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Manganese in PDB 7t0y: The Ribosomal Rna Processing 1B Protein Phosphatase-1 Holoenzyme

Enzymatic activity of The Ribosomal Rna Processing 1B Protein Phosphatase-1 Holoenzyme

All present enzymatic activity of The Ribosomal Rna Processing 1B Protein Phosphatase-1 Holoenzyme:
3.1.3.16;

Protein crystallography data

The structure of The Ribosomal Rna Processing 1B Protein Phosphatase-1 Holoenzyme, PDB code: 7t0y was solved by G.Srivastava, R.Page, W.Peti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.27 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.528, 160.387, 50.615, 90, 90, 90
R / Rfree (%) 20.8 / 24.6

Other elements in 7t0y:

The structure of The Ribosomal Rna Processing 1B Protein Phosphatase-1 Holoenzyme also contains other interesting chemical elements:

Bromine (Br) 3 atoms
Fluorine (F) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the The Ribosomal Rna Processing 1B Protein Phosphatase-1 Holoenzyme (pdb code 7t0y). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Ribosomal Rna Processing 1B Protein Phosphatase-1 Holoenzyme, PDB code: 7t0y:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7t0y

Go back to Manganese Binding Sites List in 7t0y
Manganese binding site 1 out of 4 in the The Ribosomal Rna Processing 1B Protein Phosphatase-1 Holoenzyme


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Ribosomal Rna Processing 1B Protein Phosphatase-1 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn406

b:19.2
occ:1.00
 OD2 A:ASP64 2.1 21.2 1.0
O A:HOH670 2.1 22.8 1.0
O A:HOH583 2.1 22.5 1.0
OD2 A:ASP92 2.2 15.7 1.0
NE2 A:HIS66 2.2 22.8 1.0
CE1 A:HIS66 3.1 21.9 1.0
CG A:ASP92 3.2 17.6 1.0
CD2 A:HIS66 3.2 19.0 1.0
CG A:ASP64 3.2 17.2 1.0
MN A:MN407 3.2 16.3 1.0
CB A:ASP92 3.6 14.8 1.0
O A:HOH608 3.8 19.6 1.0
CB A:ASP64 4.0 21.3 1.0
OD1 A:ASP64 4.1 23.4 1.0
O A:HOH688 4.2 28.0 1.0
O A:HIS248 4.2 20.9 1.0
CD2 A:HIS125 4.2 19.2 1.0
ND1 A:HIS66 4.3 16.6 1.0
OD1 A:ASP92 4.3 19.0 1.0
CG A:HIS66 4.3 18.1 1.0
NE2 A:HIS173 4.3 21.3 1.0
NE2 A:HIS125 4.4 20.2 1.0
CE1 A:HIS173 4.4 19.4 1.0
CE2 A:PHE267 4.4 20.8 1.0
CA A:HIS248 4.5 17.3 1.0
OH A:TYR272 4.5 27.1 1.0
C A:HIS248 4.6 19.2 1.0
OD1 A:ASN124 4.8 19.9 1.0
ND1 A:HIS248 4.8 18.3 1.0

Manganese binding site 2 out of 4 in 7t0y

Go back to Manganese Binding Sites List in 7t0y
Manganese binding site 2 out of 4 in the The Ribosomal Rna Processing 1B Protein Phosphatase-1 Holoenzyme


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Ribosomal Rna Processing 1B Protein Phosphatase-1 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn407

b:16.3
occ:1.00
 O A:HOH583 2.1 22.5 1.0
NE2 A:HIS173 2.1 21.3 1.0
ND1 A:HIS248 2.1 18.3 1.0
OD1 A:ASN124 2.1 19.9 1.0
OD2 A:ASP92 2.2 15.7 1.0
CE1 A:HIS248 3.0 20.8 1.0
CD2 A:HIS173 3.0 16.3 1.0
CE1 A:HIS173 3.1 19.4 1.0
CG A:ASN124 3.2 17.6 1.0
CG A:ASP92 3.2 17.6 1.0
CG A:HIS248 3.2 19.4 1.0
MN A:MN406 3.2 19.2 1.0
O A:HOH608 3.5 19.6 1.0
OD1 A:ASP92 3.6 19.0 1.0
CA A:HIS248 3.6 17.3 1.0
ND2 A:ASN124 3.7 16.4 1.0
CB A:HIS248 3.7 17.7 1.0
O A:HIS248 4.0 20.9 1.0
OD2 A:ASP64 4.0 21.2 1.0
NE2 A:HIS248 4.1 18.8 1.0
ND1 A:HIS173 4.2 17.9 1.0
CG A:HIS173 4.2 17.2 1.0
CD2 A:HIS125 4.2 19.2 1.0
CD2 A:HIS248 4.3 15.6 1.0
C A:HIS248 4.3 19.2 1.0
N A:ASN124 4.4 18.2 1.0
CB A:ASN124 4.5 14.7 1.0
CB A:ASP92 4.5 14.8 1.0
O A:LEU205 4.6 21.3 1.0
N A:HIS248 4.6 16.0 1.0
O A:HOH670 4.7 22.8 1.0
NE2 A:HIS125 4.8 20.2 1.0
CG A:ASP64 4.9 17.2 1.0
CA A:ASN124 4.9 19.2 1.0

