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Manganese 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:

Calcium (Ca) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Structural Mechanism of Trimeric PP2A Holoenzyme Involving PR70: Insight For CDC6 Dephosphorylation, PDB code: 4i5l:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4i5l

Go back to Manganese Binding Sites List in 4i5l
Manganese 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 Manganese with other atoms in the Mn 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
C:Mn401

b:34.7
occ:1.00
 O C:HOH559 1.9 28.3 1.0
OD1 C:ASN117 2.0 29.2 1.0
NE2 C:HIS167 2.1 26.7 1.0
ND1 C:HIS241 2.2 28.1 1.0
OD2 C:ASP85 2.4 26.0 1.0
CE1 C:HIS167 3.0 26.3 1.0
CE1 C:HIS241 3.0 29.1 1.0
CG C:ASN117 3.1 28.5 1.0
CD2 C:HIS167 3.1 26.6 1.0
CG C:ASP85 3.2 25.1 1.0
MN C:MN402 3.3 40.9 1.0
CG C:HIS241 3.3 28.1 1.0
O C:HOH532 3.3 26.3 1.0
OD1 C:ASP85 3.5 25.1 1.0
CA C:HIS241 3.5 27.1 1.0
ND2 C:ASN117 3.6 28.7 1.0
CB C:HIS241 3.7 27.3 1.0
OD2 C:ASP57 3.9 25.6 1.0
O C:HIS241 4.0 28.9 1.0
ND1 C:HIS167 4.1 26.0 1.0
CD2 C:HIS118 4.2 25.4 1.0
NE2 C:HIS241 4.2 29.6 1.0
CG C:HIS167 4.2 26.9 1.0
CB C:ASN117 4.3 28.3 1.0
C C:HIS241 4.3 27.9 1.0
N C:ASN117 4.3 25.9 1.0
CD2 C:HIS241 4.4 29.2 1.0
CB C:ASP85 4.5 23.7 1.0
N C:HIS241 4.6 26.0 1.0
O C:LEU199 4.7 27.8 1.0
CG C:ASP57 4.8 24.7 1.0
NE2 C:HIS118 4.8 26.1 1.0
CA C:ASN117 4.8 28.0 1.0
O H:HOH104 4.8 38.6 1.0
OD1 C:ASP57 4.9 25.2 1.0

Manganese binding site 2 out of 4 in 4i5l

Go back to Manganese Binding Sites List in 4i5l
Manganese 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 Manganese with other atoms in the Mn 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
C:Mn402

b:40.9
occ:1.00
 OD2 C:ASP57 2.1 25.6 1.0
OD2 C:ASP85 2.1 26.0 1.0
O C:HOH559 2.1 28.3 1.0
NE2 C:HIS59 2.2 24.2 1.0
O H:HOH104 2.2 38.6 1.0
CE1 C:HIS59 3.1 24.2 1.0
CG C:ASP85 3.1 25.1 1.0
CG C:ASP57 3.2 24.7 1.0
CD2 C:HIS59 3.2 23.7 1.0
MN C:MN401 3.3 34.7 1.0
CB C:ASP85 3.5 23.7 1.0
CB C:ASP57 3.8 23.4 1.0
O C:HOH532 3.9 26.3 1.0
O C:HIS241 4.1 28.9 1.0
OD1 C:ASP57 4.1 25.2 1.0
CD2 C:HIS118 4.1 25.4 1.0
ND1 C:HIS59 4.2 24.2 1.0
OD1 C:ASP85 4.3 25.1 1.0
NE2 C:HIS118 4.3 26.1 1.0
CG C:HIS59 4.3 23.9 1.0
CE1 C:HIS167 4.4 26.3 1.0
NE2 C:HIS167 4.5 26.7 1.0
OH C:TYR265 4.5 31.4 1.0
OXT H:FGA6 4.5 42.1 1.0
CE1 C:PHE260 4.5 23.3 1.0
CA C:HIS241 4.6 27.1 1.0
OD1 C:ASN117 4.6 29.2 1.0
C C:HIS241 4.7 27.9 1.0
O H:FGA6 4.8 41.2 1.0
ND1 C:HIS241 4.9 28.1 1.0

