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Manganese in PDB 3e7a: Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R

Enzymatic activity of Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R

All present enzymatic activity of Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R:
3.1.3.16;

Protein crystallography data

The structure of Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R, PDB code: 3e7a was solved by M.S.Kelker, R.Page, W.Peti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.57 / 1.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.354, 77.274, 132.444, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 16.9

Other elements in 3e7a:

The structure of Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R also contains other interesting chemical elements:

Iodine (I) 25 atoms
Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R (pdb code 3e7a). 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 Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R, PDB code: 3e7a:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3e7a

Go back to Manganese Binding Sites List in 3e7a
Manganese binding site 1 out of 4 in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural 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 Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:10.9
occ:1.00
 OD2 A:ASP64 2.1 12.5 1.0
O A:HOH669 2.1 11.7 1.0
NE2 A:HIS66 2.2 11.7 1.0
O C:HOH769 2.2 13.2 1.0
OD2 A:ASP92 2.2 11.7 1.0
CD2 A:HIS66 3.1 9.4 1.0
CG A:ASP64 3.2 12.2 1.0
CE1 A:HIS66 3.2 11.5 1.0
MN A:MN403 3.3 10.8 1.0
CG A:ASP92 3.3 11.7 1.0
CB A:ASP92 3.7 11.2 1.0
CB A:ASP64 4.0 10.4 1.0
O C:HOH766 4.0 13.5 1.0
OD1 A:ASP64 4.1 12.0 1.0
O A:HIS248 4.1 12.6 1.0
O C:HOH389 4.2 40.5 1.0
CD2 A:HIS125 4.3 11.7 1.0
ND1 A:HIS66 4.3 9.7 1.0
CG A:HIS66 4.3 10.6 1.0
CE2 A:PHE267 4.3 14.2 1.0
OD1 A:ASP92 4.4 11.3 1.0
OH A:TYR272 4.4 16.0 1.0
NE2 A:HIS125 4.4 11.5 1.0
CA A:HIS248 4.5 10.7 1.0
O C:FGA4 4.5 23.8 1.0
NE2 A:HIS173 4.6 11.5 1.0
C A:HIS248 4.6 12.4 1.0
CE1 A:HIS173 4.6 10.9 1.0
OD1 A:ASN124 4.7 11.7 1.0
ND1 A:HIS248 4.9 10.2 1.0
O C:HOH775 4.9 25.7 1.0
CZ A:PHE267 5.0 12.2 1.0

Manganese binding site 2 out of 4 in 3e7a

Go back to Manganese Binding Sites List in 3e7a
Manganese binding site 2 out of 4 in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural 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 Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:10.8
occ:1.00
 O A:HOH669 2.0 11.7 1.0
OD1 A:ASN124 2.1 11.7 1.0
NE2 A:HIS173 2.2 11.5 1.0
ND1 A:HIS248 2.2 10.2 1.0
OD2 A:ASP92 2.2 11.7 1.0
CE1 A:HIS248 3.1 13.9 1.0
CG A:ASP92 3.2 11.7 1.0
CG A:ASN124 3.2 11.5 1.0
CD2 A:HIS173 3.2 9.9 1.0
CE1 A:HIS173 3.2 10.9 1.0
MN A:MN402 3.3 10.9 1.0
CG A:HIS248 3.3 10.8 1.0
O C:HOH766 3.5 13.5 1.0
OD1 A:ASP92 3.5 11.3 1.0
CA A:HIS248 3.6 10.7 1.0
ND2 A:ASN124 3.7 11.6 1.0
CB A:HIS248 3.7 10.2 1.0
O A:HIS248 4.0 12.6 1.0
OD2 A:ASP64 4.0 12.5 1.0
CD2 A:HIS125 4.2 11.7 1.0
NE2 A:HIS248 4.3 12.0 1.0
ND1 A:HIS173 4.3 11.2 1.0
CG A:HIS173 4.3 9.8 1.0
C A:HIS248 4.3 12.4 1.0
CB A:ASN124 4.4 11.9 1.0
N A:ASN124 4.4 9.1 1.0
CD2 A:HIS248 4.4 11.2 1.0
CB A:ASP92 4.4 11.2 1.0
O A:LEU205 4.6 12.7 1.0
N A:HIS248 4.6 11.2 1.0
CG A:ASP64 4.8 12.2 1.0
NE2 A:HIS125 4.8 11.5 1.0
OD1 A:ASP64 4.8 12.0 1.0
CA A:ASN124 4.9 10.2 1.0
O C:HOH769 5.0 13.2 1.0

