Sodium in PDB 2iw2: Crystal Structure of Human Prolidase

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

The structure of Crystal Structure of Human Prolidase, PDB code: 2iw2 was solved by U.Mueller, F.H.Niesen, Y.Roske, F.Goetz, J.Behlke, K.Buessow, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.51 / 1.82
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	103.579, 108.518, 211.024, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 19.2

The binding sites of Sodium atom in the Crystal Structure of Human Prolidase (pdb code 2iw2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Human Prolidase, PDB code: 2iw2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of Human Prolidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Prolidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1484 b:21.6 occ:1.00 OD2 A:ASP288 2.3 25.6 1.0 NE2 A:HIS371 2.5 14.3 1.0 O A:HOH2404 2.5 31.8 1.0 OE2 A:GLU413 2.5 26.6 1.0 OE2 A:GLU453 2.5 17.9 1.0 NA A:NA1485 2.9 38.7 1.0 CD A:GLU413 3.2 25.0 1.0 CG A:ASP288 3.3 19.2 1.0 OE1 A:GLU413 3.3 25.4 1.0 CE1 A:HIS371 3.4 13.4 1.0 CD2 A:HIS371 3.4 14.6 1.0 CD A:GLU453 3.5 18.8 1.0 OD1 A:ASP288 3.7 27.2 1.0 OE1 A:GLU453 3.7 19.7 1.0 OG1 A:THR411 4.2 13.7 1.0 CG2 A:THR411 4.4 11.9 1.0 NE2 A:HIS378 4.4 17.6 1.0 CG A:GLU413 4.5 17.2 1.0 CB A:ASP288 4.5 14.1 1.0 CB A:THR411 4.5 12.6 1.0 ND1 A:HIS371 4.5 13.8 1.0 CG A:HIS371 4.6 10.9 1.0 CD2 A:HIS378 4.8 15.9 1.0 CG A:GLU453 4.8 11.6 1.0 OD2 A:ASP277 4.9 15.9 1.0 CG2 A:VAL377 4.9 16.9 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of Human Prolidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Prolidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1485 b:38.7 occ:1.00 OD1 A:ASP288 2.3 27.2 1.0 OD2 A:ASP277 2.3 15.9 1.0 OE1 A:GLU453 2.5 19.7 1.0 OD1 A:ASP277 2.5 15.6 1.0 CG A:ASP277 2.7 14.1 1.0 NA A:NA1484 2.9 21.6 1.0 OD2 A:ASP288 3.0 25.6 1.0 CG A:ASP288 3.0 19.2 1.0 CD A:GLU453 3.3 18.8 1.0 OE2 A:GLU453 3.3 17.9 1.0 OE1 A:GLU413 3.8 25.4 1.0 OG1 A:THR290 3.8 12.5 1.0 O A:HOH2404 3.9 31.8 1.0 OH A:TYR242 4.1 21.8 1.0 CB A:ASP277 4.2 10.6 1.0 CZ A:TYR242 4.3 22.4 1.0 CB A:ASP288 4.5 14.1 1.0 CE2 A:TYR242 4.5 21.1 1.0 CD A:GLU413 4.6 25.0 1.0 OE2 A:GLU413 4.6 26.6 1.0 CG A:GLU453 4.7 11.6 1.0 NE A:ARG451 4.7 16.4 1.0 NH2 A:ARG451 4.8 14.9 1.0 CE1 A:TYR242 5.0 20.7 1.0 C A:ASP288 5.0 12.6 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of Human Prolidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Human Prolidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1486 b:21.9 occ:1.00 O A:HOH2470 2.3 24.2 1.0 O A:HOH2362 2.4 18.5 1.0 O A:GLY319 2.4 13.1 1.0 C A:GLY319 3.4 12.6 1.0 CA A:GLY319 4.0 12.8 1.0 O A:MET321 4.0 13.8 1.0 N A:ALA320 4.4 12.2 1.0 O A:MET318 4.6 12.4 1.0 CA A:GLY462 4.6 15.6 1.0 O A:SER461 4.7 18.3 1.0 CA A:ALA320 4.7 12.5 1.0 C A:ALA320 4.8 13.5 1.0 N A:MET321 4.9 12.3 1.0 C A:MET321 5.0 12.9 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of Human Prolidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Human Prolidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1484 b:39.6 occ:1.00 OD1 B:ASP288 2.3 25.4 1.0 OD2 B:ASP277 2.3 17.0 1.0 O B:HOH2361 2.5 39.3 1.0 OD1 B:ASP277 2.6 18.6 1.0 OE1 B:GLU453 2.6 21.8 1.0 CG B:ASP277 2.8 17.8 1.0 NA B:NA1485 2.9 25.2 1.0 OD2 B:ASP288 2.9 23.8 1.0 CG B:ASP288 3.0 19.0 1.0 CD B:GLU453 3.3 20.3 1.0 OE2 B:GLU453 3.3 18.7 1.0 OE1 B:GLU413 3.8 26.7 1.0 OG1 B:THR290 3.9 14.5 1.0 O B:HOH2417 3.9 38.2 1.0 OH B:TYR242 4.0 18.8 1.0 CZ B:TYR242 4.2 19.0 1.0 CB B:ASP277 4.3 13.5 1.0 CB B:ASP288 4.5 14.6 1.0 CE2 B:TYR242 4.5 18.7 1.0 CD B:GLU413 4.6 22.4 1.0 OE2 B:GLU413 4.6 22.8 1.0 NH2 B:ARG451 4.7 16.2 1.0 CG B:GLU453 4.7 13.3 1.0 NE B:ARG451 4.7 17.0 1.0 CE1 B:TYR242 4.8 18.1 1.0 C B:ASP288 5.0 13.2 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of Human Prolidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Human Prolidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1485 b:25.2 occ:1.00 OD2 B:ASP288 2.3 23.8 1.0 NE2 B:HIS371 2.4 16.2 1.0 OE2 B:GLU413 2.5 22.8 1.0 OE2 B:GLU453 2.5 18.7 1.0 O B:HOH2417 2.7 38.2 1.0 NA B:NA1484 2.9 39.6 1.0 CD B:GLU413 3.2 22.4 1.0 OE1 B:GLU413 3.2 26.7 1.0 CG B:ASP288 3.2 19.0 1.0 CD2 B:HIS371 3.3 15.3 1.0 CE1 B:HIS371 3.3 14.4 1.0 CD B:GLU453 3.5 20.3 1.0 OD1 B:ASP288 3.7 25.4 1.0 OE1 B:GLU453 3.8 21.8 1.0 O B:HOH2361 3.9 39.3 1.0 OG1 B:THR411 4.1 15.1 1.0 CG2 B:THR411 4.1 14.6 1.0 CB B:THR411 4.4 14.5 1.0 NE2 B:HIS378 4.4 18.5 1.0 CB B:ASP288 4.4 14.6 1.0 ND1 B:HIS371 4.5 14.4 1.0 CG B:HIS371 4.5 13.9 1.0 CG B:GLU413 4.6 16.5 1.0 CG B:GLU453 4.7 13.3 1.0 CD2 B:HIS378 4.8 17.8 1.0 OD2 B:ASP277 4.9 17.0 1.0 CG2 B:VAL377 5.0 16.8 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.