Zinc in PDB 1kq9: Human Methionine Aminopeptidase Type II in Complex with L- Methionine

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

The structure of Human Methionine Aminopeptidase Type II in Complex with L- Methionine, PDB code: 1kq9 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)	66.00 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	90.069, 98.660, 101.370, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.7

The binding sites of Zinc atom in the Human Methionine Aminopeptidase Type II in Complex with L- Methionine (pdb code 1kq9). 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 L- Methionine, PDB code: 1kq9:
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 L- 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 L- Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn479 b:19.1 occ:1.00 OXT A:MET601 2.0 18.8 1.0 OD1 A:ASP262 2.4 16.0 1.0 N A:MET601 2.4 22.1 1.0 OE1 A:GLU459 2.4 12.5 1.0 OD1 A:ASP251 2.4 19.6 1.0 OD2 A:ASP251 2.6 17.2 1.0 CG A:ASP251 2.9 17.9 1.0 C A:MET601 3.0 36.8 1.0 CG A:ASP262 3.1 17.3 1.0 CA A:MET601 3.2 30.8 1.0 CD A:GLU459 3.2 23.1 1.0 ZN A:ZN480 3.2 20.7 1.0 OD2 A:ASP262 3.3 16.3 1.0 OE2 A:GLU459 3.4 14.7 1.0 CZ A:PHE219 3.9 17.5 1.0 O A:MET601 4.1 39.7 1.0 OE2 A:GLU364 4.2 21.4 1.0 CE2 A:PHE219 4.2 18.1 1.0 NE2 A:GLN457 4.3 14.5 1.0 O A:HOH805 4.3 39.3 1.0 CB A:ASP251 4.4 14.8 1.0 O A:HOH758 4.4 43.4 1.0 CG A:GLU459 4.5 11.3 1.0 CB A:ASP262 4.5 13.6 1.0 CB A:MET601 4.6 27.6 1.0 N A:CYS263 4.6 15.2 1.0 C A:ASP262 4.7 14.4 1.0 CE1 A:PHE219 4.7 16.3 1.0 CD A:GLU364 4.8 25.3 1.0 CB A:ALA264 4.8 16.8 1.0 CA A:ASP262 4.8 15.6 1.0 OE1 A:GLU364 4.9 25.5 1.0 CB A:GLU459 5.0 13.4 1.0 CA A:ASP251 5.0 12.8 1.0

Zinc binding site 2 out of 2 in the Human Methionine Aminopeptidase Type II in Complex with L- 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 L- Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn480 b:20.7 occ:1.00 OXT A:MET601 2.1 18.8 1.0 OE2 A:GLU459 2.4 14.7 1.0 OD2 A:ASP262 2.4 16.3 1.0 NE2 A:HIS331 2.5 20.0 1.0 OE1 A:GLU364 2.6 25.5 1.0 C A:MET601 2.9 36.8 1.0 O A:MET601 3.0 39.7 1.0 CD A:GLU364 3.2 25.3 1.0 ZN A:ZN479 3.2 19.1 1.0 CD A:GLU459 3.3 23.1 1.0 CG A:ASP262 3.3 17.3 1.0 CD2 A:HIS331 3.3 18.5 1.0 CE1 A:HIS331 3.4 18.6 1.0 OE2 A:GLU364 3.6 21.4 1.0 OE1 A:GLU459 3.6 12.5 1.0 CB A:ALA362 3.7 22.8 1.0 OD1 A:ASP262 3.8 16.0 1.0 O A:HOH787 4.0 43.4 1.0 O A:HOH805 4.2 39.3 1.0 CG A:GLU364 4.2 20.3 1.0 CA A:MET601 4.2 30.8 1.0 N A:MET601 4.4 22.1 1.0 ND1 A:HIS331 4.5 19.6 1.0 CG A:HIS331 4.5 19.6 1.0 CB A:ASP262 4.6 13.6 1.0 CG A:GLU459 4.6 11.3 1.0 CB A:GLU364 4.8 22.4 1.0 NE2 A:HIS339 4.9 50.1 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