Manganese in PDB 3d27: E. Coli Methionine Aminopeptidase with Fe Inhibitor W29

All present enzymatic activity of E. Coli Methionine Aminopeptidase with Fe Inhibitor W29:
3.4.11.18;

The structure of E. Coli Methionine Aminopeptidase with Fe Inhibitor W29, PDB code: 3d27 was solved by Q.Z.Ye, S.Chai, H.Z.He, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.86 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.510, 59.880, 54.880, 90.00, 106.47, 90.00
R / Rfree (%)	19.1 / 24.4

The binding sites of Manganese atom in the E. Coli Methionine Aminopeptidase with Fe Inhibitor W29 (pdb code 3d27). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the E. Coli Methionine Aminopeptidase with Fe Inhibitor W29, PDB code: 3d27:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the E. Coli Methionine Aminopeptidase with Fe Inhibitor W29


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of E. Coli Methionine Aminopeptidase with Fe Inhibitor W29 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1 b:20.6 occ:1.00 OD2 A:ASP108 2.2 14.2 1.0 OE2 A:GLU235 2.3 14.6 1.0 OE2 A:GLU204 2.3 16.0 1.0 NE2 A:HIS171 2.3 11.4 1.0 O2 A:W29265 2.4 32.9 1.0 O1 A:W29265 2.4 32.9 1.0 CG A:ASP108 3.1 14.7 1.0 CD2 A:HIS171 3.1 11.7 1.0 CD A:GLU204 3.2 15.5 1.0 C10 A:W29265 3.2 33.1 1.0 C05 A:W29265 3.2 32.8 1.0 CD A:GLU235 3.2 13.8 1.0 MN A:MN2 3.4 18.7 1.0 CE1 A:HIS171 3.4 11.9 1.0 OD1 A:ASP108 3.5 15.3 1.0 OE1 A:GLU235 3.5 13.6 1.0 OE1 A:GLU204 3.5 17.8 1.0 OG1 A:THR202 3.9 13.5 1.0 CB A:ASP108 4.3 14.5 1.0 CG2 A:THR202 4.3 14.1 1.0 CG A:HIS171 4.4 12.5 1.0 NE2 A:HIS178 4.4 16.8 1.0 CG A:GLU204 4.4 15.0 1.0 CB A:THR202 4.4 14.2 1.0 ND1 A:HIS171 4.5 12.2 1.0 C06 A:W29265 4.5 33.2 1.0 C03 A:W29265 4.6 33.0 1.0 CE1 A:PHE177 4.6 16.8 1.0 CG A:GLU235 4.6 13.8 1.0 O A:HOH386 4.8 20.4 1.0 CD2 A:HIS178 5.0 17.0 1.0

Manganese binding site 2 out of 2 in the E. Coli Methionine Aminopeptidase with Fe Inhibitor W29


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of E. Coli Methionine Aminopeptidase with Fe Inhibitor W29 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2 b:18.7 occ:1.00 O2 A:W29265 2.0 32.9 1.0 OD1 A:ASP97 2.1 12.9 1.0 OE1 A:GLU235 2.1 13.6 1.0 OD1 A:ASP108 2.2 15.3 1.0 O A:HOH386 2.4 20.4 1.0 OD2 A:ASP97 2.6 13.9 1.0 CG A:ASP97 2.6 13.9 1.0 C10 A:W29265 3.0 33.1 1.0 CD A:GLU235 3.1 13.8 1.0 CG A:ASP108 3.2 14.7 1.0 MN A:MN1 3.4 20.6 1.0 OE2 A:GLU235 3.5 14.6 1.0 C06 A:W29265 3.5 33.2 1.0 OD2 A:ASP108 3.5 14.2 1.0 O A:HOH272 3.7 14.5 1.0 OG1 A:THR99 3.9 15.8 1.0 CB A:ASP97 4.1 14.2 1.0 C05 A:W29265 4.2 32.8 1.0 O A:VAL98 4.3 15.1 1.0 OE1 A:GLU204 4.4 17.8 1.0 N A:THR109 4.4 14.8 1.0 CG A:GLU235 4.5 13.8 1.0 CB A:ASP108 4.5 14.5 1.0 O1 A:W29265 4.5 32.9 1.0 O A:THR109 4.6 15.1 1.0 C A:ASP108 4.7 14.6 1.0 O A:HOH388 4.7 29.1 1.0 N A:VAL98 4.7 14.5 1.0 C A:THR109 4.8 15.1 1.0 CA A:ASP97 4.8 14.3 1.0 C04 A:W29265 4.8 33.2 1.0 OE2 A:GLU204 4.8 16.0 1.0 CA A:ASP108 4.9 14.6 1.0 CB A:GLU235 4.9 14.2 1.0 C A:VAL98 4.9 15.2 1.0 C A:ASP97 4.9 14.4 1.0 CD A:GLU204 4.9 15.5 1.0 CA A:THR109 5.0 15.0 1.0

W.L.Wang, S.C.Chai, M.Huang, H.Z.He, T.D.Hurley, Q.Z.Ye. Discovery of Inhibitors of Escherichia Coli Methionine Aminopeptidase with the Fe(II)-Form Selectivity and Antibacterial Activity. J.Med.Chem. V. 51 6110 2008.
ISSN: ISSN 0022-2623
PubMed: 18785729
DOI: 10.1021/JM8005788