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Manganese in PDB 3egh: Crystal Structure of A Complex Between Protein Phosphatase 1 Alpha (PP1), the PP1 Binding and Pdz Domains of Spinophilin and the Small Natural Molecular Toxin Nodularin-R

Enzymatic activity of Crystal Structure of A Complex Between Protein Phosphatase 1 Alpha (PP1), the PP1 Binding and Pdz Domains of Spinophilin and the Small Natural Molecular Toxin Nodularin-R

All present enzymatic activity of Crystal Structure of A Complex Between Protein Phosphatase 1 Alpha (PP1), the PP1 Binding and Pdz Domains of Spinophilin and the Small Natural Molecular Toxin Nodularin-R:
3.1.3.16;

Protein crystallography data

The structure of Crystal Structure of A Complex Between Protein Phosphatase 1 Alpha (PP1), the PP1 Binding and Pdz Domains of Spinophilin and the Small Natural Molecular Toxin Nodularin-R, PDB code: 3egh was solved by M.J.Ragusa, R.Page, W.Peti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 119.409, 84.426, 109.314, 90.00, 93.58, 90.00
R / Rfree (%) 19.2 / 23.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of A Complex Between Protein Phosphatase 1 Alpha (PP1), the PP1 Binding and Pdz Domains of Spinophilin and the Small Natural Molecular Toxin Nodularin-R (pdb code 3egh). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of A Complex Between Protein Phosphatase 1 Alpha (PP1), the PP1 Binding and Pdz Domains of Spinophilin and the Small Natural Molecular Toxin Nodularin-R, PDB code: 3egh:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3egh

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Manganese binding site 1 out of 4 in the Crystal Structure of A Complex Between Protein Phosphatase 1 Alpha (PP1), the PP1 Binding and Pdz Domains of Spinophilin and the Small Natural Molecular Toxin Nodularin-R


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of A Complex Between Protein Phosphatase 1 Alpha (PP1), the PP1 Binding and Pdz Domains of Spinophilin and the Small Natural Molecular Toxin Nodularin-R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:23.9
occ:0.75
 OD2 A:ASP64 2.1 30.3 1.0
OD2 A:ASP92 2.2 26.0 1.0
O A:HOH508 2.2 28.7 1.0
O E:HOH103 2.2 38.2 1.0
NE2 A:HIS66 2.3 29.1 1.0
CE1 A:HIS66 3.1 27.0 1.0
MN A:MN405 3.2 27.3 1.0
CG A:ASP64 3.2 29.1 1.0
CG A:ASP92 3.2 27.1 1.0
CD2 A:HIS66 3.3 28.1 1.0
CB A:ASP92 3.6 26.5 1.0
O E:HOH101 3.8 32.0 1.0
CB A:ASP64 4.0 28.0 1.0
OD1 A:ASP64 4.1 28.9 1.0
O E:FGA4 4.1 36.4 0.8
CD2 A:HIS125 4.2 26.8 1.0
ND1 A:HIS66 4.3 29.9 1.0
OD1 A:ASP92 4.3 26.4 1.0
NE2 A:HIS125 4.3 28.5 1.0
O A:HIS248 4.3 26.8 1.0
CG A:HIS66 4.4 28.6 1.0
NE2 A:HIS173 4.5 28.0 1.0
CE2 A:PHE267 4.5 26.5 1.0
CE1 A:HIS173 4.5 22.5 1.0
CA A:HIS248 4.5 26.7 1.0
OH A:TYR272 4.6 30.4 1.0
OD1 A:ASN124 4.6 22.5 1.0
C A:HIS248 4.7 27.7 1.0
ND1 A:HIS248 4.9 26.9 1.0

Manganese binding site 2 out of 4 in 3egh

Go back to Manganese Binding Sites List in 3egh
Manganese binding site 2 out of 4 in the Crystal Structure of A Complex Between Protein Phosphatase 1 Alpha (PP1), the PP1 Binding and Pdz Domains of Spinophilin and the Small Natural Molecular Toxin Nodularin-R


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of A Complex Between Protein Phosphatase 1 Alpha (PP1), the PP1 Binding and Pdz Domains of Spinophilin and the Small Natural Molecular Toxin Nodularin-R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:27.3
occ:1.00
 O A:HOH508 1.9 28.7 1.0
OD1 A:ASN124 2.0 22.5 1.0
NE2 A:HIS173 2.2 28.0 1.0
OD2 A:ASP92 2.2 26.0 1.0
ND1 A:HIS248 2.3 26.9 1.0
CG A:ASN124 3.1 25.6 1.0
CE1 A:HIS173 3.1 22.5 1.0
CE1 A:HIS248 3.1 29.1 1.0
CG A:ASP92 3.2 27.1 1.0
CD2 A:HIS173 3.2 24.4 1.0
MN A:MN404 3.2 23.9 0.8
O E:HOH101 3.3 32.0 1.0
CG A:HIS248 3.5 27.8 1.0
OD1 A:ASP92 3.5 26.4 1.0
ND2 A:ASN124 3.7 24.3 1.0
CA A:HIS248 3.7 26.7 1.0
CB A:HIS248 3.9 26.8 1.0
OD2 A:ASP64 4.0 30.3 1.0
CD2 A:HIS125 4.1 26.8 1.0
O A:HIS248 4.1 26.8 1.0
ND1 A:HIS173 4.3 26.4 1.0
CB A:ASN124 4.3 26.1 1.0
CG A:HIS173 4.3 26.3 1.0
NE2 A:HIS248 4.4 29.8 1.0
N A:ASN124 4.4 27.1 1.0
CB A:ASP92 4.4 26.5 1.0
C A:HIS248 4.4 27.7 1.0
CD2 A:HIS248 4.5 29.3 1.0
N A:HIS248 4.6 26.6 1.0
O A:LEU205 4.6 26.5 1.0
NE2 A:HIS125 4.7 28.5 1.0
O E:HOH103 4.8 38.2 1.0
CG A:ASP64 4.8 29.1 1.0
CA A:ASN124 4.9 26.6 1.0
OD1 A:ASP64 5.0 28.9 1.0

