Cobalt in PDB 4hxx: Pyridinylpyrimidines Selectively Inhibit Human Methionine Aminopeptidase-1

All present enzymatic activity of Pyridinylpyrimidines Selectively Inhibit Human Methionine Aminopeptidase-1:
3.4.11.18;

The structure of Pyridinylpyrimidines Selectively Inhibit Human Methionine Aminopeptidase-1, PDB code: 4hxx was solved by S.B.Gabelli, F.Zhang, J.Liu, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.33 / 2.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.500, 77.403, 48.068, 90.00, 90.92, 90.00
R / Rfree (%)	19 / 25.8

The structure of Pyridinylpyrimidines Selectively Inhibit Human Methionine Aminopeptidase-1 also contains other interesting chemical elements:

Potassium	(K)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Cobalt atom in the Pyridinylpyrimidines Selectively Inhibit Human Methionine Aminopeptidase-1 (pdb code 4hxx). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Pyridinylpyrimidines Selectively Inhibit Human Methionine Aminopeptidase-1, PDB code: 4hxx:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Pyridinylpyrimidines Selectively Inhibit Human Methionine Aminopeptidase-1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Pyridinylpyrimidines Selectively Inhibit Human Methionine Aminopeptidase-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:34.2 occ:1.00 OE2 A:GLU367 1.9 26.5 1.0 OE1 A:GLU336 2.1 28.7 1.0 OD2 A:ASP240 2.1 21.8 1.0 NE2 A:HIS303 2.1 24.0 1.0 CD A:GLU367 2.7 25.9 1.0 OE1 A:GLU367 2.9 29.2 1.0 CO A:CO402 3.0 34.6 1.0 CG A:ASP240 3.0 31.2 1.0 CD A:GLU336 3.1 31.4 1.0 CD2 A:HIS303 3.1 30.7 1.0 CE1 A:HIS303 3.1 33.7 1.0 OD1 A:ASP240 3.3 28.2 1.0 OE2 A:GLU336 3.5 36.0 1.0 O A:HOH587 3.7 41.1 1.0 OG1 A:THR334 3.7 33.2 1.0 CG2 A:THR334 4.0 29.7 1.0 O A:HOH506 4.1 27.2 1.0 CG A:GLU367 4.2 26.5 1.0 CB A:THR334 4.2 33.8 1.0 CG A:HIS303 4.2 32.4 1.0 ND1 A:HIS303 4.2 28.1 1.0 CB A:ASP240 4.3 30.0 1.0 CG A:GLU336 4.3 31.0 1.0 O A:HOH524 4.7 27.5 1.0 NE2 A:HIS310 4.8 33.9 1.0 C24 A:1AY405 4.8 52.0 1.0 CD2 A:HIS310 4.9 37.3 1.0 CB A:GLU336 4.9 32.8 1.0 OD2 A:ASP229 5.0 30.1 1.0

Cobalt binding site 2 out of 3 in the Pyridinylpyrimidines Selectively Inhibit Human Methionine Aminopeptidase-1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Pyridinylpyrimidines Selectively Inhibit Human Methionine Aminopeptidase-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:34.6 occ:1.00 OD1 A:ASP240 2.0 28.2 1.0 O A:HOH506 2.1 27.2 1.0 OD1 A:ASP229 2.1 24.9 1.0 OE1 A:GLU367 2.1 29.2 1.0 OD2 A:ASP229 2.6 30.1 1.0 CG A:ASP229 2.7 27.0 1.0 CG A:ASP240 2.9 31.2 1.0 CO A:CO401 3.0 34.2 1.0 OD2 A:ASP240 3.1 21.8 1.0 CD A:GLU367 3.2 25.9 1.0 OE2 A:GLU367 3.5 26.5 1.0 O A:HOH587 3.9 41.1 1.0 OG1 A:THR231 4.0 28.7 1.0 O A:HOH568 4.1 33.0 1.0 CB A:ASP229 4.2 24.6 1.0 ND2 A:ASN242 4.3 28.4 1.0 OE1 A:GLU336 4.3 28.7 1.0 O A:HOH607 4.3 46.3 1.0 CB A:ASP240 4.4 30.0 1.0 OE2 A:GLU336 4.4 36.0 1.0 CG A:GLU367 4.5 26.5 1.0 O A:ILE230 4.5 27.0 1.0 N A:LEU241 4.5 30.4 1.0 O A:HOH524 4.5 27.5 1.0 O A:LEU241 4.6 28.2 1.0 CD A:GLU336 4.7 31.4 1.0 O A:HOH518 4.7 29.8 1.0 C A:LEU241 4.8 28.2 1.0 CB A:ASN242 4.9 25.4 1.0 CB A:GLU367 4.9 27.8 1.0 C A:ASP240 4.9 30.4 1.0 CA A:ASP229 4.9 24.6 1.0 CA A:ASP240 4.9 30.4 1.0 NE2 A:HIS303 4.9 24.0 1.0 N A:ILE230 5.0 24.9 1.0 CO A:CO403 5.0 47.9 1.0

Cobalt binding site 3 out of 3 in the Pyridinylpyrimidines Selectively Inhibit Human Methionine Aminopeptidase-1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Pyridinylpyrimidines Selectively Inhibit Human Methionine Aminopeptidase-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co403 b:47.9 occ:1.00 N2 A:1AY405 2.1 55.1 1.0 NE2 A:HIS212 2.2 41.4 1.0 O A:HOH587 2.3 41.1 1.0 N25 A:1AY405 2.3 51.8 1.0 O A:HOH568 2.4 33.0 1.0 O A:HOH524 2.5 27.5 1.0 C3 A:1AY405 3.0 54.4 1.0 CD2 A:HIS212 3.0 36.7 1.0 C1 A:1AY405 3.0 53.6 1.0 C4 A:1AY405 3.1 52.8 1.0 CE1 A:HIS212 3.2 39.4 1.0 C23 A:1AY405 3.3 53.2 1.0 C24 A:1AY405 3.5 52.0 1.0 NE2 A:HIS310 4.1 33.9 1.0 CG A:HIS212 4.2 34.1 1.0 ND1 A:HIS212 4.3 36.2 1.0 C5 A:1AY405 4.3 53.6 1.0 C7 A:1AY405 4.3 54.0 1.0 O A:HOH518 4.4 29.8 1.0 N9 A:1AY405 4.4 53.1 1.0 O A:HOH506 4.5 27.2 1.0 OD2 A:ASP229 4.5 30.1 1.0 OE2 A:GLU336 4.5 36.0 1.0 C21 A:1AY405 4.6 53.5 1.0 CE1 A:HIS310 4.8 35.6 1.0 C6 A:1AY405 4.8 54.1 1.0 CO A:CO402 5.0 34.6 1.0

P.Zhang, X.Yang, F.Zhang, S.B.Gabelli, R.Wang, Y.Zhang, S.Bhat, X.Chen, M.Furlani, L.M.Amzel, J.O.Liu, D.Ma. Pyridinylpyrimidines Selectively Inhibit Human Methionine Aminopeptidase-1. Bioorg.Med.Chem. V. 21 2600 2013.
ISSN: ISSN 0968-0896
PubMed: 23507151
DOI: 10.1016/J.BMC.2013.02.023