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

Go back to Phosphorus Binding Sites List in 1aa1
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

Go back to Phosphorus Binding Sites List in 1aa1
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

Go back to Phosphorus Binding Sites List in 1aa1
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

Go back to Phosphorus Binding Sites List in 1aa1
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

Go back to Phosphorus Binding Sites List in 1aa1
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

Go back to Phosphorus Binding Sites List in 1aa1
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

Go back to Phosphorus Binding Sites List in 1aa1
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

Go back to Phosphorus Binding Sites List in 1aa1
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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy