Manganese in PDB 2okn: Crystal Strcture of Human Prolidase

All present enzymatic activity of Crystal Strcture of Human Prolidase:
3.4.13.9;

The structure of Crystal Strcture of Human Prolidase, PDB code: 2okn was solved by U.Mueller, F.H.Niesen, Y.Roske, F.Goetz, J.Behlke, K.Buessow, U.Heinemann, Protein Structure Factory (Psf), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.94 / 2.45
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	103.890, 108.960, 212.010, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 23.1

The binding sites of Manganese atom in the Crystal Strcture of Human Prolidase (pdb code 2okn). 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 Strcture of Human Prolidase, PDB code: 2okn:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Strcture of Human Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Strcture of Human Prolidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn495 b:36.2 occ:1.00 O3 A:PI501 2.0 37.9 1.0 OD2 A:ASP288 2.1 35.9 1.0 OE2 A:GLU413 2.2 40.9 1.0 NE2 A:HIS371 2.3 36.4 1.0 OE2 A:GLU453 2.3 38.1 1.0 O1 A:PI501 2.8 38.5 1.0 P A:PI501 3.0 37.3 1.0 CG A:ASP288 3.1 35.4 1.0 CD A:GLU413 3.2 39.9 1.0 CD2 A:HIS371 3.2 36.7 1.0 CE1 A:HIS371 3.2 37.1 1.0 MN A:MN496 3.3 34.3 1.0 CD A:GLU453 3.3 36.6 1.0 OD1 A:ASP288 3.5 37.6 1.0 OE1 A:GLU453 3.6 35.7 1.0 OE1 A:GLU413 3.6 39.5 1.0 CG2 A:THR411 3.9 36.0 1.0 O4 A:PI501 3.9 35.7 1.0 OG1 A:THR411 4.0 37.3 1.0 O2 A:PI501 4.2 35.4 1.0 CB A:THR411 4.2 35.9 1.0 CB A:ASP288 4.3 36.4 1.0 ND1 A:HIS371 4.3 36.9 1.0 CG A:HIS371 4.4 36.9 1.0 CG A:GLU413 4.4 39.7 1.0 NE2 A:HIS378 4.5 37.6 1.0 CG A:GLU453 4.6 35.5 1.0 CD2 A:HIS378 4.7 37.2 1.0 CG2 A:VAL377 4.8 38.4 1.0 O A:HOH503 5.0 44.2 1.0

Manganese binding site 2 out of 4 in the Crystal Strcture of Human Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Strcture of Human Prolidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn496 b:34.3 occ:1.00 O3 A:PI501 2.1 37.9 1.0 OD1 A:ASP288 2.1 37.6 1.0 OE1 A:GLU453 2.2 35.7 1.0 OD1 A:ASP277 2.4 33.6 1.0 OD2 A:ASP277 2.5 34.4 1.0 CG A:ASP277 2.8 34.1 1.0 CG A:ASP288 3.0 35.4 1.0 CD A:GLU453 3.1 36.6 1.0 MN A:MN495 3.3 36.2 1.0 OD2 A:ASP288 3.3 35.9 1.0 OE2 A:GLU453 3.3 38.1 1.0 P A:PI501 3.4 37.3 1.0 O2 A:PI501 3.6 35.4 1.0 OG1 A:THR290 3.8 35.1 1.0 OH A:TYR242 3.9 46.0 1.0 CZ A:TYR242 4.1 45.9 1.0 O4 A:PI501 4.2 35.7 1.0 CB A:ASP277 4.3 34.1 1.0 CE2 A:TYR242 4.3 45.4 1.0 O1 A:PI501 4.4 38.5 1.0 CB A:ASP288 4.4 36.4 1.0 CG A:GLU453 4.5 35.5 1.0 C A:ASP288 4.6 35.5 1.0 CE1 A:TYR242 4.6 45.9 1.0 CA A:ASP288 4.7 35.0 1.0 N A:ILE289 4.7 36.5 1.0 OE2 A:GLU413 4.8 40.9 1.0 OE1 A:GLU413 4.8 39.5 1.0 NE A:ARG451 4.8 39.2 1.0 O A:ASP288 4.9 34.5 1.0 NH2 A:ARG451 5.0 38.6 1.0

