Manganese in PDB 5m4g: Crystal Structure of Wild-Type Human Prolidase with Mn Ions

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

The structure of Crystal Structure of Wild-Type Human Prolidase with Mn Ions, PDB code: 5m4g 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)	43.18 / 1.48
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	103.641, 108.282, 211.452, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 16.7

The binding sites of Manganese atom in the Crystal Structure of Wild-Type Human Prolidase with Mn Ions (pdb code 5m4g). 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, PDB code: 5m4g:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn499 b:17.0 occ:0.48 OD2 A:ASP287 2.3 19.2 1.0 OE2 A:GLU452 2.3 18.6 1.0 NE2 A:HIS370 2.4 14.5 1.0 OE2 A:GLU412 2.4 24.0 1.0 O A:OH501 2.4 26.4 1.0 O A:HOH661 2.8 33.8 1.0 CD A:GLU412 3.1 22.4 1.0 CG A:ASP287 3.2 17.6 1.0 MN A:MN500 3.2 15.8 0.4 OE1 A:GLU412 3.3 25.1 1.0 CE1 A:HIS370 3.3 13.9 1.0 CD A:GLU452 3.4 17.9 1.0 CD2 A:HIS370 3.4 15.0 1.0 OD1 A:ASP287 3.5 18.3 1.0 OE1 A:GLU452 3.7 20.3 1.0 O A:HOH791 3.9 35.1 1.0 OG1 A:THR410 4.0 14.5 1.0 CG2 A:THR410 4.1 14.5 1.0 O A:HOH616 4.3 42.0 1.0 CB A:THR410 4.3 14.0 1.0 CB A:ASP287 4.4 15.3 1.0 CG A:GLU412 4.4 17.5 1.0 ND1 A:HIS370 4.4 14.2 1.0 NE2 A:HIS377 4.5 19.4 1.0 CG A:HIS370 4.5 14.8 1.0 CG A:GLU452 4.6 14.9 1.0 CD2 A:HIS377 4.8 17.4 1.0 O A:HOH815 4.9 31.9 1.0 O A:HOH886 5.0 45.6 1.0 OD2 A:ASP276 5.0 16.8 1.0 O A:HOH1101 5.0 51.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn500 b:15.8 occ:0.39 O A:OH501 2.1 26.4 1.0 OD1 A:ASP287 2.1 18.3 1.0 O A:HOH791 2.2 35.1 1.0 OE1 A:GLU452 2.2 20.3 1.0 OD2 A:ASP276 2.2 16.8 1.0 OD1 A:ASP276 2.3 16.8 1.0 CG A:ASP276 2.6 16.2 1.0 CD A:GLU452 3.0 17.9 1.0 CG A:ASP287 3.1 17.6 1.0 MN A:MN499 3.2 17.0 0.5 OE2 A:GLU452 3.2 18.6 1.0 OD2 A:ASP287 3.3 19.2 1.0 OG1 A:THR289 3.6 14.5 1.0 OH A:TYR241 3.8 18.5 1.0 OE1 A:GLU412 3.9 25.1 1.0 CB A:ASP276 4.1 14.4 1.0 CZ A:TYR241 4.2 18.1 1.0 O A:HOH661 4.2 33.8 1.0 O A:HOH616 4.3 42.0 1.0 CB A:ASP287 4.4 15.3 1.0 CG A:GLU452 4.4 14.9 1.0 CE2 A:TYR241 4.5 18.4 1.0 C A:ASP287 4.6 13.6 1.0 CD A:GLU412 4.7 22.4 1.0 N A:ILE288 4.7 13.0 1.0 NH2 A:ARG450 4.7 16.6 1.0 NE A:ARG450 4.7 16.4 1.0 OE2 A:GLU412 4.8 24.0 1.0 CA A:ASP287 4.8 14.3 1.0 CE1 A:TYR241 4.8 17.1 1.0 O A:ILE288 4.8 12.7 1.0 CA A:ASP276 4.9 13.4 1.0 CB A:GLU452 4.9 13.7 1.0 C A:ILE288 4.9 12.2 1.0 O A:ASP287 5.0 14.2 1.0 CB A:THR289 5.0 13.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn499 b:17.4 occ:0.48 OD2 B:ASP287 2.3 18.6 1.0 OE2 B:GLU452 2.3 18.8 1.0 O B:OH501 2.4 25.7 1.0 NE2 B:HIS370 2.4 14.3 1.0 OE2 B:GLU412 2.5 23.9 1.0 O B:HOH652 2.9 34.5 1.0 CD B:GLU412 3.2 22.4 1.0 CG B:ASP287 3.2 17.5 1.0 MN B:MN500 3.3 17.9 0.4 OE1 B:GLU412 3.3 26.2 1.0 CD B:GLU452 3.4 18.1 1.0 CE1 B:HIS370 3.4 13.9 1.0 CD2 B:HIS370 3.4 14.0 1.0 OD1 B:ASP287 3.5 19.7 1.0 OE1 B:GLU452 3.7 18.8 1.0 O B:HOH830 3.8 27.1 1.0 OG1 B:THR410 4.0 15.0 1.0 CG2 B:THR410 4.1 15.1 1.0 CB B:THR410 4.3 14.2 1.0 CB B:ASP287 4.4 14.3 1.0 CG B:GLU412 4.5 16.4 1.0 ND1 B:HIS370 4.5 13.6 1.0 NE2 B:HIS377 4.5 19.7 1.0 CG B:HIS370 4.5 13.8 1.0 CG B:GLU452 4.6 15.6 1.0 CD2 B:HIS377 4.8 18.0 1.0 O B:HOH855 4.8 27.6 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn500 b:17.9 occ:0.43 O B:OH501 2.0 25.7 1.0 OD1 B:ASP287 2.1 19.7 1.0 O B:HOH830 2.1 27.1 1.0 OD2 B:ASP276 2.2 16.9 1.0 OD1 B:ASP276 2.2 16.2 1.0 OE1 B:GLU452 2.2 18.8 1.0 CG B:ASP276 2.5 16.5 1.0 CG B:ASP287 3.0 17.5 1.0 CD B:GLU452 3.1 18.1 1.0 MN B:MN499 3.3 17.4 0.5 OE2 B:GLU452 3.3 18.8 1.0 OD2 B:ASP287 3.3 18.6 1.0 OG1 B:THR289 3.6 13.0 1.0 OH B:TYR241 3.8 18.1 1.0 CB B:ASP276 4.0 15.2 1.0 OE1 B:GLU412 4.0 26.2 1.0 CZ B:TYR241 4.1 17.9 1.0 O B:HOH652 4.3 34.5 1.0 CE2 B:TYR241 4.4 19.0 1.0 CB B:ASP287 4.4 14.3 1.0 CG B:GLU452 4.5 15.6 1.0 C B:ASP287 4.7 12.9 1.0 NH2 B:ARG450 4.7 17.7 1.0 N B:ILE288 4.7 11.5 1.0 NE B:ARG450 4.7 16.5 1.0 CA B:ASP287 4.8 12.7 1.0 CD B:GLU412 4.8 22.4 1.0 CE1 B:TYR241 4.8 16.1 1.0 CA B:ASP276 4.8 13.3 1.0 O B:ILE288 4.8 12.5 1.0 OE2 B:GLU412 4.9 23.9 1.0 C B:ILE288 4.9 11.8 1.0 CB B:GLU452 4.9 14.2 1.0 CB B:THR289 5.0 12.9 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