Zinc in PDB 1kq0: Human Methionine Aminopeptidase Type II in Complex with D- Methionine

All present enzymatic activity of Human Methionine Aminopeptidase Type II in Complex with D- Methionine:
3.4.11.18;

The structure of Human Methionine Aminopeptidase Type II in Complex with D- Methionine, PDB code: 1kq0 was solved by M.C.Nonato, J.Widom, J.Clardy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	89.727, 98.938, 100.628, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 21.8

The binding sites of Zinc atom in the Human Methionine Aminopeptidase Type II in Complex with D- Methionine (pdb code 1kq0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Methionine Aminopeptidase Type II in Complex with D- Methionine, PDB code: 1kq0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Methionine Aminopeptidase Type II in Complex with D- Methionine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Methionine Aminopeptidase Type II in Complex with D- Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn479 b:32.6 occ:1.00 OD1 A:ASP262 1.9 21.4 1.0 OE1 A:GLU459 2.1 23.5 1.0 OD1 A:ASP251 2.2 18.3 1.0 OD2 A:ASP251 2.3 18.8 1.0 N A:MED601 2.5 62.5 1.0 CG A:ASP251 2.6 17.8 1.0 CG A:ASP262 2.8 20.1 1.0 OD2 A:ASP262 2.9 20.9 1.0 CD A:GLU459 3.0 22.3 1.0 ZN A:ZN480 3.1 35.6 1.0 OE2 A:GLU459 3.2 20.9 1.0 CA A:MED601 3.7 62.6 1.0 CZ A:PHE219 3.9 19.0 1.0 CB A:ASP251 4.1 17.1 1.0 NE2 A:GLN457 4.1 15.9 1.0 OE2 A:GLU364 4.2 23.4 1.0 CB A:ASP262 4.2 20.0 1.0 CE2 A:PHE219 4.3 18.9 1.0 O A:HOH747 4.3 29.9 1.0 CG A:GLU459 4.4 20.3 1.0 O A:HOH732 4.4 37.2 1.0 OE1 A:GLU364 4.5 25.0 1.0 CB A:ALA264 4.6 19.4 1.0 N A:CYS263 4.6 18.9 1.0 C A:MED601 4.6 62.7 1.0 C A:ASP262 4.6 19.3 1.0 CA A:ASP262 4.6 19.8 1.0 CD A:GLU364 4.6 23.5 1.0 CE1 A:PHE219 4.7 19.1 1.0 CB A:MED601 4.8 62.5 1.0 CA A:ASP251 4.9 17.1 1.0 CB A:GLU459 4.9 19.2 1.0

Zinc binding site 2 out of 2 in the Human Methionine Aminopeptidase Type II in Complex with D- Methionine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Methionine Aminopeptidase Type II in Complex with D- Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn480 b:35.6 occ:1.00 OD2 A:ASP262 2.0 20.9 1.0 OE2 A:GLU459 2.1 20.9 1.0 OE1 A:GLU364 2.1 25.0 1.0 CE1 A:HIS331 2.2 25.7 1.0 CD A:GLU364 3.0 23.5 1.0 CG A:ASP262 3.0 20.1 1.0 NE2 A:HIS331 3.1 26.1 1.0 CD A:GLU459 3.1 22.3 1.0 ZN A:ZN479 3.1 32.6 1.0 ND1 A:HIS331 3.2 25.9 1.0 OE2 A:GLU364 3.4 23.4 1.0 OD1 A:ASP262 3.5 21.4 1.0 OE1 A:GLU459 3.5 23.5 1.0 OXT A:MED601 3.6 62.7 1.0 N A:MED601 3.6 62.5 1.0 CA A:MED601 3.6 62.6 1.0 C A:MED601 3.6 62.7 1.0 CB A:ALA362 3.8 22.9 1.0 CG A:GLU364 4.1 23.0 1.0 O A:HOH747 4.1 29.9 1.0 CB A:ASP262 4.2 20.0 1.0 CD2 A:HIS331 4.3 24.8 1.0 O A:MED601 4.3 62.7 1.0 CG A:HIS331 4.4 24.9 1.0 CG A:GLU459 4.4 20.3 1.0 CB A:GLU364 4.8 22.1 1.0 OD2 A:ASP251 4.8 18.8 1.0

M.C.Nonato, J.Widom, J.Clardy. Human Methionine Aminopeptidase Type 2 in Complex with L- and D-Methionine Bioorg.Med.Chem.Lett. V. 16 2580 2006.
ISSN: ISSN 0960-894X
PubMed: 16540317
DOI: 10.1016/J.BMCL.2006.02.047