Manganese binding site 3 out of 4 in the Crystal Strcture of Human Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Strcture of Human Prolidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn495 b:38.0 occ:1.00 OE2 B:GLU413 2.0 40.4 1.0 O3 B:PI502 2.0 45.5 1.0 OD2 B:ASP288 2.2 39.5 1.0 OE2 B:GLU453 2.2 43.0 1.0 NE2 B:HIS371 2.3 40.9 1.0 CD B:GLU413 3.0 41.3 1.0 O2 B:PI502 3.0 44.4 1.0 P B:PI502 3.1 45.2 1.0 CG B:ASP288 3.1 40.5 1.0 CD B:GLU453 3.2 41.6 1.0 CD2 B:HIS371 3.2 41.0 1.0 CE1 B:HIS371 3.3 40.3 1.0 MN B:MN496 3.3 39.0 1.0 OE1 B:GLU413 3.4 42.3 1.0 OD1 B:ASP288 3.5 42.0 1.0 OE1 B:GLU453 3.5 42.3 1.0 CG2 B:THR411 3.7 40.1 1.0 O4 B:PI502 3.7 43.7 1.0 OG1 B:THR411 3.9 37.7 1.0 CB B:THR411 4.1 40.3 1.0 CG B:GLU413 4.3 39.9 1.0 O B:HOH567 4.3 26.9 1.0 O1 B:PI502 4.3 42.2 1.0 CB B:ASP288 4.4 39.8 1.0 CG B:HIS371 4.4 41.4 1.0 ND1 B:HIS371 4.4 41.2 1.0 CG B:GLU453 4.5 41.2 1.0 NE2 B:HIS378 4.7 44.7 1.0 CD2 B:HIS378 4.9 44.5 1.0 O B:HOH573 4.9 39.4 1.0 CB B:GLU413 4.9 39.2 1.0

Manganese binding site 4 out of 4 in the Crystal Strcture of Human Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Strcture of Human Prolidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn496 b:39.0 occ:1.00 OD1 B:ASP288 2.0 42.0 1.0 O3 B:PI502 2.2 45.5 1.0 OD1 B:ASP277 2.2 39.4 1.0 OE1 B:GLU453 2.3 42.3 1.0 O B:HOH567 2.3 26.9 1.0 OD2 B:ASP277 2.4 43.4 1.0 CG B:ASP277 2.6 41.0 1.0 CG B:ASP288 3.0 40.5 1.0 CD B:GLU453 3.1 41.6 1.0 OD2 B:ASP288 3.2 39.5 1.0 OE2 B:GLU453 3.3 43.0 1.0 MN B:MN495 3.3 38.0 1.0 P B:PI502 3.4 45.2 1.0 O1 B:PI502 3.8 42.2 1.0 OG1 B:THR290 3.9 40.8 1.0 OH B:TYR242 3.9 49.5 1.0 O4 B:PI502 4.1 43.7 1.0 CB B:ASP277 4.1 40.2 1.0 CZ B:TYR242 4.1 50.1 1.0 CB B:ASP288 4.4 39.8 1.0 CE2 B:TYR242 4.4 49.9 1.0 CG B:GLU453 4.5 41.2 1.0 O2 B:PI502 4.6 44.4 1.0 N B:ILE289 4.6 40.5 1.0 C B:ASP288 4.6 40.1 1.0 OE1 B:GLU413 4.7 42.3 1.0 CA B:ASP288 4.7 40.1 1.0 NH2 B:ARG451 4.7 36.0 1.0 OE2 B:GLU413 4.8 40.4 1.0 CE1 B:TYR242 4.8 49.4 1.0 NE B:ARG451 4.9 37.7 1.0 CA B:ASP277 4.9 39.6 1.0 CD B:GLU413 5.0 41.3 1.0

U.Mueller, F.H.Niesen, Y.Roske, F.Goetz, J.Behlke, K.Buessow, U.Heinemann. Crystal Structure of Human Prolidase: the Molecular Basis of Pd Disease. To Be Published.