Manganese binding site 3 out of 4 in 3e7a

Go back to Manganese Binding Sites List in 3e7a
Manganese binding site 3 out of 4 in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural 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 Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:11.2
occ:1.00
 OD2 B:ASP64 2.1 13.3 1.0
O B:HOH698 2.1 11.7 1.0
O D:HOH724 2.1 12.8 1.0
NE2 B:HIS66 2.2 11.6 1.0
OD2 B:ASP92 2.2 11.4 1.0
CE1 B:HIS66 3.2 12.0 1.0
CD2 B:HIS66 3.2 12.7 1.0
CG B:ASP64 3.2 12.5 1.0
CG B:ASP92 3.3 12.7 1.0
MN B:MN403 3.3 11.0 1.0
CB B:ASP92 3.7 12.8 1.0
O D:HOH720 3.9 12.6 1.0
CB B:ASP64 3.9 12.2 1.0
OD1 B:ASP64 4.1 13.3 1.0
O B:HIS248 4.2 13.7 1.0
CD2 B:HIS125 4.3 11.6 1.0
ND1 B:HIS66 4.3 12.6 1.0
CG B:HIS66 4.3 11.7 1.0
CE1 B:PHE267 4.3 13.1 1.0
OD1 B:ASP92 4.4 11.9 1.0
NE2 B:HIS125 4.4 15.0 1.0
OH B:TYR272 4.4 18.5 1.0
O D:FGA4 4.4 21.2 1.0
CA B:HIS248 4.5 11.9 1.0
NE2 B:HIS173 4.5 12.5 1.0
CE1 B:HIS173 4.6 12.9 1.0
C B:HIS248 4.6 13.4 1.0
OD1 B:ASN124 4.8 11.2 1.0
O D:HOH721 4.8 25.2 1.0
ND1 B:HIS248 4.9 11.7 1.0
CZ B:PHE267 4.9 11.8 1.0

Manganese binding site 4 out of 4 in 3e7a

Go back to Manganese Binding Sites List in 3e7a
Manganese binding site 4 out of 4 in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural 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 Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:11.0
occ:1.00
 O B:HOH698 2.0 11.7 1.0
OD1 B:ASN124 2.1 11.2 1.0
NE2 B:HIS173 2.2 12.5 1.0
OD2 B:ASP92 2.2 11.4 1.0
ND1 B:HIS248 2.2 11.7 1.0
CE1 B:HIS248 3.1 12.3 1.0
CG B:ASP92 3.1 12.7 1.0
CE1 B:HIS173 3.1 12.9 1.0
CD2 B:HIS173 3.2 12.9 1.0
CG B:ASN124 3.2 10.6 1.0
MN B:MN402 3.3 11.2 1.0
CG B:HIS248 3.3 11.8 1.0
O D:HOH720 3.3 12.6 1.0
OD1 B:ASP92 3.5 11.9 1.0
CA B:HIS248 3.6 11.9 1.0
ND2 B:ASN124 3.7 11.0 1.0
CB B:HIS248 3.7 12.5 1.0
OD2 B:ASP64 4.0 13.3 1.0
O B:HIS248 4.0 13.7 1.0
CD2 B:HIS125 4.2 11.6 1.0
ND1 B:HIS173 4.3 10.4 1.0
NE2 B:HIS248 4.3 11.1 1.0
CG B:HIS173 4.3 10.6 1.0
C B:HIS248 4.3 13.4 1.0
N B:ASN124 4.4 11.5 1.0
CB B:ASN124 4.4 12.3 1.0
CD2 B:HIS248 4.4 12.9 1.0
CB B:ASP92 4.4 12.8 1.0
O B:LEU205 4.6 12.2 1.0
N B:HIS248 4.6 12.0 1.0
CG B:ASP64 4.8 12.5 1.0
NE2 B:HIS125 4.8 15.0 1.0
CA B:ASN124 4.9 11.2 1.0
OD1 B:ASP64 4.9 13.3 1.0
O D:HOH724 4.9 12.8 1.0

Reference:

M.S.Kelker, R.Page, W.Peti. Crystal Structures of Protein Phosphatase-1 Bound to Nodularin-R and Tautomycin: A Novel Scaffold For Structure-Based Drug Design of Serine/Threonine Phosphatase Inhibitors J.Mol.Biol. V. 385 11 2009.
ISSN: ISSN 0022-2836
PubMed: 18992256
DOI: 10.1016/J.JMB.2008.10.053
Page generated: Sat Oct 5 16:08:56 2024

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