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Manganese 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:

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

Manganese binding site 1 out of 4 in 4i5n

Go back to Manganese Binding Sites List in 4i5n
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:Mn501

b:52.5
occ:1.00
 OD2 C:ASP85 1.9 49.3 1.0
OD2 C:ASP57 2.0 49.6 1.0
O C:HOH634 2.1 38.3 1.0
O C:HOH611 2.1 31.8 1.0
NE2 C:HIS59 2.1 50.5 1.0
MN C:MN502 2.8 43.0 1.0
CG C:ASP85 2.9 41.8 1.0
CE1 C:HIS59 2.9 48.1 1.0
CG C:ASP57 3.1 45.7 1.0
CD2 C:HIS59 3.3 46.3 1.0
CB C:ASP85 3.4 39.4 1.0
O H:HOH101 3.4 23.4 1.0
O C:HIS241 3.9 46.0 1.0
OD1 C:ASP57 3.9 44.6 1.0
OD1 C:ASP85 3.9 44.3 1.0
CD2 C:HIS118 4.0 47.4 1.0
OXT H:FGA6 4.0 78.2 1.0
ND1 C:HIS59 4.1 45.9 1.0
CB C:ASP57 4.1 43.5 1.0
CE1 C:HIS167 4.2 38.4 1.0
NE2 C:HIS118 4.2 47.5 1.0
NE2 C:HIS167 4.2 40.2 1.0
CG C:HIS59 4.3 42.0 1.0
OD1 C:ASN117 4.3 44.9 1.0
ND1 C:HIS241 4.3 52.7 1.0
CA C:HIS241 4.4 48.0 1.0
C C:HIS241 4.5 47.4 1.0
OH C:TYR265 4.6 62.0 1.0
O H:FGA6 4.7 85.5 1.0
C H:FGA6 4.8 81.3 1.0
CE1 C:PHE260 4.9 37.0 1.0
CG C:HIS118 4.9 47.2 1.0
CA C:ASP85 4.9 38.5 1.0

Manganese binding site 2 out of 4 in 4i5n

Go back to Manganese Binding Sites List in 4i5n
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:Mn502

b:43.0
occ:1.00
 OD1 C:ASN117 1.9 44.9 1.0
OD2 C:ASP85 2.0 49.3 1.0
O C:HOH634 2.1 38.3 1.0
NE2 C:HIS167 2.1 40.2 1.0
ND1 C:HIS241 2.1 52.7 1.0
MN C:MN501 2.8 52.5 1.0
CE1 C:HIS241 2.8 54.5 1.0
CE1 C:HIS167 2.9 38.4 1.0
CG C:ASN117 3.0 47.6 1.0
CG C:ASP85 3.1 41.8 1.0
CG C:HIS241 3.2 51.6 1.0
CD2 C:HIS167 3.2 39.4 1.0
ND2 C:ASN117 3.4 47.5 1.0
OD1 C:ASP85 3.5 44.3 1.0
O H:HOH101 3.5 23.4 1.0
CA C:HIS241 3.5 48.0 1.0
CB C:HIS241 3.8 49.0 1.0
OD2 C:ASP57 3.8 49.6 1.0
O C:HIS241 3.9 46.0 1.0
NE2 C:HIS241 4.0 51.3 1.0
ND1 C:HIS167 4.1 38.8 1.0
CD2 C:HIS241 4.2 51.6 1.0
C C:HIS241 4.2 47.4 1.0
CD2 C:HIS118 4.2 47.4 1.0
CG C:HIS167 4.3 37.7 1.0
CB C:ASN117 4.3 44.8 1.0
N C:ASN117 4.4 44.8 1.0
CB C:ASP85 4.4 39.4 1.0
O C:HOH611 4.5 31.8 1.0
N C:HIS241 4.5 51.5 1.0
CG C:ASP57 4.6 45.7 1.0
OD1 C:ASP57 4.6 44.6 1.0
NE2 C:HIS59 4.7 50.5 1.0
NE2 C:HIS118 4.8 47.5 1.0
O C:LEU199 4.9 42.1 1.0
CA C:ASN117 4.9 45.5 1.0

