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Calcium in PDB 4i5n: 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: 4i5n 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) 49.08 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.100, 101.077, 347.164, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 25

Other elements in 4i5n:

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 4i5n). 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: 4i5n:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4i5n

Go back to Calcium Binding Sites List in 4i5n
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:49.5
occ:1.00
 OE1 B:GLU412 2.3 43.3 1.0
OE2 B:GLU412 2.3 40.8 1.0
O B:ALA407 2.3 46.3 1.0
OD1 B:ASP405 2.3 54.6 1.0
OD1 B:ASP403 2.3 53.4 1.0
OD1 B:ASP401 2.3 48.9 1.0
CD B:GLU412 2.4 44.8 1.0
CG B:ASP403 3.1 49.1 1.0
CG B:ASP405 3.3 57.6 1.0
OD2 B:ASP403 3.4 49.8 1.0
C B:ALA407 3.5 47.9 1.0
CG B:ASP401 3.6 47.7 1.0
OD2 B:ASP405 3.8 62.6 1.0
CG B:GLU412 3.9 46.5 1.0
N B:SER409 4.2 46.7 1.0
N B:ASP403 4.3 43.8 1.0
CB B:ASP403 4.3 47.5 1.0
N B:ALA407 4.3 48.9 1.0
CA B:LEU408 4.4 45.2 1.0
N B:ASP405 4.4 54.6 1.0
OD2 B:ASP401 4.4 50.1 1.0
N B:LEU408 4.4 47.6 1.0
CB B:ASP405 4.4 54.0 1.0
CA B:ASP401 4.4 41.4 1.0
CA B:ALA407 4.5 48.5 1.0
CB B:ASP401 4.6 42.8 1.0
C B:ASP401 4.6 43.1 1.0
N B:LEU402 4.6 43.4 1.0
OG B:SER409 4.6 51.7 1.0
N B:GLY404 4.7 53.8 1.0
CA B:ASP403 4.7 46.5 1.0
CB B:SER409 4.8 50.1 1.0
CB B:GLU412 4.8 46.4 1.0
C B:LEU408 4.8 46.1 1.0
CA B:ASP405 4.9 53.6 1.0
N B:GLY406 4.9 47.2 1.0
CB B:ALA407 5.0 50.7 1.0

Calcium binding site 2 out of 4 in 4i5n

Go back to Calcium Binding Sites List in 4i5n
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:56.5
occ:1.00
 OD1 B:ASP331 2.3 67.3 1.0
OD2 B:ASP331 2.3 71.0 1.0
O B:LEU333 2.3 51.0 1.0
O B:HOH723 2.3 52.1 1.0
OD1 B:ASP327 2.3 52.5 1.0
OD2 B:ASP329 2.4 76.3 1.0
CG B:ASP331 2.4 67.0 1.0
OD1 B:ASP329 2.4 85.8 1.0
CG B:ASP329 2.7 78.0 1.0
C B:LEU333 3.6 52.2 1.0
CG B:ASP327 3.6 48.7 1.0
O B:HOH727 3.6 58.4 1.0
CB B:ASP331 3.8 61.9 1.0
N B:ASP331 4.1 65.1 1.0
CB B:ASP329 4.2 72.3 1.0
N B:LEU333 4.4 54.2 1.0
CA B:ASP327 4.4 51.2 1.0
CA B:ASP331 4.4 59.9 1.0
OD2 B:ASP327 4.5 41.7 1.0
CA B:LEU333 4.5 53.6 1.0
CB B:ASP327 4.5 50.1 1.0
N B:ILE334 4.5 52.0 1.0
OD2 B:ASP338 4.5 62.1 1.0
C B:ASP327 4.5 54.4 1.0
CD1 B:ILE334 4.6 64.8 1.0
CA B:ILE334 4.6 51.8 1.0
N B:ASP329 4.7 66.6 1.0
N B:HIS330 4.8 66.2 1.0
CB B:LEU333 4.8 54.6 1.0
O B:ASP327 4.8 49.9 1.0
CA B:ASP329 4.9 67.4 1.0
C B:ASP329 4.9 66.6 1.0
N B:LEU332 4.9 58.3 1.0
C B:ASP331 4.9 57.8 1.0
N B:THR328 4.9 59.9 1.0