Manganese binding site 3 out of 4 in 3egh

Go back to Manganese Binding Sites List in 3egh
Manganese binding site 3 out of 4 in the Crystal Structure of A Complex Between Protein Phosphatase 1 Alpha (PP1), the PP1 Binding and Pdz Domains of Spinophilin and the Small Natural Molecular Toxin Nodularin-R


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of A Complex Between Protein Phosphatase 1 Alpha (PP1), the PP1 Binding and Pdz Domains of Spinophilin and the Small Natural Molecular Toxin Nodularin-R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:21.1
occ:0.75
 O B:HOH514 1.9 25.1 1.0
OD2 B:ASP64 2.0 33.0 1.0
O F:HOH101 2.2 29.8 1.0
NE2 B:HIS66 2.2 31.3 1.0
OD2 B:ASP92 2.3 25.9 1.0
CG B:ASP64 3.1 30.3 1.0
MN B:MN402 3.2 22.2 1.0
CD2 B:HIS66 3.2 26.8 1.0
CE1 B:HIS66 3.2 28.9 1.0
CG B:ASP92 3.3 26.4 1.0
CB B:ASP92 3.7 25.0 1.0
O F:HOH102 3.7 23.3 1.0
CB B:ASP64 4.0 26.9 1.0
OD1 B:ASP64 4.0 33.3 1.0
CD2 B:HIS125 4.3 23.6 1.0
O B:HIS248 4.3 27.7 1.0
ND1 B:HIS66 4.3 29.1 1.0
CG B:HIS66 4.3 29.6 1.0
CE1 B:HIS173 4.4 24.6 1.0
OD1 B:ASP92 4.4 25.4 1.0
NE2 B:HIS173 4.4 27.9 1.0
CE2 B:PHE267 4.5 25.6 1.0
NE2 B:HIS125 4.5 25.1 1.0
O F:FGA4 4.5 31.4 0.8
OH B:TYR272 4.5 35.3 1.0
CA B:HIS248 4.5 26.4 1.0
OD1 B:ASN124 4.7 25.9 1.0
C B:HIS248 4.7 27.0 1.0
ND1 B:HIS248 4.8 25.5 1.0

Manganese binding site 4 out of 4 in 3egh

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Manganese binding site 4 out of 4 in the Crystal Structure of A Complex Between Protein Phosphatase 1 Alpha (PP1), the PP1 Binding and Pdz Domains of Spinophilin and the Small Natural Molecular Toxin Nodularin-R


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of A Complex Between Protein Phosphatase 1 Alpha (PP1), the PP1 Binding and Pdz Domains of Spinophilin and the Small Natural Molecular Toxin Nodularin-R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:22.2
occ:1.00
 OD1 B:ASN124 2.0 25.9 1.0
NE2 B:HIS173 2.1 27.9 1.0
O B:HOH514 2.2 25.1 1.0
OD2 B:ASP92 2.2 25.9 1.0
ND1 B:HIS248 2.3 25.5 1.0
CE1 B:HIS248 3.0 20.9 1.0
CE1 B:HIS173 3.0 24.6 1.0
O F:HOH102 3.0 23.3 1.0
CG B:ASN124 3.1 26.6 1.0
MN B:MN401 3.2 21.1 0.8
CG B:ASP92 3.2 26.4 1.0
CD2 B:HIS173 3.2 24.5 1.0
CG B:HIS248 3.4 24.8 1.0
OD1 B:ASP92 3.6 25.4 1.0
ND2 B:ASN124 3.7 27.0 1.0
CA B:HIS248 3.7 26.4 1.0
CB B:HIS248 3.9 26.1 1.0
OD2 B:ASP64 4.0 33.0 1.0
O B:HIS248 4.2 27.7 1.0
ND1 B:HIS173 4.2 26.3 1.0
NE2 B:HIS248 4.2 23.8 1.0
CD2 B:HIS125 4.2 23.6 1.0
CG B:HIS173 4.3 26.0 1.0
CB B:ASN124 4.4 24.8 1.0
CB B:ASP92 4.4 25.0 1.0
N B:ASN124 4.4 25.8 1.0
CD2 B:HIS248 4.5 25.2 1.0
C B:HIS248 4.5 27.0 1.0
O B:LEU205 4.6 27.3 1.0
N B:HIS248 4.7 26.8 1.0
O F:HOH101 4.8 29.8 1.0
CG B:ASP64 4.8 30.3 1.0
NE2 B:HIS125 4.8 25.1 1.0
OD1 B:ASP64 4.9 33.3 1.0
CA B:ASN124 4.9 25.8 1.0

Reference:

M.J.Ragusa, B.Dancheck, D.A.Critton, A.C.Nairn, R.Page, W.Peti. Spinophilin Directs Protein Phosphatase 1 Specificity By Blocking Substrate Binding Sites. Nat.Struct.Mol.Biol. V. 17 459 2010.
ISSN: ISSN 1545-9993
PubMed: 20305656
DOI: 10.1038/NSMB.1786
Page generated: Sat Oct 5 16:12:58 2024

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