Manganese binding site 3 out of 4 in 7t0y

Go back to Manganese Binding Sites List in 7t0y
Manganese binding site 3 out of 4 in the The Ribosomal Rna Processing 1B Protein Phosphatase-1 Holoenzyme


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Ribosomal Rna Processing 1B Protein Phosphatase-1 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn407

b:20.5
occ:1.00
 OD2 C:ASP64 2.0 22.8 1.0
O C:HOH520 2.1 22.2 1.0
O C:HOH651 2.1 27.6 1.0
OD2 C:ASP92 2.2 18.9 1.0
NE2 C:HIS66 2.2 18.3 1.0
CE1 C:HIS66 3.1 20.6 1.0
CD2 C:HIS66 3.2 21.1 1.0
CG C:ASP92 3.2 20.1 1.0
CG C:ASP64 3.2 21.6 1.0
MN C:MN408 3.3 17.8 1.0
CB C:ASP92 3.6 20.0 1.0
O C:HOH587 3.8 22.8 1.0
CB C:ASP64 3.9 20.1 1.0
OD1 C:ASP64 4.1 20.5 1.0
O C:HOH653 4.2 29.5 1.0
O C:HIS248 4.2 25.1 1.0
CD2 C:HIS125 4.2 22.3 1.0
ND1 C:HIS66 4.3 17.3 1.0
OD1 C:ASP92 4.3 20.0 1.0
CG C:HIS66 4.3 19.0 1.0
CE1 C:HIS173 4.4 16.9 1.0
NE2 C:HIS173 4.4 23.2 1.0
NE2 C:HIS125 4.4 20.9 1.0
OH C:TYR272 4.4 28.2 1.0
CE1 C:PHE267 4.4 18.7 1.0
CA C:HIS248 4.5 24.3 1.0
C C:HIS248 4.6 21.0 1.0
OD1 C:ASN124 4.8 20.2 1.0
ND1 C:HIS248 4.8 19.2 1.0

Manganese binding site 4 out of 4 in 7t0y

Go back to Manganese Binding Sites List in 7t0y
Manganese binding site 4 out of 4 in the The Ribosomal Rna Processing 1B Protein Phosphatase-1 Holoenzyme


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Ribosomal Rna Processing 1B Protein Phosphatase-1 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn408

b:17.8
occ:1.00
 O C:HOH520 1.8 22.2 1.0
NE2 C:HIS173 2.0 23.2 1.0
OD1 C:ASN124 2.0 20.2 1.0
ND1 C:HIS248 2.1 19.2 1.0
OD2 C:ASP92 2.2 18.9 1.0
CE1 C:HIS248 2.9 27.1 1.0
CE1 C:HIS173 3.0 16.9 1.0
CD2 C:HIS173 3.1 22.1 1.0
CG C:ASN124 3.1 24.5 1.0
CG C:ASP92 3.2 20.1 1.0
MN C:MN407 3.3 20.5 1.0
CG C:HIS248 3.3 22.7 1.0
O C:HOH587 3.5 22.8 1.0
ND2 C:ASN124 3.5 18.9 1.0
OD1 C:ASP92 3.5 20.0 1.0
CA C:HIS248 3.6 24.3 1.0
CB C:HIS248 3.8 24.2 1.0
O C:HIS248 4.0 25.1 1.0
OD2 C:ASP64 4.0 22.8 1.0
ND1 C:HIS173 4.1 19.5 1.0
NE2 C:HIS248 4.1 20.9 1.0
CG C:HIS173 4.2 19.8 1.0
CD2 C:HIS125 4.2 22.3 1.0
C C:HIS248 4.3 21.0 1.0
CD2 C:HIS248 4.3 24.1 1.0
N C:ASN124 4.3 22.1 1.0
CB C:ASN124 4.4 18.7 1.0
CB C:ASP92 4.5 20.0 1.0
O C:LEU205 4.6 20.7 1.0
N C:HIS248 4.6 20.1 1.0
O C:HOH651 4.7 27.6 1.0
NE2 C:HIS125 4.8 20.9 1.0
CA C:ASN124 4.9 19.8 1.0
CG C:ASP64 4.9 21.6 1.0
NH1 C:ARG221 4.9 28.3 1.0
O C:HOH653 5.0 29.5 1.0

Reference:

G.Srivastava, R.Bajaj, G.S.Kumar, A.Gaudreau-Lapierre, H.Nicolas, D.Chamousset, D.Kreitler, W.Peti, L.Trinkle-Mulcahy, R.Page. The Ribosomal Rna Processing 1B:Protein Phosphatase 1 Holoenzyme Reveals Non-Canonical PP1 Interaction Motifs. Cell Rep V. 41 11726 2022.
ISSN: ESSN 2211-1247
PubMed: 36450254
DOI: 10.1016/J.CELREP.2022.111726
Page generated: Sun Oct 6 10:35:16 2024

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