Manganese binding site 3 out of 4 in 4i5l

Go back to Manganese Binding Sites List in 4i5l
Manganese 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 Manganese with other atoms in the Mn 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
F:Mn401

b:34.0
occ:1.00
 OD1 F:ASN117 1.9 34.2 1.0
O F:HOH547 1.9 25.5 1.0
OD2 F:ASP85 2.0 38.4 1.0
NE2 F:HIS167 2.1 33.2 1.0
ND1 F:HIS241 2.1 39.5 1.0
CE1 F:HIS241 2.9 38.1 1.0
CE1 F:HIS167 3.0 30.2 1.0
CG F:ASN117 3.0 32.4 1.0
CG F:ASP85 3.0 30.6 1.0
MN F:MN402 3.1 43.8 1.0
CD2 F:HIS167 3.1 31.1 1.0
CG F:HIS241 3.2 37.4 1.0
O F:HOH548 3.4 34.6 1.0
OD1 F:ASP85 3.4 30.4 1.0
ND2 F:ASN117 3.5 32.2 1.0
CA F:HIS241 3.6 34.8 1.0
CB F:HIS241 3.7 35.5 1.0
OD2 F:ASP57 3.8 38.0 1.0
O F:HIS241 4.0 36.8 1.0
NE2 F:HIS241 4.1 38.8 1.0
CD2 F:HIS118 4.1 30.4 1.0
ND1 F:HIS167 4.1 29.2 1.0
CG F:HIS167 4.2 30.2 1.0
CD2 F:HIS241 4.2 38.8 1.0
CB F:ASN117 4.3 31.6 1.0
C F:HIS241 4.3 36.0 1.0
N F:ASN117 4.3 28.6 1.0
CB F:ASP85 4.4 29.6 1.0
O F:HOH546 4.6 28.3 1.0
N F:HIS241 4.6 33.2 1.0
NE2 F:HIS118 4.7 31.0 1.0
CG F:ASP57 4.7 34.8 1.0
O F:LEU199 4.7 32.3 1.0
CA F:ASN117 4.8 29.8 1.0
OD1 F:ASP57 4.9 34.6 1.0
NE2 F:HIS59 4.9 40.3 1.0

Manganese binding site 4 out of 4 in 4i5l

Go back to Manganese Binding Sites List in 4i5l
Manganese 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 Manganese with other atoms in the Mn 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
F:Mn402

b:43.8
occ:1.00
 O F:HOH546 1.9 28.3 1.0
OD2 F:ASP57 1.9 38.0 1.0
OD2 F:ASP85 2.0 38.4 1.0
NE2 F:HIS59 2.1 40.3 1.0
O F:HOH547 2.4 25.5 1.0
CG F:ASP85 2.9 30.6 1.0
CE1 F:HIS59 3.0 37.3 1.0
MN F:MN401 3.1 34.0 1.0
CG F:ASP57 3.1 34.8 1.0
CD2 F:HIS59 3.2 36.1 1.0
CB F:ASP85 3.4 29.6 1.0
CB F:ASP57 3.8 33.5 1.0
O F:HOH548 3.9 34.6 1.0
CD2 F:HIS118 4.0 30.4 1.0
OD1 F:ASP85 4.0 30.4 1.0
OD1 F:ASP57 4.0 34.6 1.0
ND1 F:HIS59 4.1 35.8 1.0
NE2 F:HIS118 4.2 31.0 1.0
O F:HIS241 4.2 36.8 1.0
CE1 F:HIS167 4.2 30.2 1.0
CG F:HIS59 4.3 35.0 1.0
NE2 F:HIS167 4.3 33.2 1.0
OXT G:FGA6 4.3 50.1 1.0
OD1 F:ASN117 4.5 34.2 1.0
CA F:HIS241 4.5 34.8 1.0
OH F:TYR265 4.5 38.1 1.0
CE1 F:PHE260 4.6 28.6 1.0
ND1 F:HIS241 4.7 39.5 1.0
C F:HIS241 4.7 36.0 1.0
CA F:ASP85 4.9 28.0 1.0
CG F:HIS118 5.0 29.9 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: Sat Oct 5 19:46:50 2024

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