Manganese in PDB 8eip: Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg

The structure of Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg, PDB code: 8eip was solved by I.Sharon, T.M.Schmeing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.04 / 2.24
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	151.529, 126.648, 109.516, 90, 130.39, 90
R / Rfree (%)	22.6 / 25.8

The structure of Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Manganese atom in the Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg (pdb code 8eip). 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 Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg, PDB code: 8eip:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg


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 Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:106.2 occ:1.00 CE1 A:HIS315 3.7 49.1 1.0 NE2 A:HIS315 4.0 56.2 1.0 OG A:SER330 4.0 43.5 1.0 CB A:SER330 4.1 45.2 1.0 CD2 B:LEU260 4.2 56.4 1.0 CG2 A:THR338 4.3 47.7 1.0 CD1 B:LEU260 4.3 58.6 1.0 CG2 A:VAL332 4.4 37.7 1.0 CG1 A:VAL313 4.5 50.5 1.0 CG B:LEU260 4.8 61.2 1.0 NZ A:LYS327 4.9 55.4 1.0 ND1 A:HIS315 4.9 54.4 1.0 OD1 A:ASP340 5.0 61.8 1.0 CB A:VAL313 5.0 51.4 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg


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 Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:155.6 occ:1.00 CE1 B:HIS315 3.5 42.6 1.0 NE2 B:HIS315 3.7 47.5 1.0 OG B:SER330 3.8 42.5 1.0 CB B:SER330 3.8 37.8 1.0 O B:HOH590 3.9 62.0 1.0 OH A:TYR62 4.3 60.9 1.0 CG2 B:VAL332 4.4 43.2 1.0 CG1 B:VAL313 4.4 33.2 1.0 CG2 B:THR338 4.4 51.1 1.0 CD1 A:LEU260 4.6 65.9 1.0 ND1 B:HIS315 4.8 46.8 1.0 CB B:VAL313 4.8 31.4 1.0 OD1 B:ASP340 4.9 58.6 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg


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 Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn403 b:99.9 occ:1.00 O C:HOH524 3.4 52.5 1.0 CE1 C:HIS315 3.6 43.7 1.0 NE2 C:HIS315 3.9 52.3 1.0 CB C:SER330 4.0 46.1 1.0 OG C:SER330 4.0 49.6 1.0 CD2 D:LEU260 4.0 70.3 1.0 CG2 C:VAL332 4.2 40.6 1.0 CG2 C:THR338 4.3 55.1 1.0 CG1 C:VAL313 4.3 48.3 1.0 CD1 D:LEU260 4.5 68.0 1.0 OH D:TYR62 4.7 70.7 1.0 CB C:VAL313 4.7 42.7 1.0 CG D:LEU260 4.8 64.5 1.0 ND1 C:HIS315 4.9 46.7 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg


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 Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn403 b:80.9 occ:1.00 O D:HOH520 3.2 52.1 1.0 CE1 D:HIS315 3.5 43.2 1.0 NE2 D:HIS315 3.7 53.9 1.0 OG D:SER330 3.8 49.9 1.0 CB D:SER330 3.9 40.7 1.0 CD1 C:LEU260 4.1 59.7 1.0 CD2 C:LEU260 4.2 55.0 1.0 CG1 D:VAL313 4.3 35.3 1.0 CG2 D:THR338 4.4 39.8 1.0 CG2 D:VAL332 4.5 50.2 1.0 CG C:LEU260 4.7 57.2 1.0 ND1 D:HIS315 4.7 50.0 1.0 CB D:VAL313 4.8 48.7 1.0 OD1 D:ASP340 5.0 45.2 1.0 NZ D:LYS327 5.0 59.3 1.0

I.Sharon, G.A.Mckay, D.Nguyen, T.M.Schmeing. Discovery of Cyanophycin Dipeptide Hydrolase Enzymes Suggests Widespread Utility of the Natural Biopolymer Cyanophycin. Proc.Natl.Acad.Sci.Usa V. 120 47120 2023.
ISSN: ESSN 1091-6490
PubMed: 36800389
DOI: 10.1073/PNAS.2216547120