Cobalt in PDB 5d6e: Structure of Human Methionine Aminopeptidase 2 with Covalent Spiroepoxytriazole Inhibitor (-)-31B

All present enzymatic activity of Structure of Human Methionine Aminopeptidase 2 with Covalent Spiroepoxytriazole Inhibitor (-)-31B:
3.4.11.18;

The structure of Structure of Human Methionine Aminopeptidase 2 with Covalent Spiroepoxytriazole Inhibitor (-)-31B, PDB code: 5d6e was solved by R.Janowski, A.K.Miller, D.Niessing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.49
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	89.600, 98.790, 101.430, 90.00, 90.00, 90.00
R / Rfree (%)	11 / 15.6

The binding sites of Cobalt atom in the Structure of Human Methionine Aminopeptidase 2 with Covalent Spiroepoxytriazole Inhibitor (-)-31B (pdb code 5d6e). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Structure of Human Methionine Aminopeptidase 2 with Covalent Spiroepoxytriazole Inhibitor (-)-31B, PDB code: 5d6e:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Structure of Human Methionine Aminopeptidase 2 with Covalent Spiroepoxytriazole Inhibitor (-)-31B


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Human Methionine Aminopeptidase 2 with Covalent Spiroepoxytriazole Inhibitor (-)-31B within 5.0Å range: probe atom residue distance (Å) B Occ A:Co502 b:18.0 occ:0.50 O A:HOH655 1.7 39.9 1.0 OD1 A:ASP262 1.9 22.5 1.0 OD1 A:ASP251 2.0 19.7 1.0 OE1 A:GLU459 2.0 26.8 1.0 OD2 A:ASP251 2.2 22.0 1.0 CG A:ASP251 2.4 19.1 1.0 CG A:ASP262 2.8 22.0 1.0 CD A:GLU459 2.9 24.7 1.0 OD2 A:ASP262 3.2 33.3 1.0 OE2 A:GLU459 3.2 21.4 1.0 CO A:CO503 3.4 26.5 0.3 C8 A:94A501 3.6 30.1 1.0 CZ A:PHE219 3.8 21.4 1.0 CB A:ASP251 3.9 16.8 1.0 O A:HOH852 4.1 46.4 1.0 OE1 A:GLU364 4.1 31.3 1.0 CB A:ASP262 4.1 23.3 1.0 NE2 A:GLN457 4.2 18.1 1.0 CE1 A:PHE219 4.3 18.2 1.0 N A:CYS263 4.3 16.8 1.0 CB A:ALA264 4.3 16.8 1.0 CG A:GLU459 4.3 19.3 1.0 O A:HOH633 4.4 29.3 1.0 C A:ASP262 4.4 16.2 1.0 OE2 A:GLU364 4.4 29.1 1.0 CA A:ASP262 4.5 18.9 1.0 CD A:GLU364 4.6 27.4 1.0 O1 A:94A501 4.6 30.4 1.0 CA A:ASP251 4.7 15.6 1.0 O A:CYS263 4.7 17.7 1.0 CB A:GLU459 4.8 16.6 1.0 CE2 A:PHE219 4.8 21.7 1.0 C A:CYS263 4.8 17.9 1.0 C5 A:94A501 4.8 27.5 1.0 C4 A:94A501 4.9 31.6 1.0 CA A:CYS263 5.0 16.3 1.0 O A:ASP262 5.0 18.7 1.0 C A:ASP251 5.0 15.7 1.0

Cobalt binding site 2 out of 2 in the Structure of Human Methionine Aminopeptidase 2 with Covalent Spiroepoxytriazole Inhibitor (-)-31B


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Human Methionine Aminopeptidase 2 with Covalent Spiroepoxytriazole Inhibitor (-)-31B within 5.0Å range: probe atom residue distance (Å) B Occ A:Co503 b:26.5 occ:0.30 OE2 A:GLU459 2.1 21.4 1.0 NE2 A:HIS331 2.1 29.1 1.0 OD2 A:ASP262 2.2 33.3 1.0 OE2 A:GLU364 2.3 29.1 1.0 C8 A:94A501 2.5 30.1 1.0 CD2 A:HIS331 3.1 28.0 1.0 CG A:ASP262 3.1 22.0 1.0 O A:HOH655 3.1 39.9 1.0 CD A:GLU364 3.1 27.4 1.0 CE1 A:HIS331 3.1 25.8 1.0 CD A:GLU459 3.2 24.7 1.0 C4 A:94A501 3.4 31.6 1.0 CO A:CO502 3.4 18.0 0.5 N1 A:94A501 3.4 28.9 1.0 OD1 A:ASP262 3.6 22.5 1.0 OE1 A:GLU459 3.6 26.8 1.0 C2 A:94A501 3.6 28.4 1.0 C5 A:94A501 3.7 27.5 1.0 OE1 A:GLU364 3.7 31.3 1.0 CB A:ALA362 3.7 19.8 1.0 CG A:GLU364 4.0 29.8 1.0 CB A:ASP262 4.1 23.3 1.0 N6 A:94A501 4.2 30.8 1.0 CG A:HIS331 4.2 22.3 1.0 ND1 A:HIS331 4.2 27.0 1.0 O1 A:94A501 4.3 30.4 1.0 C3 A:94A501 4.4 27.3 1.0 CG A:GLU459 4.5 19.3 1.0 N5 A:94A501 4.8 30.6 1.0 CB A:GLU364 4.9 32.8 1.0 C19 A:94A501 4.9 27.3 1.0 C7 A:94A501 4.9 29.3 1.0 OD2 A:ASP251 4.9 22.0 1.0

M.Morgen, C.Jost, M.Malz, R.Janowski, D.Niessing, C.D.Klein, N.Gunkel, A.K.Miller. Spiroepoxytriazoles Are Fumagillin-Like Irreversible Inhibitors of METAP2 with Potent Cellular Activity. Acs Chem.Biol. V. 11 1001 2016.
ISSN: ESSN 1554-8937
PubMed: 26686773
DOI: 10.1021/ACSCHEMBIO.5B00755