Manganese in PDB 5x49: Crystal Structure of Human Mitochondrial X-Prolyl Aminopeptidase (XPNPEP3)

All present enzymatic activity of Crystal Structure of Human Mitochondrial X-Prolyl Aminopeptidase (XPNPEP3):
3.4.11.9;

The structure of Crystal Structure of Human Mitochondrial X-Prolyl Aminopeptidase (XPNPEP3), PDB code: 5x49 was solved by R.Singh, A.Kumar, B.Ghosh, S.Jamdar, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.98 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.897, 135.103, 67.205, 90.00, 99.87, 90.00
R / Rfree (%)	15.4 / 17.8

The binding sites of Manganese atom in the Crystal Structure of Human Mitochondrial X-Prolyl Aminopeptidase (XPNPEP3) (pdb code 5x49). 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 Human Mitochondrial X-Prolyl Aminopeptidase (XPNPEP3), PDB code: 5x49:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Human Mitochondrial X-Prolyl Aminopeptidase (XPNPEP3)


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 Human Mitochondrial X-Prolyl Aminopeptidase (XPNPEP3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:11.4 occ:1.00 OD2 A:ASP342 2.2 12.8 1.0 OE2 A:GLU475 2.2 12.4 1.0 O2 A:01B604 2.2 12.9 1.0 OE2 A:GLU451 2.2 12.6 1.0 NE2 A:HIS424 2.2 12.7 1.0 OXT A:01B604 2.3 14.2 1.0 CD A:GLU451 3.1 13.0 1.0 CG A:ASP342 3.1 12.0 1.0 C3 A:01B604 3.1 15.5 1.0 C2 A:01B604 3.1 14.5 1.0 CD2 A:HIS424 3.2 12.2 1.0 CE1 A:HIS424 3.3 11.2 1.0 OE1 A:GLU451 3.3 13.9 1.0 CD A:GLU475 3.3 14.8 1.0 MN A:MN602 3.4 11.6 1.0 OD1 A:ASP342 3.4 11.5 1.0 C1 A:01B604 3.6 12.2 1.0 OE1 A:GLU475 3.7 11.0 1.0 OG1 A:THR449 3.9 12.1 1.0 CG2 A:THR449 4.1 10.6 1.0 N2 A:01B604 4.2 10.3 1.0 CB A:THR449 4.3 9.7 1.0 C2 A:DMS607 4.3 37.5 1.0 O3 A:01B604 4.3 14.5 1.0 CG A:HIS424 4.3 13.7 1.0 ND1 A:HIS424 4.4 10.5 1.0 CB A:ASP342 4.4 12.4 1.0 CG A:GLU451 4.5 12.8 1.0 CG A:GLU475 4.6 13.3 1.0 NE2 A:HIS431 4.6 14.6 1.0 C6 A:01B604 4.8 13.5 1.0 CG1 A:VAL430 4.9 13.6 1.0 CD2 A:HIS431 5.0 13.7 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Human Mitochondrial X-Prolyl Aminopeptidase (XPNPEP3)


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 Human Mitochondrial X-Prolyl Aminopeptidase (XPNPEP3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:11.6 occ:1.00 OD1 A:ASP342 2.1 11.5 1.0 OE1 A:GLU475 2.1 11.0 1.0 O2 A:01B604 2.1 12.9 1.0 OD1 A:ASP331 2.3 11.9 1.0 OD2 A:ASP331 2.3 11.2 1.0 N2 A:01B604 2.3 10.3 1.0 CG A:ASP331 2.6 9.7 1.0 CD A:GLU475 3.0 14.8 1.0 C2 A:01B604 3.0 14.5 1.0 C1 A:01B604 3.0 12.2 1.0 CG A:ASP342 3.1 12.0 1.0 OE2 A:GLU475 3.2 12.4 1.0 MN A:MN601 3.4 11.4 1.0 OD2 A:ASP342 3.5 12.8 1.0 OG1 A:THR344 3.7 11.2 1.0 OH A:TYR300 3.7 12.2 1.0 OE1 A:GLU451 3.9 13.9 1.0 CB A:ASP331 4.1 12.6 1.0 CZ A:TYR300 4.2 12.2 1.0 C3 A:01B604 4.3 15.5 1.0 CG A:GLU475 4.3 13.3 1.0 C A:ASP342 4.4 11.9 1.0 CB A:ASP342 4.4 12.4 1.0 C6 A:01B604 4.5 13.5 1.0 N A:ILE343 4.5 10.3 1.0 CE1 A:TYR300 4.5 10.0 1.0 OXT A:01B604 4.6 14.2 1.0 O A:ILE343 4.6 12.0 1.0 CD A:GLU451 4.7 13.0 1.0 CA A:ASP342 4.7 11.8 1.0 O A:ASP342 4.7 11.9 1.0 OE2 A:GLU451 4.7 12.6 1.0 C A:ILE343 4.7 10.2 1.0 CE2 A:TYR300 4.8 13.4 1.0 CB A:GLU475 4.9 9.8 1.0 CA A:ASP331 4.9 12.4 1.0 NE A:ARG473 4.9 10.6 1.0 NH2 A:ARG473 5.0 11.4 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Human Mitochondrial X-Prolyl Aminopeptidase (XPNPEP3)


