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Manganese in PDB 2bcd: X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound

Enzymatic activity of X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound

All present enzymatic activity of X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound:
3.1.3.16;

Protein crystallography data

The structure of X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound, PDB code: 2bcd was solved by J.T.Maynes, H.A.Luu, M.M.Cherney, R.J.Andersen, D.Williams, C.F.Holmes, M.N.James, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.75 / 2.10
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.955, 100.955, 63.485, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 26.4

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound (pdb code 2bcd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound, PDB code: 2bcd:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 2bcd

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Manganese binding site 1 out of 8 in the X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn400

b:13.0
occ:1.00
 OD1 A:ASN124 1.9 13.7 1.0
OD2 A:ASP92 2.0 13.7 1.0
NE2 A:HIS173 2.0 10.5 1.0
ND1 A:HIS248 2.1 12.2 1.0
CE1 A:HIS248 2.9 13.2 1.0
CG A:ASP92 3.0 11.0 1.0
CE1 A:HIS173 3.0 9.9 1.0
CD2 A:HIS173 3.1 10.6 1.0
CG A:ASN124 3.1 10.9 1.0
CG A:HIS248 3.2 12.9 1.0
MN A:MN401 3.3 20.9 1.0
OD1 A:ASP92 3.3 13.4 1.0
O A:HOH608 3.5 13.1 1.0
CA A:HIS248 3.6 14.8 1.0
ND2 A:ASN124 3.7 12.9 1.0
CB A:HIS248 3.7 14.5 1.0
OD2 A:ASP64 3.9 13.1 1.0
O A:HIS248 4.0 17.1 1.0
NE2 A:HIS248 4.1 11.4 1.0
ND1 A:HIS173 4.1 8.2 1.0
CG A:HIS173 4.2 9.9 1.0
CD2 A:HIS125 4.2 11.5 1.0
CD2 A:HIS248 4.3 11.9 1.0
CB A:ASN124 4.3 10.0 1.0
C A:HIS248 4.3 16.4 1.0
CB A:ASP92 4.4 11.6 1.0
N A:ASN124 4.4 9.5 1.0
N A:HIS248 4.6 14.9 1.0
O A:LEU205 4.7 11.6 1.0
CG A:ASP64 4.8 14.9 1.0
O A:HOH638 4.8 16.8 1.0
NE2 A:HIS125 4.8 12.8 1.0
CA A:ASN124 4.9 10.1 1.0
OD1 A:ASP64 4.9 13.2 1.0
NE2 A:HIS66 5.0 13.6 1.0

Manganese binding site 2 out of 8 in 2bcd

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Manganese binding site 2 out of 8 in the X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:20.9
occ:1.00
 OD2 A:ASP64 1.9 13.1 1.0
OD2 A:ASP92 2.0 13.7 1.0
NE2 A:HIS66 2.1 13.6 1.0
O A:HOH638 2.1 16.8 1.0
CG A:ASP92 3.0 11.0 1.0
CE1 A:HIS66 3.0 14.4 1.0
CD2 A:HIS66 3.1 12.2 1.0
CG A:ASP64 3.1 14.9 1.0
MN A:MN400 3.3 13.0 1.0
CB A:ASP92 3.5 11.6 1.0
CB A:ASP64 3.9 14.8 1.0
OD1 A:ASP64 4.1 13.2 1.0
O A:HOH608 4.1 13.1 1.0
OD1 A:ASP92 4.1 13.4 1.0
ND1 A:HIS66 4.2 13.8 1.0
O A:HIS248 4.2 17.1 1.0
CG A:HIS66 4.2 13.9 1.0
CD2 A:HIS125 4.2 11.5 1.0
CE1 A:PHE267 4.4 14.5 1.0
NE2 A:HIS125 4.5 12.8 1.0
CA A:HIS248 4.5 14.8 1.0
NE2 A:HIS173 4.5 10.5 1.0
CE1 A:HIS173 4.5 9.9 1.0
OH A:TYR272 4.6 21.6 1.0
C A:HIS248 4.6 16.4 1.0
OD1 A:ASN124 4.7 13.7 1.0
ND1 A:HIS248 4.8 12.2 1.0
O A:HOH673 4.8 34.4 1.0
O B:FGA4 4.9 28.1 1.0
CZ A:PHE267 4.9 16.7 1.0

Manganese binding site 3 out of 8 in 2bcd

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Manganese binding site 3 out of 8 in the X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:53.2
occ:1.00
 N A:ILE146 3.6 19.4 1.0
CB A:ASN145 3.8 20.2 1.0
CB A:ILE146 4.1 20.4 1.0
N A:LYS147 4.1 20.0 1.0
CA A:ILE146 4.2 20.5 1.0
C A:ASN145 4.5 19.7 1.0
CA A:ASN145 4.6 19.8 1.0
C A:ILE146 4.6 20.2 1.0
CG A:ASN145 4.7 19.9 1.0
OD1 A:ASN145 4.8 22.8 1.0
CG1 A:ILE146 4.8 20.2 1.0
CB A:LYS147 4.9 20.8 1.0

