Manganese in PDB 6obu: PP1 Y134K in Complex with Microcystin Lr

All present enzymatic activity of PP1 Y134K in Complex with Microcystin Lr:
3.1.3.16;

The structure of PP1 Y134K in Complex with Microcystin Lr, PDB code: 6obu was solved by M.S.Choy, T.M.Moon, J.A.Bray, T.L.Archuleta, W.Shi, W.Peti, R.Page, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.17 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.348, 78.362, 134.038, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 20.2

The structure of PP1 Y134K in Complex with Microcystin Lr also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the PP1 Y134K in Complex with Microcystin Lr (pdb code 6obu). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the PP1 Y134K in Complex with Microcystin Lr, PDB code: 6obu:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the PP1 Y134K in Complex with Microcystin Lr


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of PP1 Y134K in Complex with Microcystin Lr within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:20.6 occ:1.00 O A:HOH527 2.1 17.4 1.0 OD2 A:ASP64 2.1 21.4 1.0 OD2 A:ASP92 2.2 17.7 1.0 O C:HOH403 2.2 24.3 1.0 NE2 A:HIS66 2.2 18.5 1.0 CE1 A:HIS66 3.1 17.2 1.0 CG A:ASP64 3.2 18.3 1.0 CD2 A:HIS66 3.2 18.0 1.0 CG A:ASP92 3.2 17.9 1.0 MN A:MN402 3.3 19.0 1.0 CB A:ASP92 3.7 16.4 1.0 O C:HOH404 3.8 20.9 1.0 CB A:ASP64 3.9 15.3 1.0 O A:HIS248 4.1 20.8 1.0 OD1 A:ASP64 4.1 18.5 1.0 CD2 A:HIS125 4.2 17.9 1.0 OXT C:FGA6 4.2 33.8 1.0 NE2 A:HIS125 4.3 22.2 1.0 ND1 A:HIS66 4.3 18.3 1.0 CE1 A:PHE267 4.3 21.1 1.0 OD1 A:ASP92 4.3 18.5 1.0 CG A:HIS66 4.4 18.5 1.0 OH A:TYR272 4.5 29.7 1.0 CA A:HIS248 4.5 19.4 1.0 CE1 A:HIS173 4.6 18.7 1.0 NE2 A:HIS173 4.6 17.8 1.0 C A:HIS248 4.6 23.0 1.0 O C:FGA6 4.8 33.9 1.0 OD1 A:ASN124 4.9 17.4 1.0 C C:FGA6 4.9 36.0 1.0 CZ A:PHE267 4.9 20.1 1.0 ND1 A:HIS248 5.0 20.1 1.0

Manganese binding site 2 out of 4 in the PP1 Y134K in Complex with Microcystin Lr


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of PP1 Y134K in Complex with Microcystin Lr within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:19.0 occ:1.00 O A:HOH527 1.9 17.4 1.0 OD1 A:ASN124 2.1 17.4 1.0 NE2 A:HIS173 2.1 17.8 1.0 OD2 A:ASP92 2.2 17.7 1.0 ND1 A:HIS248 2.3 20.1 1.0 CE1 A:HIS173 3.1 18.7 1.0 CE1 A:HIS248 3.1 19.4 1.0 CG A:ASP92 3.1 17.9 1.0 CG A:ASN124 3.2 20.3 1.0 CD2 A:HIS173 3.2 16.3 1.0 MN A:MN401 3.3 20.6 1.0 O C:HOH404 3.3 20.9 1.0 CG A:HIS248 3.4 20.9 1.0 OD1 A:ASP92 3.4 18.5 1.0 CA A:HIS248 3.6 19.4 1.0 ND2 A:ASN124 3.7 19.1 1.0 CB A:HIS248 3.8 19.1 1.0 O A:HIS248 4.0 20.8 1.0 OD2 A:ASP64 4.1 21.4 1.0 CD2 A:HIS125 4.1 17.9 1.0 ND1 A:HIS173 4.2 15.3 1.0 CG A:HIS173 4.3 18.4 1.0 C A:HIS248 4.3 23.0 1.0 NE2 A:HIS248 4.3 20.3 1.0 N A:ASN124 4.4 18.6 1.0 CB A:ASN124 4.4 17.1 1.0 CB A:ASP92 4.5 16.4 1.0 CD2 A:HIS248 4.5 23.8 1.0 O A:LEU205 4.6 20.0 1.0 NE2 A:HIS125 4.7 22.2 1.0 N A:HIS248 4.7 17.5 1.0 CG A:ASP64 4.9 18.3 1.0 OD1 A:ASP64 4.9 18.5 1.0 CA A:ASN124 4.9 18.8 1.0 O C:HOH403 5.0 24.3 1.0

