Manganese in PDB 5wg8: Structure of PP5C with Lb-100; 7-Oxabicyclo[2.2.1]Heptane-2,3- Dicarbonyl Moiety Modeled in the Density

All present enzymatic activity of Structure of PP5C with Lb-100; 7-Oxabicyclo[2.2.1]Heptane-2,3- Dicarbonyl Moiety Modeled in the Density:
3.1.3.16;

The structure of Structure of PP5C with Lb-100; 7-Oxabicyclo[2.2.1]Heptane-2,3- Dicarbonyl Moiety Modeled in the Density, PDB code: 5wg8 was solved by B.M.D'arcy, M.R.Swingle, R.E.Honkanen, A.Prakash, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.34 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.656, 91.150, 95.494, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19.6

The binding sites of Manganese atom in the Structure of PP5C with Lb-100; 7-Oxabicyclo[2.2.1]Heptane-2,3- Dicarbonyl Moiety Modeled in the Density (pdb code 5wg8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of PP5C with Lb-100; 7-Oxabicyclo[2.2.1]Heptane-2,3- Dicarbonyl Moiety Modeled in the Density, PDB code: 5wg8:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of PP5C with Lb-100; 7-Oxabicyclo[2.2.1]Heptane-2,3- Dicarbonyl Moiety Modeled in the Density


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of PP5C with Lb-100; 7-Oxabicyclo[2.2.1]Heptane-2,3- Dicarbonyl Moiety Modeled in the Density within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:9.1 occ:1.00 OD1 A:ASN303 2.1 4.3 1.0 O04 A:LB1503 2.1 10.3 1.0 NE2 A:HIS352 2.2 3.6 1.0 ND1 A:HIS427 2.2 2.5 1.0 OD2 A:ASP271 2.3 5.5 1.0 C14 A:LB1503 2.8 10.9 1.0 CE1 A:HIS427 3.0 3.7 1.0 CD2 A:HIS352 3.1 3.0 1.0 CG A:ASN303 3.1 3.7 1.0 CG A:ASP271 3.2 4.1 1.0 CE1 A:HIS352 3.2 4.7 1.0 CG A:HIS427 3.3 3.3 1.0 MN A:MN502 3.4 6.9 1.0 OD1 A:ASP271 3.5 3.8 1.0 ND2 A:ASN303 3.7 3.6 1.0 CA A:HIS427 3.7 4.3 1.0 CB A:HIS427 3.7 3.6 1.0 O02 A:LB1503 3.9 10.3 1.0 OD2 A:ASP242 4.0 4.8 1.0 NE2 A:HIS427 4.2 3.6 1.0 O A:HIS427 4.3 4.7 1.0 CG A:HIS352 4.3 2.6 1.0 ND1 A:HIS352 4.3 3.6 1.0 C10 A:LB1503 4.3 11.2 1.0 CD2 A:HIS427 4.3 2.6 1.0 CB A:ASN303 4.4 4.0 1.0 N A:ASN303 4.4 3.7 1.0 C A:HIS427 4.5 5.1 1.0 CD2 A:HIS304 4.5 5.9 1.0 CB A:ASP271 4.5 3.7 1.0 O A:LEU385 4.7 3.7 1.0 N A:HIS427 4.7 4.9 1.0 C13 A:LB1503 4.7 10.3 1.0 O A:HOH785 4.8 22.7 1.0 C09 A:LB1503 4.8 11.2 1.0 CA A:ASN303 4.9 3.6 1.0 CG A:ASP242 4.9 4.7 1.0 O01 A:LB1503 4.9 10.8 1.0

Manganese binding site 2 out of 2 in the Structure of PP5C with Lb-100; 7-Oxabicyclo[2.2.1]Heptane-2,3- Dicarbonyl Moiety Modeled in the Density


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of PP5C with Lb-100; 7-Oxabicyclo[2.2.1]Heptane-2,3- Dicarbonyl Moiety Modeled in the Density within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:6.9 occ:1.00 OD2 A:ASP242 2.1 4.8 1.0 OD2 A:ASP271 2.1 5.5 1.0 NE2 A:HIS244 2.1 4.0 1.0 O04 A:LB1503 2.2 10.3 1.0 O02 A:LB1503 2.2 10.3 1.0 O01 A:LB1503 2.3 10.8 1.0 C14 A:LB1503 2.9 10.9 1.0 CE1 A:HIS244 3.0 4.0 1.0 C09 A:LB1503 3.1 11.2 1.0 CG A:ASP271 3.1 4.1 1.0 C13 A:LB1503 3.2 10.3 1.0 CD2 A:HIS244 3.2 3.8 1.0 C08 A:LB1503 3.2 11.5 1.0 C10 A:LB1503 3.3 11.2 1.0 CG A:ASP242 3.3 4.7 1.0 MN A:MN501 3.4 9.1 1.0 C07 A:LB1503 3.4 11.0 1.0 CB A:ASP271 3.5 3.7 1.0 CB A:ASP242 4.0 4.9 1.0 CD2 A:HIS304 4.2 5.9 1.0 ND1 A:HIS244 4.2 3.6 1.0 OD1 A:ASP271 4.2 3.8 1.0 OD1 A:ASP242 4.3 5.0 1.0 CG A:HIS244 4.3 3.5 1.0 NE2 A:HIS352 4.4 3.6 1.0 C12 A:LB1503 4.4 11.9 1.0 CE1 A:HIS352 4.5 4.7 1.0 C11 A:LB1503 4.5 12.4 1.0 CE1 A:PHE446 4.6 4.7 1.0 NE2 A:HIS304 4.6 7.2 1.0 CA A:HIS427 4.7 4.3 1.0 OD1 A:ASN303 4.8 4.3 1.0 O A:HIS427 5.0 4.7 1.0 CA A:ASP271 5.0 3.5 1.0

B.M.D'arcy, M.R.Swingle, C.M.Papke, K.A.Abney, E.S.Bouska, A.Prakash, R.E.Honkanen. The Antitumor Drug Lb-100 Is A Catalytic Inhibitor of Protein Phosphatase 2A (PPP2CA) and 5 (PPP5C) Coordinating with the Active-Site Catalytic Metals in PPP5C. Mol. Cancer Ther. V. 18 556 2019.
ISSN: ESSN 1538-8514
PubMed: 30679389
DOI: 10.1158/1535-7163.MCT-17-1143