Manganese in PDB 5m4q: Crystal Structure of Wild-Type Human Prolidase with Mn Ions and Pro Ligand

All present enzymatic activity of Crystal Structure of Wild-Type Human Prolidase with Mn Ions and Pro Ligand:
3.4.13.9;

The structure of Crystal Structure of Wild-Type Human Prolidase with Mn Ions and Pro Ligand, PDB code: 5m4q was solved by P.Wilk, M.S.Weiss, U.Mueller, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.65 / 1.73
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	103.429, 107.005, 216.125, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 18

The binding sites of Manganese atom in the Crystal Structure of Wild-Type Human Prolidase with Mn Ions and Pro Ligand (pdb code 5m4q). 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 Wild-Type Human Prolidase with Mn Ions and Pro Ligand, PDB code: 5m4q:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Wild-Type Human Prolidase with Mn Ions and Pro Ligand


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 Wild-Type Human Prolidase with Mn Ions and Pro Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn499 b:22.2 occ:0.69 OD2 A:ASP287 2.2 26.3 1.0 OE2 A:GLU452 2.2 21.9 1.0 NE2 A:HIS370 2.2 19.7 1.0 O A:OH501 2.2 30.4 1.0 OE2 A:GLU412 2.3 24.5 1.0 O A:HOH619 2.7 54.0 1.0 CD A:GLU412 3.1 27.0 1.0 CG A:ASP287 3.1 26.1 1.0 CD2 A:HIS370 3.2 18.6 1.0 CE1 A:HIS370 3.2 22.1 1.0 OE1 A:GLU412 3.2 29.5 1.0 CD A:GLU452 3.3 23.9 1.0 MN A:MN500 3.3 24.6 0.7 OD1 A:ASP287 3.5 27.8 1.0 OE1 A:GLU452 3.7 26.6 1.0 OG1 A:THR410 3.9 21.6 1.0 CG2 A:THR410 3.9 21.0 1.0 O A:HOH877 3.9 35.7 1.0 N A:PRO504 4.1 66.8 1.0 CA A:PRO504 4.1 76.2 1.0 CB A:THR410 4.2 19.3 1.0 ND1 A:HIS370 4.3 20.1 1.0 CB A:ASP287 4.3 24.3 1.0 CG A:HIS370 4.3 23.9 1.0 CG A:GLU412 4.4 21.4 1.0 CG A:GLU452 4.6 22.7 1.0 NE2 A:HIS377 4.6 24.0 1.0 CD2 A:HIS377 4.8 22.8 1.0 C A:PRO504 4.9 67.1 1.0 CG2 A:VAL376 5.0 27.0 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Wild-Type Human Prolidase with Mn Ions and Pro Ligand


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 Wild-Type Human Prolidase with Mn Ions and Pro Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn500 b:24.6 occ:0.70 O A:OH501 2.1 30.4 1.0 OD1 A:ASP287 2.2 27.8 1.0 OD2 A:ASP276 2.2 23.7 1.0 OE1 A:GLU452 2.2 26.6 1.0 OD1 A:ASP276 2.3 25.4 1.0 O A:HOH877 2.5 35.7 1.0 CG A:ASP276 2.5 19.3 1.0 CD A:GLU452 3.1 23.9 1.0 CG A:ASP287 3.1 26.1 1.0 OE2 A:GLU452 3.2 21.9 1.0 MN A:MN499 3.3 22.2 0.7 OD2 A:ASP287 3.4 26.3 1.0 OG1 A:THR289 3.6 22.6 1.0 OH A:TYR241 3.8 29.5 1.0 O A:HOH619 3.8 54.0 1.0 CB A:ASP276 4.0 21.5 1.0 OE1 A:GLU412 4.1 29.5 1.0 CZ A:TYR241 4.2 33.2 1.0 CE2 A:TYR241 4.4 31.9 1.0 CB A:ASP287 4.5 24.3 1.0 N A:PRO504 4.5 66.8 1.0 CG A:GLU452 4.5 22.7 1.0 CD A:PRO504 4.6 72.0 1.0 C A:ASP287 4.7 23.1 1.0 N A:ILE288 4.7 21.7 1.0 NE A:ARG450 4.7 19.9 1.0 CD A:GLU412 4.8 27.0 1.0 CA A:ASP287 4.8 18.9 1.0 CA A:ASP276 4.8 19.1 1.0 OE2 A:GLU412 4.8 24.5 1.0 O A:ILE288 4.8 21.1 1.0 CE1 A:TYR241 4.9 28.2 1.0 NH2 A:ARG450 4.9 25.2 1.0 C A:ILE288 5.0 24.6 1.0 CB A:GLU452 5.0 20.2 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Wild-Type Human Prolidase with Mn Ions and Pro Ligand