Manganese binding site 3 out of 4 in the PP1 Y134K in Complex with Microcystin Lr


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of PP1 Y134K in Complex with Microcystin Lr within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:22.1 occ:1.00 O B:HOH533 2.1 21.3 1.0 OD2 B:ASP64 2.1 21.8 1.0 OD2 B:ASP92 2.2 18.0 1.0 O D:HOH101 2.2 24.1 1.0 NE2 B:HIS66 2.2 21.3 1.0 CE1 B:HIS66 3.2 19.3 1.0 CG B:ASP64 3.2 19.8 1.0 CG B:ASP92 3.2 17.6 1.0 MN B:MN402 3.2 20.6 1.0 CD2 B:HIS66 3.3 20.5 1.0 CB B:ASP92 3.7 16.6 1.0 O D:HOH102 3.8 23.2 1.0 CB B:ASP64 3.9 20.3 1.0 OD1 B:ASP64 4.1 22.0 1.0 O D:FGA6 4.2 41.7 1.0 O B:HIS248 4.2 27.4 1.0 ND1 B:HIS66 4.3 20.9 1.0 NE2 B:HIS125 4.3 21.9 1.0 CD2 B:HIS125 4.3 19.9 1.0 OD1 B:ASP92 4.3 18.6 1.0 CE1 B:PHE267 4.4 18.3 1.0 CG B:HIS66 4.4 18.1 1.0 NE2 B:HIS173 4.5 20.3 1.0 CE1 B:HIS173 4.5 17.9 1.0 CA B:HIS248 4.6 19.8 1.0 OH B:TYR272 4.6 34.0 1.0 OXT D:FGA6 4.6 42.9 1.0 C B:HIS248 4.7 24.2 1.0 C D:FGA6 4.8 38.1 1.0 OD1 B:ASN124 4.9 19.1 1.0 ND1 B:HIS248 4.9 23.7 1.0

Manganese binding site 4 out of 4 in the PP1 Y134K in Complex with Microcystin Lr


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of PP1 Y134K in Complex with Microcystin Lr within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:20.6 occ:1.00 O B:HOH533 1.9 21.3 1.0 NE2 B:HIS173 2.1 20.3 1.0 OD1 B:ASN124 2.1 19.1 1.0 OD2 B:ASP92 2.2 18.0 1.0 ND1 B:HIS248 2.3 23.7 1.0 CE1 B:HIS248 3.1 25.0 1.0 CE1 B:HIS173 3.1 17.9 1.0 CG B:ASP92 3.1 17.6 1.0 CD2 B:HIS173 3.2 17.7 1.0 CG B:ASN124 3.2 20.6 1.0 MN B:MN401 3.2 22.1 1.0 O D:HOH102 3.4 23.2 1.0 CG B:HIS248 3.4 23.0 1.0 OD1 B:ASP92 3.4 18.6 1.0 CA B:HIS248 3.6 19.8 1.0 ND2 B:ASN124 3.7 18.5 1.0 CB B:HIS248 3.8 20.3 1.0 O B:HIS248 4.0 27.4 1.0 OD2 B:ASP64 4.0 21.8 1.0 ND1 B:HIS173 4.2 19.0 1.0 CD2 B:HIS125 4.2 19.9 1.0 NE2 B:HIS248 4.3 24.4 1.0 CG B:HIS173 4.3 17.3 1.0 C B:HIS248 4.3 24.2 1.0 CB B:ASP92 4.4 16.6 1.0 CD2 B:HIS248 4.4 23.1 1.0 N B:ASN124 4.4 17.7 1.0 CB B:ASN124 4.5 20.1 1.0 O B:LEU205 4.7 19.4 1.0 N B:HIS248 4.7 18.8 1.0 NE2 B:HIS125 4.7 21.9 1.0 CG B:ASP64 4.8 19.8 1.0 OD1 B:ASP64 4.9 22.0 1.0 O D:HOH101 5.0 24.1 1.0 CA B:ASN124 5.0 19.2 1.0

M.S.Choy, T.M.Moon, R.Ravindran, J.A.Bray, L.C.Robinson, T.L.Archuleta, W.Shi, W.Peti, K.Tatchell, R.Page. SDS22 Selectively Recognizes and Traps Metal-Deficient Inactive PP1. Proc.Natl.Acad.Sci.Usa V. 116 20472 2019.
ISSN: ESSN 1091-6490
PubMed: 31548429
DOI: 10.1073/PNAS.1908718116