Manganese binding site 3 out of 4 in 4i5n

Go back to Manganese Binding Sites List in 4i5n
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:Mn601

b:41.7
occ:1.00
 OD1 F:ASN117 1.9 35.7 1.0
OD2 F:ASP85 2.0 46.6 1.0
O F:HOH731 2.0 52.5 1.0
ND1 F:HIS241 2.1 43.2 1.0
NE2 F:HIS167 2.1 38.4 1.0
MN F:MN602 2.8 53.8 1.0
CG F:ASN117 2.9 35.5 1.0
CE1 F:HIS241 2.9 45.0 1.0
CE1 F:HIS167 3.1 37.1 1.0
CG F:ASP85 3.1 38.9 1.0
CD2 F:HIS167 3.1 39.8 1.0
CG F:HIS241 3.1 43.5 1.0
ND2 F:ASN117 3.3 35.8 1.0
O F:HOH703 3.4 35.1 1.0
CA F:HIS241 3.6 43.3 1.0
OD1 F:ASP85 3.6 38.9 1.0
OD1 F:ASP57 3.6 49.4 1.0
CB F:HIS241 3.6 43.8 1.0
O F:HIS241 4.0 49.3 1.0
NE2 F:HIS241 4.1 41.7 1.0
CD2 F:HIS118 4.2 37.5 1.0
ND1 F:HIS167 4.2 35.4 1.0
CD2 F:HIS241 4.2 43.4 1.0
CG F:HIS167 4.2 37.0 1.0
CB F:ASN117 4.3 34.9 1.0
C F:HIS241 4.3 45.3 1.0
CB F:ASP85 4.3 37.3 1.0
O F:HOH728 4.4 34.4 1.0
N F:ASN117 4.5 34.6 1.0
CG F:ASP57 4.6 47.8 1.0
N F:HIS241 4.6 40.3 1.0
OD2 F:ASP57 4.6 63.4 1.0
NE2 F:HIS118 4.7 38.4 1.0
NE2 F:HIS59 4.8 42.4 1.0
O F:LEU199 4.8 41.5 1.0
CA F:ASN117 4.9 34.7 1.0

Manganese binding site 4 out of 4 in 4i5n

Go back to Manganese Binding Sites List in 4i5n
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:Mn602

b:53.8
occ:1.00
 OD2 F:ASP85 2.0 46.6 1.0
OD1 F:ASP57 2.1 49.4 1.0
OD2 F:ASP57 2.1 63.4 1.0
NE2 F:HIS59 2.2 42.4 1.0
O F:HOH728 2.2 34.4 1.0
O F:HOH731 2.4 52.5 1.0
CG F:ASP57 2.5 47.8 1.0
MN F:MN601 2.8 41.7 1.0
CG F:ASP85 2.9 38.9 1.0
CE1 F:HIS59 3.0 40.6 1.0
CB F:ASP85 3.3 37.3 1.0
CD2 F:HIS59 3.3 38.9 1.0
O F:HOH703 3.5 35.1 1.0
NE2 F:HIS167 3.9 38.4 1.0
CE1 F:HIS167 3.9 37.1 1.0
CB F:ASP57 4.0 44.6 1.0
OD1 F:ASP85 4.1 38.9 1.0
CD2 F:HIS118 4.2 37.5 1.0
ND1 F:HIS59 4.2 36.6 1.0
CA F:HIS241 4.2 43.3 1.0
CG F:HIS59 4.4 36.6 1.0
OD1 F:ASN117 4.4 35.7 1.0
ND1 F:HIS241 4.4 43.2 1.0
O F:HIS241 4.4 49.3 1.0
NE2 F:HIS118 4.4 38.4 1.0
OXT G:FGA6 4.4 63.4 1.0
C F:HIS241 4.6 45.3 1.0
CE1 F:PHE260 4.7 34.6 1.0
CA F:ASP85 4.8 36.7 1.0
OH F:TYR265 4.9 46.0 1.0
CA F:ASP57 4.9 40.1 1.0
N F:HIS241 4.9 40.3 1.0
O G:FGA6 4.9 64.3 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 19:46:56 2024

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