Manganese in PDB 7a12: Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9)

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9):
3.4.11.18;

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9), PDB code: 7a12 was solved by J.H.Thorpe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.76 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.424, 100.628, 99.031, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 19.8

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9) (pdb code 7a12). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9), PDB code: 7a12:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9)


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 Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn511 b:23.3 occ:1.00 OD1 A:ASP262 2.0 22.7 1.0 OE2 A:GLU459 2.1 20.1 1.0 O A:HOH610 2.2 22.7 1.0 O A:HOH773 2.2 24.7 1.0 OD2 A:ASP251 2.3 19.6 1.0 OD1 A:ASP251 2.3 18.3 1.0 CG A:ASP251 2.6 19.6 1.0 CD A:GLU459 2.9 29.1 1.0 CG A:ASP262 3.0 23.3 1.0 OE1 A:GLU459 3.1 21.3 1.0 MN A:MN512 3.4 24.8 1.0 OD2 A:ASP262 3.4 22.5 1.0 CZ A:PHE219 4.0 23.1 1.0 O A:HOH780 4.1 21.1 0.5 NE2 A:GLN457 4.1 16.1 1.0 CB A:ASP251 4.1 17.1 1.0 O A:HOH742 4.1 38.8 1.0 OE2 A:GLU364 4.2 26.8 1.0 CE1 A:PHE219 4.3 23.8 1.0 O A:HOH603 4.3 38.6 1.0 O03 A:QVK510 4.3 36.9 0.5 CG A:GLU459 4.3 24.0 1.0 CB A:ASP262 4.4 22.3 1.0 O A:HOH835 4.4 48.8 1.0 N A:CYS263 4.6 20.2 1.0 CB A:ALA264 4.6 20.9 1.0 C A:ASP262 4.6 24.9 1.0 CA A:ASP262 4.7 21.1 1.0 CD A:GLU364 4.8 39.6 1.0 OE1 A:GLU364 4.8 28.8 1.0 CB A:GLU459 4.9 21.4 1.0 CE2 A:PHE219 4.9 25.3 1.0 CA A:ASP251 5.0 16.9 1.0 N05 A:QVK510 5.0 36.0 0.5

Manganese binding site 2 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9)


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 Methionine Aminopeptidase-2 in Complex with An Inhibitor GW557358X (Compound 9) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn512 b:24.8 occ:1.00 OD2 A:ASP262 2.2 22.5 1.0 O03 A:QVK510 2.2 36.9 0.5 OE1 A:GLU459 2.2 21.3 1.0 O A:HOH780 2.2 21.1 0.5 O A:HOH610 2.3 22.7 1.0 NE2 A:HIS331 2.3 29.2 1.0 OE1 A:GLU364 2.3 28.8 1.0 CG A:ASP262 3.0 23.3 1.0 CD A:GLU364 3.1 39.6 1.0 CE1 A:HIS331 3.3 29.0 1.0 C02 A:QVK510 3.3 36.1 0.5 CD A:GLU459 3.3 29.1 1.0 CD2 A:HIS331 3.3 29.4 1.0 MN A:MN511 3.4 23.3 1.0 OD1 A:ASP262 3.4 22.7 1.0 OE2 A:GLU364 3.5 26.8 1.0 OE2 A:GLU459 3.8 20.1 1.0 O A:HOH773 3.9 24.7 1.0 CB A:ALA362 3.9 25.4 1.0 N01 A:QVK510 3.9 35.1 0.5 O1 A:PO4501 4.2 70.5 1.0 CB A:ASP262 4.3 22.3 1.0 CG A:GLU364 4.3 25.9 1.0 O A:HOH742 4.3 38.8 1.0 C04 A:QVK510 4.4 36.4 0.5 ND1 A:HIS331 4.4 29.8 1.0 CG A:HIS331 4.5 28.7 1.0 N05 A:QVK510 4.5 36.0 0.5 CG A:GLU459 4.6 24.0 1.0 O3 A:PO4501 4.7 70.7 1.0

D.J.Hirst, M.Brandt, G.Bruton, E.Christodoulou, L.Cutler, N.Deeks, J.D.Goodacre, T.Jack, M.Lindon, A.Miah, K.Page, N.Parr, L.Shukla, M.Sims, P.Thomas, J.Thorpe, D.S.Holmes. Structure-Based Optimisation of Orally Active & Reversible Metap-2 Inhibitors Maintaining A Tight 'Molecular Budget'. Bioorg.Med.Chem.Lett. V. 30 27533 2020.
ISSN: ESSN 1464-3405
PubMed: 32919012
DOI: 10.1016/J.BMCL.2020.127533