Calcium binding site 3 out of 4 in 4i5n

Go back to Calcium Binding Sites List in 4i5n
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:43.5
occ:1.00
 OD1 E:ASP403 2.3 51.6 1.0
OE2 E:GLU412 2.3 41.8 1.0
OE1 E:GLU412 2.3 39.3 1.0
OD2 E:ASP403 2.3 46.0 1.0
O E:ALA407 2.3 46.8 1.0
OD1 E:ASP405 2.4 41.4 1.0
OD1 E:ASP401 2.4 41.1 1.0
CG E:ASP403 2.4 44.5 1.0
CD E:GLU412 2.4 40.6 1.0
O E:HOH815 2.5 42.9 1.0
CG E:ASP405 3.3 42.9 1.0
C E:ALA407 3.6 43.3 1.0
CG E:ASP401 3.6 40.1 1.0
OD2 E:ASP405 3.8 41.2 1.0
CB E:ASP403 3.8 41.8 1.0
CG E:GLU412 3.9 41.0 1.0
N E:ASP403 4.1 41.3 1.0
CB E:ASP405 4.3 42.8 1.0
N E:ALA407 4.3 42.8 1.0
N E:ASP405 4.3 43.3 1.0
N E:SER409 4.4 44.4 1.0
OD2 E:ASP401 4.4 39.8 1.0
CA E:ASP403 4.5 40.3 1.0
CA E:ASP401 4.5 37.5 1.0
CA E:ALA407 4.5 43.0 1.0
N E:LEU408 4.5 41.4 1.0
C E:ASP401 4.5 37.5 1.0
CA E:LEU408 4.6 41.0 1.0
CB E:ASP401 4.6 36.9 1.0
N E:GLY404 4.7 40.0 1.0
N E:LEU402 4.7 38.7 1.0
CA E:ASP405 4.8 43.7 1.0
CB E:GLU412 4.8 41.0 1.0
OG E:SER409 4.9 46.4 1.0
C E:ASP403 4.9 42.2 1.0
O E:ASP401 4.9 36.5 1.0
N E:GLY406 5.0 45.8 1.0
CB E:SER409 5.0 46.9 1.0

Calcium binding site 4 out of 4 in 4i5n

Go back to Calcium Binding Sites List in 4i5n
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:68.8
occ:1.00
 OD1 E:ASP329 2.3 88.0 1.0
OD2 E:ASP329 2.3 83.0 1.0
OD1 E:ASP327 2.3 68.7 1.0
O E:LEU333 2.3 60.0 1.0
CG E:ASP329 2.3 85.0 1.0
OD2 E:ASP331 2.4 76.7 1.0
OD1 E:ASP331 2.4 78.6 1.0
O E:HOH824 2.6 79.5 1.0
CG E:ASP331 2.7 73.3 1.0
C E:LEU333 3.4 58.7 1.0
CG E:ASP327 3.5 69.4 1.0
CB E:ASP329 3.7 79.5 1.0
CB E:ASP331 4.1 68.1 1.0
N E:ASP331 4.2 68.3 1.0
OD2 E:ASP338 4.2 59.6 1.0
OD2 E:ASP327 4.3 66.5 1.0
N E:LEU333 4.3 62.5 1.0
CA E:ASP329 4.3 75.6 1.0
CA E:LEU333 4.3 59.3 1.0
C E:ASP329 4.3 74.8 1.0
N E:ILE334 4.4 57.0 1.0
N E:ASP329 4.4 78.8 1.0
N E:HIS330 4.4 76.6 1.0
CA E:ASP327 4.4 66.9 1.0
CA E:ILE334 4.5 56.5 1.0
CG2 E:ILE334 4.5 58.4 1.0
CB E:ASP327 4.5 67.2 1.0
CB E:LEU333 4.6 58.5 1.0
CA E:ASP331 4.7 69.1 1.0
O E:ASP329 4.7 73.0 1.0
C E:ASP327 4.8 72.7 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 08:01:45 2024

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