3.9 22.0 1.0
CA E:GLY403 3.9 24.0 1.0
N E:GLY381 4.0 28.7 1.0
O E:HOH638 4.1 29.3 1.0
C2 E:3PG477 4.1 41.2 1.0
NZ E:LYS175 4.3 45.3 1.0
C E:GLY403 4.4 27.3 1.0
O E:HOH670 4.7 53.5 1.0
CA E:GLY381 4.7 28.6 1.0
CA E:GLY380 4.7 29.7 1.0
O3 E:3PG477 4.7 35.7 1.0
N E:GLY380 4.7 30.2 1.0
C E:GLY380 4.8 30.2 1.0
CA E:GLY404 4.9 26.5 1.0

Phosphorus binding site 6 out of 8 in 1aa1

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Phosphorus binding site 6 out of 8 in the Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:P478

b:44.0
occ:1.00
 P E:3PG478 0.0 44.0 1.0
O2P E:3PG478 1.5 45.2 1.0
O3P E:3PG478 1.5 46.0 1.0
O4P E:3PG478 1.5 43.4 1.0
O1P E:3PG478 1.7 42.0 1.0
C3 E:3PG478 2.6 42.3 1.0
NH2 E:ARG295 3.7 10.2 1.0
NE E:ARG295 3.7 10.1 1.0
NE2 E:HIS298 3.8 3.9 1.0
O E:HOH674 3.8 43.1 1.0
C2 E:3PG478 3.9 44.2 1.0
O E:HOH636 3.9 26.3 1.0
CZ E:ARG295 4.1 12.8 1.0
O E:HOH627 4.5 22.2 1.0
CD2 E:HIS298 4.6 4.8 1.0
CE1 E:HIS298 4.6 3.8 1.0
O3 E:3PG478 4.6 41.3 1.0
C1 E:3PG478 4.7 47.2 1.0
CG E:ARG295 4.8 9.2 1.0
CD E:ARG295 4.8 9.3 1.0

Phosphorus binding site 7 out of 8 in 1aa1

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Phosphorus binding site 7 out of 8 in the Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:P477

b:36.4
occ:1.00
 P H:3PG477 0.0 36.4 1.0
O4P H:3PG477 1.5 38.9 1.0
O2P H:3PG477 1.5 37.1 1.0
O3P H:3PG477 1.5 40.0 1.0
O1P H:3PG477 1.7 38.1 1.0
C3 H:3PG477 2.8 38.4 1.0
O H:HOH524 3.6 17.6 1.0
O H:HOH628 3.7 23.1 1.0
N H:GLY404 3.8 27.4 1.0
N H:GLY403 3.9 22.0 1.0
CA H:GLY403 3.9 24.0 1.0
N H:GLY381 4.0 28.7 1.0
O H:HOH641 4.1 29.3 1.0
C2 H:3PG477 4.1 41.2 1.0
NZ H:LYS175 4.3 45.3 1.0
C H:GLY403 4.4 27.3 1.0
O H:HOH673 4.7 53.5 1.0
CA H:GLY381 4.7 28.6 1.0
CA H:GLY380 4.7 29.7 1.0
O3 H:3PG477 4.7 35.7 1.0
N H:GLY380 4.7 30.2 1.0
C H:GLY380 4.8 30.2 1.0
CA H:GLY404 4.9 26.5 1.0

Phosphorus binding site 8 out of 8 in 1aa1

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Phosphorus binding site 8 out of 8 in the Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Activated Spinach Rubisco in Complex with the Product 3- Phosphoglycerate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:P478

b:44.0
occ:1.00
 P H:3PG478 0.0 44.0 1.0
O2P H:3PG478 1.5 45.2 1.0
O3P H:3PG478 1.5 46.0 1.0
O4P H:3PG478 1.5 43.4 1.0
O1P H:3PG478 1.7 42.0 1.0
C3 H:3PG478 2.6 42.3 1.0
NH2 H:ARG295 3.7 10.2 1.0
NE H:ARG295 3.7 10.1 1.0
NE2 H:HIS298 3.8 3.9 1.0
O H:HOH677 3.8 43.1 1.0
C2 H:3PG478 3.9 44.2 1.0
O H:HOH639 3.9 26.3 1.0
CZ H:ARG295 4.1 12.8 1.0
O H:HOH630 4.5 22.2 1.0
CD2 H:HIS298 4.6 4.8 1.0
CE1 H:HIS298 4.6 3.8 1.0
O3 H:3PG478 4.6 41.3 1.0
C1 H:3PG478 4.7 47.2 1.0
CG H:ARG295 4.8 9.2 1.0
CD H:ARG295 4.8 9.3 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: Fri Sep 25 12:40:11 2020

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