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Calcium in PDB 4i5l: Structural Mechanism of Trimeric PP2A Holoenzyme Involving PR70: Insight For CDC6 Dephosphorylation

Enzymatic activity of Structural Mechanism of Trimeric PP2A Holoenzyme Involving PR70: Insight For CDC6 Dephosphorylation

All present enzymatic activity of Structural Mechanism of Trimeric PP2A Holoenzyme Involving PR70: Insight For CDC6 Dephosphorylation:
3.1.3.16;

Protein crystallography data

The structure of Structural Mechanism of Trimeric PP2A Holoenzyme Involving PR70: Insight For CDC6 Dephosphorylation, PDB code: 4i5l was solved by N.Wlodarchak, K.A.Satyshur, F.Guo, Y.Xing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.85 / 2.43
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.234, 101.071, 343.396, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22.8

Other elements in 4i5l:

The structure of Structural Mechanism of Trimeric PP2A Holoenzyme Involving PR70: Insight For CDC6 Dephosphorylation also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural Mechanism of Trimeric PP2A Holoenzyme Involving PR70: Insight For CDC6 Dephosphorylation (pdb code 4i5l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structural Mechanism of Trimeric PP2A Holoenzyme Involving PR70: Insight For CDC6 Dephosphorylation, PDB code: 4i5l:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4i5l

Go back to Calcium Binding Sites List in 4i5l
Calcium binding site 1 out of 4 in the Structural Mechanism of Trimeric PP2A Holoenzyme Involving PR70: Insight For CDC6 Dephosphorylation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Mechanism of Trimeric PP2A Holoenzyme Involving PR70: Insight For CDC6 Dephosphorylation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:22.5
occ:1.00
 OE2 B:GLU412 2.3 32.0 1.0
OE1 B:GLU412 2.3 29.7 1.0
O B:ALA407 2.3 29.9 1.0
OD1 B:ASP401 2.3 29.1 1.0
OD1 B:ASP405 2.3 33.6 1.0
OD1 B:ASP403 2.3 32.6 1.0
O B:HOH742 2.4 21.6 1.0
CD B:GLU412 2.4 30.9 1.0
CG B:ASP405 3.2 32.5 1.0
CG B:ASP403 3.3 31.8 1.0
C B:ALA407 3.5 28.8 1.0
CG B:ASP401 3.5 27.7 1.0
OD2 B:ASP405 3.6 34.3 1.0
OD2 B:ASP403 3.6 32.9 1.0
CG B:GLU412 4.0 31.1 1.0
N B:ASP405 4.2 29.5 1.0
N B:ALA407 4.2 28.3 1.0
OD2 B:ASP401 4.3 28.0 1.0
CB B:ASP405 4.4 32.2 1.0
N B:SER409 4.4 31.6 1.0
CA B:ASP401 4.4 25.2 1.0
CA B:ALA407 4.4 28.8 1.0
N B:ASP403 4.4 27.5 1.0
N B:LEU408 4.4 28.5 1.0
CA B:LEU408 4.5 29.1 1.0
CB B:ASP401 4.5 25.7 1.0
C B:ASP401 4.5 25.4 1.0
CB B:ASP403 4.6 30.8 1.0
N B:GLY404 4.6 28.0 1.0
N B:LEU402 4.6 25.5 1.0
N B:GLY406 4.7 29.2 1.0
CA B:ASP405 4.7 31.4 1.0
CB B:SER409 4.8 32.8 1.0
OG B:SER409 4.9 34.3 1.0
CA B:ASP403 4.9 29.4 1.0
C B:LEU408 4.9 30.4 1.0
CB B:GLU412 4.9 30.8 1.0
CB B:ALA407 4.9 28.7 1.0
C B:ASP405 5.0 30.6 1.0
C B:ASP403 5.0 29.4 1.0

Calcium binding site 2 out of 4 in 4i5l

Go back to Calcium Binding Sites List in 4i5l
Calcium binding site 2 out of 4 in the Structural Mechanism of Trimeric PP2A Holoenzyme Involving PR70: Insight For CDC6 Dephosphorylation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Mechanism of Trimeric PP2A Holoenzyme Involving PR70: Insight For CDC6 Dephosphorylation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:43.7
occ:1.00
 O B:HOH740 2.2 44.2 1.0
OD1 B:ASP331 2.3 57.6 1.0
OD1 B:ASP327 2.3 44.9 1.0
O B:LEU333 2.3 44.7 1.0
OD2 B:ASP331 2.3 60.5 1.0
OD2 B:ASP329 2.4 62.4 1.0
OD1 B:ASP329 2.6 59.7 1.0
CG B:ASP331 2.6 57.9 1.0
O B:HOH762 2.8 51.1 1.0
CG B:ASP329 2.8 59.9 1.0
CG B:ASP327 3.5 41.4 1.0
C B:LEU333 3.6 40.2 1.0
O B:HOH753 3.9 50.8 1.0
CB B:ASP331 4.1 55.3 1.0
CA B:ASP327 4.1 39.2 1.0
N B:ASP331 4.2 53.3 1.0
CB B:ASP329 4.2 58.2 1.0
CD1 B:ILE334 4.3 38.9 1.0
N B:LEU333 4.3 40.2 1.0
CB B:ASP327 4.4 39.8 1.0
OD2 B:ASP338 4.4 40.6 1.0
CA B:LEU333 4.4 41.1 1.0
OD2 B:ASP327 4.4 40.4 1.0
C B:ASP327 4.5 41.5 1.0
N B:ASP329 4.5 53.5 1.0
N B:ILE334 4.6 37.5 1.0
N B:HIS330 4.6 51.5 1.0
CB B:LEU333 4.7 42.6 1.0
CA B:ASP331 4.7 52.9 1.0
CA B:ILE334 4.7 36.6 1.0
N B:THR328 4.7 43.2 1.0
CA B:ASP329 4.8 55.0 1.0
O B:ASP327 4.9 41.5 1.0
C B:ASP329 5.0 53.5 1.0

