Cobalt in PDB 1qxy: Crystal Structure of S. Aureus Methionine Aminopeptidase in Complex with A Ketoheterocycle 618

All present enzymatic activity of Crystal Structure of S. Aureus Methionine Aminopeptidase in Complex with A Ketoheterocycle 618:
3.4.11.18;

The structure of Crystal Structure of S. Aureus Methionine Aminopeptidase in Complex with A Ketoheterocycle 618, PDB code: 1qxy was solved by A.Douangamath, G.E.Dale, A.D'arcy, C.Oefner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.970, 76.690, 41.660, 90.00, 104.50, 90.00
R / Rfree (%)	14.2 / 16.5

The binding sites of Cobalt atom in the Crystal Structure of S. Aureus Methionine Aminopeptidase in Complex with A Ketoheterocycle 618 (pdb code 1qxy). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Crystal Structure of S. Aureus Methionine Aminopeptidase in Complex with A Ketoheterocycle 618, PDB code: 1qxy:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Crystal Structure of S. Aureus Methionine Aminopeptidase in Complex with A Ketoheterocycle 618


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of S. Aureus Methionine Aminopeptidase in Complex with A Ketoheterocycle 618 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1001 b:7.6 occ:1.00 OE2 A:GLU233 2.0 6.4 1.0 NE2 A:HIS168 2.1 7.2 1.0 OA A:M2C3001 2.1 8.4 1.0 OD2 A:ASP104 2.1 6.4 1.0 OE2 A:GLU202 2.2 8.4 1.0 O8 A:M2C3001 2.3 12.5 1.0 C7 A:M2C3001 2.7 11.9 1.0 CG A:ASP104 3.0 5.5 1.0 CD A:GLU202 3.0 8.0 1.0 CE1 A:HIS168 3.1 7.0 1.0 CD2 A:HIS168 3.1 7.2 1.0 CD A:GLU233 3.1 5.4 1.0 CO A:CO1002 3.3 6.5 1.0 OE1 A:GLU202 3.3 9.6 1.0 OD1 A:ASP104 3.4 6.0 1.0 OE1 A:GLU233 3.5 6.1 1.0 CO A:CO1003 3.7 5.8 0.3 C1 A:M2C3001 3.7 14.2 1.0 N10 A:M2C3001 3.8 12.8 1.0 C9 A:M2C3001 3.9 12.8 1.0 CB A:ALA200 3.9 7.6 1.0 N6 A:M2C3001 4.1 16.3 1.0 CB A:ASP104 4.2 4.5 1.0 ND1 A:HIS168 4.2 7.8 1.0 CG A:HIS168 4.2 7.2 1.0 CG A:GLU202 4.3 8.5 1.0 CG A:GLU233 4.4 5.4 1.0 O A:HOH3148 4.5 18.2 1.0 NE2 A:HIS175 4.6 16.5 1.0 C2 A:M2C3001 4.7 13.9 1.0 C11 A:M2C3001 4.9 13.0 1.0 OD1 A:ASP93 5.0 7.2 1.0

Cobalt binding site 2 out of 3 in the Crystal Structure of S. Aureus Methionine Aminopeptidase in Complex with A Ketoheterocycle 618


