Manganese in PDB 3ctz: Structure of Human Cytosolic X-Prolyl Aminopeptidase

All present enzymatic activity of Structure of Human Cytosolic X-Prolyl Aminopeptidase:
3.4.11.9;

The structure of Structure of Human Cytosolic X-Prolyl Aminopeptidase, PDB code: 3ctz was solved by X.Li, Z.Lou, Z.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.62 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.444, 131.429, 169.076, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 19.6

The structure of Structure of Human Cytosolic X-Prolyl Aminopeptidase also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Sodium	(Na)	1 atom

The binding sites of Manganese atom in the Structure of Human Cytosolic X-Prolyl Aminopeptidase (pdb code 3ctz). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of Human Cytosolic X-Prolyl Aminopeptidase, PDB code: 3ctz:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of Human Cytosolic X-Prolyl Aminopeptidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Human Cytosolic X-Prolyl Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn624 b:17.7 occ:1.00 O A:HOH1519 2.2 25.1 1.0 OE2 A:GLU537 2.3 14.4 1.0 OE2 A:GLU523 2.3 15.6 1.0 NE2 A:HIS489 2.3 13.6 1.0 O A:HOH644 2.3 15.3 1.0 OD2 A:ASP426 2.4 14.5 1.0 O A:HOH1520 2.7 33.2 1.0 CD A:GLU523 3.1 13.9 1.0 CD2 A:HIS489 3.2 15.4 1.0 OE1 A:GLU523 3.3 15.7 1.0 CG A:ASP426 3.3 14.1 1.0 CE1 A:HIS489 3.3 14.1 1.0 CD A:GLU537 3.4 13.7 1.0 MN A:MN625 3.4 14.8 1.0 OD1 A:ASP426 3.5 14.2 1.0 O A:HOH1518 3.8 19.5 1.0 OE1 A:GLU537 3.9 13.2 1.0 CG2 A:THR521 4.0 14.0 1.0 OG1 A:THR521 4.1 12.8 1.0 O A:HOH659 4.3 36.4 1.0 CG A:HIS489 4.4 14.3 1.0 ND1 A:HIS489 4.4 15.2 1.0 CB A:THR521 4.4 13.1 1.0 NE2 A:HIS498 4.5 22.0 1.0 CG A:GLU523 4.5 12.8 1.0 CB A:ASP426 4.5 13.3 1.0 CG A:GLU537 4.6 12.0 1.0 CD2 A:HIS498 4.7 20.1 1.0 O A:HOH792 4.7 29.2 1.0 C11 A:P6G628 4.8 21.0 1.0 O13 A:P6G628 4.9 25.0 1.0

Manganese binding site 2 out of 2 in the Structure of Human Cytosolic X-Prolyl Aminopeptidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Human Cytosolic X-Prolyl Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn625 b:14.8 occ:1.00 OD1 A:ASP426 2.1 14.2 1.0 OD1 A:ASP415 2.2 13.0 1.0 OE1 A:GLU537 2.2 13.2 1.0 O A:HOH644 2.2 15.3 1.0 O A:HOH1518 2.3 19.5 1.0 OD2 A:ASP415 2.3 13.4 1.0 CG A:ASP415 2.6 12.1 1.0 CD A:GLU537 2.9 13.7 1.0 OE2 A:GLU537 3.0 14.4 1.0 CG A:ASP426 3.2 14.1 1.0 MN A:MN624 3.4 17.7 1.0 OD2 A:ASP426 3.5 14.5 1.0 OG1 A:THR428 3.6 12.2 1.0 CZ A:PHE381 3.7 12.7 1.0 O A:HOH1519 3.7 25.1 1.0 O A:HOH792 3.8 29.2 1.0 CB A:ASP415 4.1 13.2 1.0 OE1 A:GLU523 4.2 15.7 1.0 CE1 A:PHE381 4.2 14.8 1.0 CE2 A:PHE381 4.3 14.0 1.0 CG A:GLU537 4.4 12.0 1.0 N A:VAL427 4.4 12.1 1.0 CB A:ASP426 4.5 13.3 1.0 O1 A:P6G628 4.5 41.0 1.0 O A:VAL427 4.7 11.9 1.0 C A:ASP426 4.7 12.3 1.0 C A:VAL427 4.7 12.6 1.0 NE A:ARG535 4.8 12.2 1.0 CA A:ASP426 4.8 12.2 1.0 CA A:ASP415 4.9 11.9 1.0 CD A:GLU523 4.9 13.9 1.0 OE2 A:GLU523 4.9 15.6 1.0 N A:THR428 4.9 11.7 1.0 O A:HOH1520 4.9 33.2 1.0 CB A:GLU537 5.0 10.8 1.0 NH2 A:ARG535 5.0 13.2 1.0

X.Li, Z.Lou, X.Li, W.Zhou, M.Ma, Y.Cao, Y.Geng, M.Bartlam, X.C.Zhang, Z.Rao. Structure of Human Cytosolic X-Prolyl Aminopeptidase: A Double Mn(II)-Dependent Dimeric Enzyme with A Novel Three-Domain Subunit J.Biol.Chem. V. 283 22858 2008.
ISSN: ISSN 0021-9258
PubMed: 18515364
DOI: 10.1074/JBC.M710274200