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 Human Mitochondrial X-Prolyl Aminopeptidase (XPNPEP3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn601 b:12.1 occ:1.00 OD2 B:ASP342 2.1 13.2 1.0 O2 B:01B604 2.2 13.7 1.0 NE2 B:HIS424 2.2 14.5 1.0 OE2 B:GLU451 2.2 12.6 1.0 OE1 B:GLU475 2.2 12.4 1.0 O3 B:01B604 2.3 15.6 1.0 C2 B:01B604 3.0 15.7 1.0 C3 B:01B604 3.1 15.8 1.0 CD B:GLU451 3.1 14.2 1.0 CG B:ASP342 3.1 12.9 1.0 CD2 B:HIS424 3.2 12.3 1.0 CE1 B:HIS424 3.2 10.4 1.0 OE1 B:GLU451 3.3 14.3 1.0 CD B:GLU475 3.3 13.0 1.0 OD1 B:ASP342 3.4 12.6 1.0 MN B:MN602 3.4 11.8 1.0 C1 B:01B604 3.5 12.4 1.0 OE2 B:GLU475 3.7 11.4 1.0 OG1 B:THR449 3.9 13.2 1.0 CG2 B:THR449 4.1 11.0 1.0 N2 B:01B604 4.2 11.4 1.0 OXT B:01B604 4.3 15.9 1.0 CB B:THR449 4.3 12.5 1.0 ND1 B:HIS424 4.3 11.4 1.0 CG B:HIS424 4.3 13.3 1.0 CB B:ASP342 4.4 13.0 1.0 CG B:GLU451 4.4 14.3 1.0 NE2 B:HIS431 4.6 14.7 1.0 CG B:GLU475 4.6 14.5 1.0 C6 B:01B604 4.8 13.8 1.0 CD2 B:HIS431 4.9 15.0 1.0 CG1 B:VAL430 4.9 13.3 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Human Mitochondrial X-Prolyl Aminopeptidase (XPNPEP3)


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 Human Mitochondrial X-Prolyl Aminopeptidase (XPNPEP3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn602 b:11.8 occ:1.00 OD1 B:ASP342 2.1 12.6 1.0 O2 B:01B604 2.1 13.7 1.0 OE2 B:GLU475 2.2 11.4 1.0 OD1 B:ASP331 2.3 13.7 1.0 OD2 B:ASP331 2.3 10.9 1.0 N2 B:01B604 2.3 11.4 1.0 CG B:ASP331 2.6 12.5 1.0 C2 B:01B604 3.0 15.7 1.0 C1 B:01B604 3.0 12.4 1.0 CD B:GLU475 3.0 13.0 1.0 CG B:ASP342 3.1 12.9 1.0 OE1 B:GLU475 3.3 12.4 1.0 MN B:MN601 3.4 12.1 1.0 OD2 B:ASP342 3.4 13.2 1.0 OG1 B:THR344 3.7 11.6 1.0 OH B:TYR300 3.7 11.3 1.0 OE1 B:GLU451 3.9 14.3 1.0 CB B:ASP331 4.1 12.0 1.0 CZ B:TYR300 4.2 11.8 1.0 C3 B:01B604 4.3 15.8 1.0 CG B:GLU475 4.4 14.5 1.0 C B:ASP342 4.4 11.5 1.0 CB B:ASP342 4.4 13.0 1.0 C6 B:01B604 4.5 13.8 1.0 N B:ILE343 4.5 11.7 1.0 CE1 B:TYR300 4.5 10.7 1.0 O3 B:01B604 4.6 15.6 1.0 O B:ILE343 4.6 12.8 1.0 CD B:GLU451 4.7 14.2 1.0 CA B:ASP342 4.7 11.4 1.0 C B:ILE343 4.7 11.2 1.0 OE2 B:GLU451 4.8 12.6 1.0 O B:ASP342 4.8 12.7 1.0 CE2 B:TYR300 4.8 11.3 1.0 CB B:GLU475 4.9 11.5 1.0 CA B:ASP331 4.9 10.7 1.0 NH2 B:ARG473 4.9 12.2 1.0 NE B:ARG473 4.9 11.7 1.0

R.Singh, S.N.Jamdar, V.D.Goyal, A.Kumar, B.Ghosh, R.D.Makde. Structure of the Human Aminopeptidase XPNPEP3 and Comparison of Its in Vitro Activity with ICP55 Orthologs: Insights Into Diverse Cellular Processes. J. Biol. Chem. V. 292 10035 2017.
ISSN: ESSN 1083-351X
PubMed: 28476889
DOI: 10.1074/JBC.M117.783357