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of S. Aureus Methionine Aminopeptidase in Complex with A Ketoheterocycle 618 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1002 b:6.5 occ:1.00 OD1 A:ASP104 2.0 6.0 1.0 OE1 A:GLU233 2.0 6.1 1.0 OA A:M2C3001 2.0 8.4 1.0 OD2 A:ASP93 2.0 7.9 1.0 N10 A:M2C3001 2.1 12.8 1.0 OD1 A:ASP93 2.3 7.2 1.0 CG A:ASP93 2.5 6.7 1.0 C9 A:M2C3001 2.9 12.8 1.0 CD A:GLU233 2.9 5.4 1.0 CG A:ASP104 3.0 5.5 1.0 C7 A:M2C3001 3.0 11.9 1.0 OE2 A:GLU233 3.2 6.4 1.0 OD2 A:ASP104 3.2 6.4 1.0 CO A:CO1001 3.3 7.6 1.0 O8 A:M2C3001 3.8 12.5 1.0 CB A:ASP93 4.0 5.9 1.0 OE1 A:GLU202 4.0 9.6 1.0 C1 A:M2C3001 4.0 14.2 1.0 O A:HOH3035 4.2 11.3 1.0 C2 A:M2C3001 4.2 13.9 1.0 NE2 A:GLN231 4.2 7.4 1.0 O A:THR105 4.2 7.3 1.0 CB A:ASP104 4.3 4.5 1.0 CG A:GLU233 4.3 5.4 1.0 N A:THR105 4.3 4.8 1.0 C11 A:M2C3001 4.4 13.0 1.0 C A:THR105 4.6 5.3 1.0 C A:ASP104 4.6 4.7 1.0 OE2 A:GLU202 4.7 8.4 1.0 CD A:GLU202 4.7 8.0 1.0 CA A:ASP104 4.7 4.4 1.0 CA A:ASP93 4.8 4.5 1.0 CB A:GLU233 4.9 5.1 1.0 C A:ASP93 4.9 4.8 1.0 CA A:THR105 4.9 4.7 1.0 CB A:SER95 5.0 7.7 1.0 O A:HOH3069 5.0 12.0 1.0

Cobalt binding site 3 out of 3 in the Crystal Structure of S. Aureus Methionine Aminopeptidase in Complex with A Ketoheterocycle 618


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of S. Aureus Methionine Aminopeptidase in Complex with A Ketoheterocycle 618 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1003 b:5.8 occ:0.30 O8 A:M2C3001 1.8 12.5 1.0 N6 A:M2C3001 2.1 16.3 1.0 NE2 A:HIS175 2.1 16.5 1.0 O A:HOH3148 2.1 18.2 1.0 O A:HOH3172 2.4 22.8 1.0 C7 A:M2C3001 2.8 11.9 1.0 C1 A:M2C3001 2.8 14.2 1.0 CE1 A:HIS175 3.0 16.1 1.0 C5 A:M2C3001 3.2 16.9 1.0 CD2 A:HIS175 3.2 15.6 1.0 NE2 A:HIS168 3.6 7.2 1.0 CD2 A:HIS168 3.7 7.2 1.0 C11 A:M2C3001 3.7 13.0 1.0 CO A:CO1001 3.7 7.6 1.0 C9 A:M2C3001 3.8 12.8 1.0 OA A:M2C3001 3.8 8.4 1.0 OE2 A:GLU202 4.0 8.4 1.0 O A:HOH3293 4.1 33.9 1.0 C2 A:M2C3001 4.1 13.9 1.0 ND1 A:HIS175 4.2 16.5 1.0 CG A:HIS175 4.3 13.3 1.0 C4 A:M2C3001 4.4 16.4 1.0 CE1 A:HIS168 4.5 7.0 1.0 CG A:HIS168 4.5 7.2 1.0 O A:THR166 4.5 8.4 1.0 O A:HOH3263 4.7 31.2 1.0 O A:HOH3287 4.7 62.7 1.0 O A:HOH3219 4.8 30.8 1.0 CD A:GLU202 4.8 8.0 1.0 C3 A:M2C3001 4.8 16.4 1.0 N10 A:M2C3001 4.8 12.8 1.0 OD2 A:ASP104 4.8 6.4 1.0 O A:HOH3093 4.8 20.1 1.0 OE1 A:GLU202 4.9 9.6 1.0 ND1 A:HIS168 4.9 7.8 1.0

A.Douangamath, G.E.Dale, A.D'arcy, M.Almstetter, R.Eckl, A.Frutos-Hoener, B.Henkel, K.Illgen, S.Nerdinger, H.Schulz, A.Macsweeney, M.Thormann, A.Treml, S.Pierau, S.Wadman, C.Oefner. Crystal Structures of Staphylococcusaureus Methionine Aminopeptidase Complexed with Keto Heterocycle and Aminoketone Inhibitors Reveal the Formation of A Tetrahedral Intermediate. J.Med.Chem. V. 47 1325 2004.
ISSN: ISSN 0022-2623
PubMed: 14998322
DOI: 10.1021/JM034188J