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 Wild-Type Human Prolidase with Mn Ions and Pro Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn499 b:27.3 occ:0.86 OE2 B:GLU452 2.2 26.0 1.0 NE2 B:HIS370 2.2 22.7 1.0 OE2 B:GLU412 2.3 25.6 1.0 OD2 B:ASP287 2.3 26.6 1.0 O B:OH501 2.3 30.1 1.0 O B:HOH631 2.8 62.1 1.0 CD B:GLU412 3.0 32.1 1.0 CG B:ASP287 3.2 25.2 1.0 CD2 B:HIS370 3.2 22.9 1.0 OE1 B:GLU412 3.2 33.1 1.0 CE1 B:HIS370 3.2 24.1 1.0 CD B:GLU452 3.2 22.6 1.0 MN B:MN500 3.3 21.7 0.6 OD1 B:ASP287 3.5 24.8 1.0 OE1 B:GLU452 3.6 28.2 1.0 CG2 B:THR410 3.9 20.4 1.0 OG1 B:THR410 3.9 23.9 1.0 CB B:THR410 4.1 18.9 1.0 O B:HOH871 4.2 36.4 1.0 N B:PRO504 4.2 78.5 1.0 CA B:PRO504 4.3 74.1 1.0 ND1 B:HIS370 4.3 22.9 1.0 CG B:HIS370 4.3 20.9 1.0 CB B:ASP287 4.4 18.4 1.0 CG B:GLU412 4.4 23.7 1.0 CG B:GLU452 4.5 23.1 1.0 NE2 B:HIS377 4.6 26.5 1.0 CD2 B:HIS377 4.8 30.4 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Wild-Type Human Prolidase with Mn Ions and Pro Ligand


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 Wild-Type Human Prolidase with Mn Ions and Pro Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn500 b:21.7 occ:0.57 OD1 B:ASP287 2.1 24.8 1.0 O B:OH501 2.1 30.1 1.0 OE1 B:GLU452 2.2 28.2 1.0 OD1 B:ASP276 2.2 24.4 1.0 OD2 B:ASP276 2.3 25.6 1.0 O B:HOH871 2.5 36.4 1.0 CG B:ASP276 2.6 24.9 1.0 CG B:ASP287 3.0 25.2 1.0 CD B:GLU452 3.1 22.6 1.0 OE2 B:GLU452 3.3 26.0 1.0 OD2 B:ASP287 3.3 26.6 1.0 MN B:MN499 3.3 27.3 0.9 OG1 B:THR289 3.7 24.6 1.0 OH B:TYR241 3.7 26.6 1.0 O B:HOH631 3.8 62.1 1.0 CB B:ASP276 4.0 24.9 1.0 CZ B:TYR241 4.1 34.3 1.0 OE1 B:GLU412 4.1 33.1 1.0 CE2 B:TYR241 4.4 38.7 1.0 CB B:ASP287 4.4 18.4 1.0 CG B:GLU452 4.5 23.1 1.0 C B:ASP287 4.6 21.6 1.0 N B:PRO504 4.6 78.5 1.0 CD B:PRO504 4.7 68.1 1.0 N B:ILE288 4.7 21.0 1.0 CE1 B:TYR241 4.7 29.9 1.0 NE B:ARG450 4.8 26.0 1.0 CA B:ASP287 4.8 18.9 1.0 CD B:GLU412 4.8 32.1 1.0 CA B:ASP276 4.8 24.2 1.0 O B:ILE288 4.9 20.8 1.0 OE2 B:GLU412 4.9 25.6 1.0 O B:ASP287 4.9 21.3 1.0 NH2 B:ARG450 4.9 28.2 1.0 C B:ILE288 4.9 19.7 1.0 CB B:GLU452 5.0 21.1 1.0

P.Wilk, M.Uehlein, J.Kalms, H.Dobbek, U.Mueller, M.S.Weiss. Substrate Specificity and Reaction Mechanism of Human Prolidase. Febs J. V. 284 2870 2017.
ISSN: ISSN 1742-4658
PubMed: 28677335
DOI: 10.1111/FEBS.14158