Manganese binding site 4 out of 8 in 2bcd

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Manganese binding site 4 out of 8 in the X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:68.4
occ:0.50
 O A:HOH668 3.5 37.0 1.0
CB A:SER22 3.8 38.1 1.0
OG A:SER22 3.9 38.6 1.0
CA A:SER22 3.9 37.8 1.0
N A:LYS23 4.0 36.7 1.0
NZ A:LYS26 4.3 38.5 1.0
C A:SER22 4.5 37.0 1.0
CD A:LYS26 4.6 33.6 1.0
CB A:LYS23 4.9 36.5 1.0

Manganese binding site 5 out of 8 in 2bcd

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Manganese binding site 5 out of 8 in the X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:75.3
occ:1.00
 N A:MET183 3.4 33.6 1.0
O A:HOH671 3.6 58.4 1.0
CB A:MET183 3.6 34.1 1.0
CA A:MET183 4.0 34.3 1.0
N A:GLU184 4.1 35.7 1.0
CB A:SER182 4.1 32.9 1.0
CG A:MET183 4.1 34.0 1.0
C A:SER182 4.4 33.1 1.0
NH1 A:ARG187 4.4 41.2 1.0
C A:MET183 4.5 35.3 1.0
CA A:SER182 4.5 32.7 1.0
OG A:SER182 4.7 31.7 1.0

Manganese binding site 6 out of 8 in 2bcd

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Manganese binding site 6 out of 8 in the X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:54.9
occ:1.00
 N A:LYS260 3.6 21.2 1.0
N A:ALA259 3.6 21.3 1.0
O A:HOH633 3.9 23.4 1.0
CA A:ALA259 4.0 21.7 1.0
NZ A:LYS260 4.3 22.8 1.0
NZ A:LYS211 4.3 38.7 1.0
C A:ALA259 4.3 21.2 1.0
C A:PHE258 4.5 22.5 1.0
CA A:LYS260 4.6 20.8 1.0
CA A:PHE258 4.8 23.7 1.0
CG A:LYS260 4.9 21.8 1.0
CD A:LYS260 4.9 24.9 1.0
CG A:LYS211 4.9 35.1 1.0

Manganese binding site 7 out of 8 in 2bcd

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Manganese binding site 7 out of 8 in the X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn406

b:72.2
occ:1.00
 NE A:ARG261 3.8 30.3 1.0
O A:HOH633 4.0 23.4 1.0
NH2 A:ARG261 4.2 32.6 1.0
CB A:PHE257 4.3 24.2 1.0
CG A:ARG261 4.5 24.5 1.0
CZ A:ARG261 4.5 34.6 1.0
CD A:ARG261 4.7 27.0 1.0

Manganese binding site 8 out of 8 in 2bcd

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Manganese binding site 8 out of 8 in the X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of X-Ray Crystal Structure of Protein Phosphatase-1 with the Marine Toxin Motuporin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn407

b:87.1
occ:1.00
 N A:GLU252 3.9 26.0 1.0
CA A:GLU252 4.0 27.4 1.0
CD2 A:PHE276 4.1 41.4 1.0
CB A:GLU252 4.2 27.7 1.0
C A:VAL251 4.3 24.6 1.0
O A:HOH644 4.4 25.6 1.0
CG A:GLU252 4.5 29.7 1.0
CB A:ASN278 4.6 30.3 1.0
CE2 A:PHE276 4.6 41.1 1.0
CA A:VAL251 4.7 23.7 1.0
O A:VAL250 4.7 20.4 1.0
CG1 A:VAL250 4.8 21.6 1.0
CG A:PHE276 4.9 41.0 1.0
C A:VAL250 4.9 21.3 1.0
N A:VAL251 5.0 22.3 1.0
O A:VAL251 5.0 24.4 1.0

Reference:

J.T.Maynes, H.A.Luu, M.M.Cherney, R.J.Andersen, D.Williams, C.F.Holmes, M.N.James. Crystal Structures of Protein Phosphatase-1 Bound to Motuporin and Dihydromicrocystin-La: Elucidation of the Mechanism of Enzyme Inhibition By Cyanobacterial Toxins. J.Mol.Biol. V. 356 111 2006.
ISSN: ISSN 0022-2836
PubMed: 16343532
DOI: 10.1016/J.JMB.2005.11.019
Page generated: Sat Oct 5 13:32:54 2024

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