Cobalt in PDB 1yvm: E. Coli Methionine Aminopeptidase in Complex with Thiabendazole

All present enzymatic activity of E. Coli Methionine Aminopeptidase in Complex with Thiabendazole:
3.4.11.18;

The structure of E. Coli Methionine Aminopeptidase in Complex with Thiabendazole, PDB code: 1yvm was solved by R.Schiffmann, A.Heine, G.Klebe, C.D.Klein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.910, 66.130, 48.530, 90.00, 111.25, 90.00
R / Rfree (%)	17 / 23.3

The structure of E. Coli Methionine Aminopeptidase in Complex with Thiabendazole also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Cobalt atom in the E. Coli Methionine Aminopeptidase in Complex with Thiabendazole (pdb code 1yvm). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the E. Coli Methionine Aminopeptidase in Complex with Thiabendazole, PDB code: 1yvm:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the E. Coli Methionine Aminopeptidase in Complex with Thiabendazole


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of E. Coli Methionine Aminopeptidase in Complex with Thiabendazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:25.1 occ:1.00 O A:HOH3071 2.0 19.0 1.0 N7 A:TMG501 2.1 20.3 1.0 N11 A:TMG501 2.2 27.2 1.0 NE2 A:HIS79 2.3 25.2 1.0 O A:HOH3196 2.3 26.4 1.0 O A:HOH3149 2.3 21.8 1.0 C9 A:TMG501 2.9 27.9 1.0 C10 A:TMG501 2.9 28.6 1.0 CD2 A:HIS79 3.1 16.9 1.0 C2 A:TMG501 3.2 30.9 1.0 C12 A:TMG501 3.3 32.8 1.0 CE1 A:HIS79 3.3 28.7 1.0 C1 A:TMG501 3.8 27.2 1.0 O A:HOH3158 4.1 17.5 1.0 N8 A:TMG501 4.1 28.7 1.0 NE2 A:HIS178 4.2 20.8 1.0 C14 A:TMG501 4.2 30.1 1.0 C6 A:TMG501 4.2 26.1 1.0 O A:HOH3053 4.2 17.6 1.0 CG A:HIS79 4.3 19.7 1.0 O A:HOH3165 4.4 14.9 1.0 ND1 A:HIS79 4.4 24.1 1.0 OD2 A:ASP97 4.6 18.8 1.0 O A:HOH3107 4.7 32.9 1.0 S13 A:TMG501 4.7 40.2 1.0 CE1 A:HIS178 4.9 20.4 1.0

Cobalt binding site 2 out of 4 in the E. Coli Methionine Aminopeptidase in Complex with Thiabendazole


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of E. Coli Methionine Aminopeptidase in Complex with Thiabendazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:16.7 occ:1.00 OD1 A:ASP108 1.9 16.4 1.0 O A:HOH3158 2.1 17.5 1.0 OD1 A:ASP97 2.1 15.9 1.0 O A:HOH3165 2.2 14.9 1.0 OE1 A:GLU235 2.2 12.9 1.0 OD2 A:ASP97 2.5 18.8 1.0 CG A:ASP97 2.5 12.5 1.0 CG A:ASP108 2.9 20.8 1.0 CD A:GLU235 3.0 17.7 1.0 CO A:CO403 3.1 18.0 1.0 OD2 A:ASP108 3.1 16.2 1.0 OE2 A:GLU235 3.3 15.6 1.0 O A:HOH3149 3.8 21.8 1.0 O A:HOH3194 3.9 16.4 1.0 OG1 A:THR99 4.0 16.9 1.0 CB A:ASP97 4.1 14.1 1.0 OE1 A:GLU204 4.2 20.3 1.0 O A:HOH3071 4.3 19.0 1.0 O A:HOH3033 4.3 27.6 1.0 CB A:ASP108 4.3 18.9 1.0 CG A:GLU235 4.4 14.3 1.0 N A:THR109 4.5 13.5 1.0 O A:VAL98 4.6 15.7 1.0 OE2 A:GLU204 4.6 15.6 1.0 O A:HOH3053 4.7 17.6 1.0 CD A:GLU204 4.7 17.3 1.0 C A:ASP108 4.7 15.4 1.0 O A:THR109 4.8 15.6 1.0 CA A:ASP108 4.8 17.6 1.0 CA A:ASP97 4.8 13.7 1.0 CB A:GLU235 4.9 13.5 1.0 C A:THR109 4.9 14.1 1.0 N A:VAL98 4.9 14.8 1.0 C A:ASP97 5.0 18.4 1.0

Cobalt binding site 3 out of 4 in the E. Coli Methionine Aminopeptidase in Complex with Thiabendazole


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of E. Coli Methionine Aminopeptidase in Complex with Thiabendazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Co403 b:18.0 occ:1.00 O A:HOH3158 1.9 17.5 1.0 OD2 A:ASP108 2.1 16.2 1.0 OE2 A:GLU235 2.1 15.6 1.0 NE2 A:HIS171 2.1 14.4 1.0 OE2 A:GLU204 2.2 15.6 1.0 CD A:GLU235 3.0 17.7 1.0 CG A:ASP108 3.0 20.8 1.0 CD2 A:HIS171 3.0 16.7 1.0 CE1 A:HIS171 3.0 14.6 1.0 CD A:GLU204 3.1 17.3 1.0 CO A:CO402 3.1 16.7 1.0 OE1 A:GLU235 3.3 12.9 1.0 OD1 A:ASP108 3.3 16.4 1.0 OE1 A:GLU204 3.4 20.3 1.0 OG1 A:THR202 3.6 15.2 1.0 O A:HOH3149 3.7 21.8 1.0 CG2 A:THR202 3.9 21.1 1.0 CB A:THR202 4.0 15.1 1.0 ND1 A:HIS171 4.2 17.7 1.0 CG A:HIS171 4.2 15.2 1.0 CB A:ASP108 4.2 18.9 1.0 O A:HOH3165 4.3 14.9 1.0 CG A:GLU235 4.3 14.3 1.0 CG A:GLU204 4.4 16.7 1.0 CB A:GLU204 4.9 15.6 1.0 CE1 A:PHE177 5.0 22.9 1.0

Cobalt binding site 4 out of 4 in the E. Coli Methionine Aminopeptidase in Complex with Thiabendazole


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of E. Coli Methionine Aminopeptidase in Complex with Thiabendazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Co404 b:54.9 occ:1.00 O A:HOH3213 2.0 42.8 1.0 O A:HOH3222 2.2 45.6 1.0 O A:HOH3093 2.3 42.4 1.0 OE2 A:GLU123 2.5 43.3 1.0 O A:HOH3269 2.8 63.2 1.0 CD A:GLU123 3.4 46.4 1.0 OE1 A:GLU123 3.8 42.8 1.0 O A:HOH3264 4.4 43.6 1.0 O A:HOH3129 4.5 35.1 1.0 CG A:GLU123 4.7 36.3 1.0 CD1 A:ILE120 4.9 34.0 1.0

R.Schiffmann, A.Heine, G.Klebe, C.D.Klein. Metal Ions As Cofactors For the Binding of Inhibitors to Methionine Aminopeptidase: A Critical View of the Relevance of in Vitro Metalloenzyme Assays. Angew.Chem.Int.Ed.Engl. V. 44 3620 2005.
ISSN: ISSN 1433-7851
PubMed: 15880695
DOI: 10.1002/ANIE.200500592