Calcium binding site 3 out of 4 in 4i5l

Go back to Calcium Binding Sites List in 4i5l
Calcium binding site 3 out of 4 in the Structural Mechanism of Trimeric PP2A Holoenzyme Involving PR70: Insight For CDC6 Dephosphorylation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Mechanism of Trimeric PP2A Holoenzyme Involving PR70: Insight For CDC6 Dephosphorylation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca701

b:27.5
occ:1.00
 O E:ALA407 2.3 36.2 1.0
OD1 E:ASP401 2.3 33.9 1.0
OD1 E:ASP405 2.3 36.8 1.0
OD1 E:ASP403 2.3 37.7 1.0
OE1 E:GLU412 2.3 42.5 1.0
OE2 E:GLU412 2.3 43.0 1.0
OD2 E:ASP403 2.4 40.2 1.0
O E:HOH838 2.5 29.6 1.0
CD E:GLU412 2.7 41.3 1.0
CG E:ASP403 2.7 36.5 1.0
CG E:ASP405 3.1 34.5 1.0
OD2 E:ASP405 3.4 36.4 1.0
C E:ALA407 3.5 34.1 1.0
CG E:ASP401 3.5 31.7 1.0
CB E:ASP403 4.1 35.8 1.0
N E:ASP405 4.1 31.5 1.0
CG E:GLU412 4.1 41.0 1.0
N E:ALA407 4.2 31.8 1.0
OD2 E:ASP401 4.2 31.3 1.0
N E:ASP403 4.3 33.5 1.0
CB E:ASP405 4.3 32.9 1.0
CA E:ALA407 4.4 33.5 1.0
N E:LEU408 4.5 34.6 1.0
N E:GLY404 4.5 31.9 1.0
CA E:ASP401 4.5 31.2 1.0
C E:ASP401 4.6 31.7 1.0
N E:LEU402 4.6 31.7 1.0
N E:SER409 4.6 35.7 1.0
CA E:LEU408 4.6 34.6 1.0
CB E:ASP401 4.6 31.4 1.0
CA E:ASP405 4.6 32.4 1.0
CA E:ASP403 4.7 33.8 1.0
N E:GLY406 4.7 31.6 1.0
O E:HOH841 4.7 33.4 1.0
OG E:SER409 4.7 35.4 1.0
C E:ASP403 4.9 32.7 1.0
CB E:ALA407 5.0 32.0 1.0
C E:ASP405 5.0 32.4 1.0

Calcium binding site 4 out of 4 in 4i5l

Go back to Calcium Binding Sites List in 4i5l
Calcium binding site 4 out of 4 in the Structural Mechanism of Trimeric PP2A Holoenzyme Involving PR70: Insight For CDC6 Dephosphorylation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Mechanism of Trimeric PP2A Holoenzyme Involving PR70: Insight For CDC6 Dephosphorylation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca702

b:48.6
occ:1.00
 OD1 E:ASP329 2.3 70.9 1.0
O E:LEU333 2.3 51.4 1.0
O E:HOH873 2.3 47.1 1.0
OD1 E:ASP327 2.3 54.2 1.0
OD2 E:ASP331 2.3 68.8 1.0
OD2 E:ASP329 2.3 72.7 1.0
CG E:ASP329 2.7 70.9 1.0
OD1 E:ASP331 2.7 67.0 1.0
CG E:ASP331 2.8 65.8 1.0
C E:LEU333 3.5 45.6 1.0
CG E:ASP327 3.6 51.0 1.0
CB E:ASP331 4.1 64.3 1.0
CB E:ASP329 4.2 69.7 1.0
N E:ASP331 4.2 62.7 1.0
N E:LEU333 4.3 48.0 1.0
OD2 E:ASP338 4.3 51.9 1.0
OD2 E:ASP327 4.4 51.6 1.0
CA E:LEU333 4.4 45.8 1.0
CA E:ASP327 4.4 51.6 1.0
CB E:ASP327 4.5 49.5 1.0
N E:ILE334 4.5 43.7 1.0
CA E:ILE334 4.6 41.7 1.0
CA E:ASP331 4.7 61.7 1.0
CB E:LEU333 4.7 45.8 1.0
C E:ASP327 4.7 53.8 1.0
N E:HIS330 4.7 63.8 1.0
N E:ASP329 4.8 66.5 1.0
CG2 E:ILE334 4.9 40.2 1.0
CA E:ASP329 4.9 67.3 1.0
N E:THR328 4.9 57.7 1.0

Reference:

N.Wlodarchak, F.Guo, K.A.Satyshur, L.Jiang, P.D.Jeffrey, T.Sun, V.Stanevich, M.C.Mumby, Y.Xing. Structure of the Ca(2+)-Dependent PP2A Heterotrimer and Insights Into CDC6 Dephosphorylation. Cell Res. V. 23 931 2013.
ISSN: ISSN 1001-0602
PubMed: 23752926
DOI: 10.1038/CR.2013.77
Page generated: Sun Jul 14 08:01:33 2024

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